Quantifying the uncertainty in forecasts of anthropogenic climate change

The contributions of climate and land use/cover changes to water yield services considering geographic scale

Background

Water yield services are critical for maintaining ecological sustainability and regional economies. Climate change and land use/cover change (LUCC) significantly affect regional water yield, but the spatiotemporal variability of water yield services has been overlooked in previous studies. This study aims to explore the relative contributions of climate and land use/cover changes to water yield services at both grid and subwatershed scales.

Methods

This study employed the InVEST model to calculate the water yield in the study area and employed a multi-scenario simulation approach to investigate the impacts of climate change and LUCC on water yield at both grid and subwatershed scales. Furthermore, the contributions of these two types of changes to water yield were quantified.

Results

Firstly, upstream areas experience significantly lower annual average precipitation, temperature, and potential evapotranspiration than downstream areas, with worsening drought severity. Secondly, urbanization led to significant LUCC, with decreases in farmland and grassland and increases in forest, water, building land, and unused land. Thirdly, the spatial heterogeneity of water yield services remains consistent across different scales, but more pronounced spatial clustering is observed at the subwatershed scale. Fourthly, climate change is the primary factor affecting regional water yield services, surpassing the influence of LUCC. Lastly, LUCC significantly impacts water cycling in watersheds, with vegetation coverage being a critical factor affecting water yield.

Conclusion

These findings highlight the need to consider the complex relationships between climate change, LUCC, and water yield services at multiple scales in water resource management.

Opportunities for centralized regional mode of manure and sewage management in pig farming: The evidence from environmental and economic performance

Pig breeding is moving toward more intensive development and is accompanied by the integrated generation of pig waste. This has disrupted the synergy between the original manure and sewage management mode and corresponding farmland at the household level. Centralized bio-energy mode is proposed to relieve environmental pressure, increase the resource recovery efficiency and rebuild the breeding and cropping. However, there is a lack of comprehensive information on a regional scale, particularly regarding evaluation, applicability and feasibility. Therefore, compared to the individual and traditional mode at the household level, this study was conducted using life cycle assessment and life cycle cost analysis, systematically assessed the environmental performance and economic viability of the centralized bio-energy mode at the regional scale, and further explored the adaptability of multi-subjects (various pig farms and biogas enterprise) and regional feasibility. Results revealed that the centralized bio-energy mode appeared to be a better alternative in terms of global warming, terrestrial acidification and marine eutrophication, with the significant reductions of 49.49 %, 6.8 % and 4.67 % respectively. Moreover, the study demonstrated a substantial profit of 48.5 CNY1 per ton of managed pig waste. Furthermore, both environmental and economic performance could be improved through scale expansion and transport optimization, with an optimal collection radius of less than 31.45 km. Conclusions clarified the potential of centralized bio-energy mode and provided valuable references for its implementation in various regions. Ultimately, further contributing to a more efficient, cost-effective, and regulated manner for resource recovery, culminating in the sustainability of pig farming and achieving environmental-friendly agriculture practices in regional contexts.

Observationally-constrained projections of an ice-free Arctic even under a low emission scenario

The sixth assessment report of the IPCC assessed that the Arctic is projected to be on average practically ice-free in September near mid-century under intermediate and high greenhouse gas emissions scenarios, though not under low emissions scenarios, based on simulations from the latest generation Coupled Model Intercomparison Project Phase 6 (CMIP6) models. Here we show, using an attribution analysis approach, that a dominant influence of greenhouse gas increases on Arctic sea ice area is detectable in three observational datasets in all months of the year, but is on average underestimated by CMIP6 models. By scaling models' sea ice response to greenhouse gases to best match the observed trend in an approach validated in an imperfect model test, we project an ice-free Arctic in September under all scenarios considered. These results emphasize the profound impacts of greenhouse gas emissions on the Arctic, and demonstrate the importance of planning for and adapting to a seasonally ice-free Arctic in the near future.

Machine learning for weather and climate are worlds apart

Modern weather and climate models share a common heritage and often even components; however, they are used in different ways to answer fundamentally different questions. As such, attempts to emulate them using machine learning should reflect this. While the use of machine learning to emulate weather forecast models is a relatively new endeavour, there is a rich history of climate model emulation. This is primarily because while weather modelling is an initial condition problem, which intimately depends on the current state of the atmosphere, climate modelling is predominantly a boundary condition problem. To emulate the response of the climate to different drivers therefore, representation of the full dynamical evolution of the atmosphere is neither necessary, or in many cases, desirable. Climate scientists are typically interested in different questions also. Indeed emulating the steady-state climate response has been possible for many years and provides significant speed increases that allow solving inverse problems for e.g. parameter estimation. Nevertheless, the large datasets, non-linear relationships and limited training data make climate a domain which is rich in interesting machine learning challenges. Here, I seek to set out the current state of climate model emulation and demonstrate how, despite some challenges, recent advances in machine learning provide new opportunities for creating useful statistical models of the climate. This article is part of the theme issue 'Machine learning for weather and climate modelling'.

Making climate projections conditional on historical observations

Many studies have sought to constrain climate projections based on recent observations. Until recently, these constraints had limited impact, and projected warming ranges were driven primarily by model outputs. Here, we use the newest climate model ensemble, improved observations, and a new statistical method to narrow uncertainty on estimates of past and future human-induced warming. Cross-validation suggests that our method produces robust results and is not overconfident. We derive consistent observationally constrained estimates of attributable warming to date and warming rate, the response to a range of future scenarios, and metrics of climate sensitivity. We find that historical observations narrow uncertainty on projected future warming by about 50%. Our results suggest that using an unconstrained multimodel ensemble is no longer the best choice for global mean temperature projections and that the lower end of previous estimates of 21st century warming can now be excluded.

Uncertainty quantification based cloud parameterization sensitivity analysis in the NCAR community atmosphere model

Using uncertainty quantification techniques, we carry out a sensitivity analysis of a large number (17) of parameters used in the NCAR CAM5 cloud parameterization schemes. The LLNL PSUADE software is used to identify the most sensitive parameters by performing sensitivity analysis. Using Morris One-At-a-Time (MOAT) method, we find that the simulations of global annual mean total precipitation, convective, large-scale precipitation, cloud fractions (total, low, mid, and high), shortwave cloud forcing, longwave cloud forcing, sensible heat flux, and latent heat flux are very sensitive to the threshold-relative-humidity-for-stratiform-low-clouds ([Formula: see text] and the auto-conversion-size-threshold-for-ice-to-snow [Formula: see text] The seasonal and regime specific dependence of some parameters in the simulation of precipitation is also found for the global monsoons and storm track regions. Through sensitivity analysis, we find that the Somali jet strength and the tropical easterly jet associated with the south Asian summer monsoon (SASM) show a systematic dependence on [Formula: see text] and [Formula: see text]. The timing of the withdrawal of SASM over India shows a monotonic increase (delayed withdrawal) with an increase in [Formula: see text]. Overall, we find that [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] are the most sensitive cloud parameters and thus are of high priority in the model tuning process, in order to reduce uncertainty in the simulation of past, present, and future climate.

Climate change impact on karstic aquifer hydrodynamics in southern Europe semi-arid region using the KAGIS model

Nowadays, there are many urban settlements in arid and semiarid areas supplied by groundwater from adjacent small aquifers. Climate projections with expected decreases in averages precipitation values jointly with increases in the frequency of heavy rainfall events does not show a clear pattern to how water resources in karstic aquifers are going to evolve. This paper, focused in the province of Alicante (Southeast of Spain), assesses the behaviour of a small karstic aquifer, the Mela aquifer, whose resources supply urban water consumption for close municipalities. We assess the hydrogeological response of the aquifer, through the KAGIS black-box GIS-based model, for the present climate conditions and for the long period analysing the four scenarios provided by the International Panel of Climate Change. Main results prove that, if we do not diminish the greenhouse gas emissions, the climate change impact on the hydrological response of the study aquifer shows a decrease in the flow rate from its unique spring and will be non-existent during the summer months. So, it will be necessary to design supply strategies for these municipalities and to carry out them, meeting budget restrictions and avoiding potential water shortages.

PortWeather: A Lightweight Onboard Solution for Real-Time Weather Prediction

Maritime journeys significantly depend on weather conditions, and so meteorology has always had a key role in maritime businesses. Nowadays, the new era of innovative machine learning approaches along with the availability of a wide range of sensors and microcontrollers creates increasing perspectives for providing on-board reliable short-range forecasting of main meteorological variables. The main goal of this study is to propose a lightweight on-board solution for real-time weather prediction. The system is composed of a commercial weather station integrated with an industrial IOT-edge data processing module that computes the wind direction and speed forecasts without the need of an Internet connection. A regression machine learning algorithm was chosen so as to require the smallest amount of resources (memory, CPU) and be able to run in a microcontroller. The algorithm has been designed and coded following specific conditions and specifications. The system has been tested on real weather data gathered from static weather stations and onboard during a test trip. The efficiency of the system has been proven through various error metrics.

Anthropogenically-driven increases in the risks of summertime compound hot extremes

Compared to individual hot days/nights, compound hot extremes that combine daytime and nighttime heat are more impactful. However, past and future changes in compound hot extremes as well as their underlying drivers and societal impacts remain poorly understood. Here we show that during 1960-2012, significant increases in Northern Hemisphere average frequency (~1.03 days decade^-1) and intensity (~0.28 °C decade^-1) of summertime compound hot extremes arise primarily from summer-mean warming. The forcing of rising greenhouse gases (GHGs) is robustly detected and largely accounts for observed trends. Observationally-constrained projections suggest an approximate eightfold increase in hemispheric-average frequency and a threefold growth in intensity of summertime compound hot extremes by 2100 (relative to 2012), given uncurbed GHG emissions. Accordingly, end-of-century population exposure to compound hot extremes is projected to be four to eight times the 2010s level, dependent on demographic and climate scenarios.

Bias Correction of Climate Model’s Precipitation Using the Copula Method and Its Application in River Basin Simulation

During the last few decades, the utilization of the data from climate models in hydrological studies has increased as they can provide data in the regions that lack raw meteorological information. The data from climate models data often present biases compared to the observed data and consequently, several methods have been developed for correcting statistical biases. The present study uses the copula for modeling the dependence between the daily mean and total monthly precipitation using E-OBS data in the Mesta/Nestos river basin in order to use this relationship for the bias correction of the MPI climate model monthly precipitation. Additionally, both the non-corrected and bias corrected data are tested as they are used as the inputs to a spatial distributed hydrological model for simulating the basin runoff. The results showed that the MPI model significantly overestimates the E-OBS data while the differences are reduced sufficiently after the bias correction. The outputs from the hydrological models were proven to coincide with the precipitation analysis results and hence, the simulated discharges in the case of copula corrected data present an increased correlation with the observed flows.

Experimental Investigation and Numerical Simulation of CO2–Brine–Rock Interactions during CO2 Sequestration in a Deep Saline Aquifer

CO2 mineralization is a long-term and secure solution for geological CO2 storage that primarily depends on the CO2–brine–rock interaction during CO2 sequestration in subsurface formations. In this study, lab experiments were conducted to investigate the CO2–brine–rock interaction over short timescales, and numerical simulations were performed to reveal dynamic interactions and equilibrium interactions by applying TOUGHREACT and PHREEQC, respectively. In the experiments, the main ions of HCO3− and Ca2+ were detected in the solution, and calcite dissolution and dawsonite precipitation were observed from SEM images. The simulation results showed that the CO2 dissolution and the solution pH were affected by the temperatures, pressures, types of solutions, and solution concentrations and were further influenced by mineral dissolution and precipitation. The results of the equilibrium simulation showed that the dissolved minerals were albite, anhydrite, calcite, Ca-montmorillonite, illite, K-feldspar, and chlorite, and the precipitated minerals were dolomite, kaolinite, and quartz, which led to HCO3−, K+, and Na+ being the main ions in solutions. The results of the dynamic simulation showed that calcite and dolomite dissolved in the early period, while other minerals began to dissolve or precipitate after 100 years. The dissolved minerals were mainly albite, kaolinite, K-feldspar, and chlorite, and precipitated minerals were Ca-montmorillonite, illite, and quartz. Anhydrite and pyrite did not change during the simulation period, and the main ions were HCO3−, Na+, Ca2+, and Mg2+ in the simulation period. This study provides an effective approach for analyzing the CO2–brine–rock interaction at different stages during CO2 storage, and the results are helpful for understanding the CO2 mineralization processes in deep saline aquifers.

Non-linear effect of sea ice: Spectacled Eider survival declines at both extremes of the ice spectrum

Understanding the relationship between environmental factors and vital rates is an important step in predicting a species' response to environmental change. Species associated with sea ice are of particular concern because sea ice is projected to decrease rapidly in polar environments with continued levels of greenhouse gas emissions. The relationship between sea ice and the vital rates of the Spectacled Eider, a threatened species that breeds in Alaska and Russia and winters in the Bering Sea, appears to be complex. While severe ice can impede foraging for benthic prey, ice also suppresses wave action and provides a platform on which eiders roost, thereby reducing thermoregulation costs. We analyzed a 23-year mark-recapture dataset for Spectacled Eiders nesting on Kigigak Island in western Alaska, and tested survival models containing different ice and weather-related covariates. We found that much of the variation in eider survival could be explained by the number of days per year with >95% sea ice concentration at the Bering Sea core wintering area. Furthermore, the data supported a quadratic relationship with sea ice rather than a linear one, indicating that intermediate sea ice concentrations were optimal for survival. We then used matrix population models to project population trajectories using General Circulation Model (GCM) outputs of daily sea ice cover. GCMs projected reduced sea ice at the wintering area by year 2100 under a moderated emissions scenario (RCP 4.5) and nearly ice-free conditions under an unabated emissions scenario (RCP 8.5). Under RCP 4.5, stochastic models projected an increase in population size until 2069 coincident with moderate ice conditions, followed by a decline in population size as ice conditions shifted from intermediate to mostly ice-free. Under RCP 8.5, eider abundance increased until 2040 and then decreased to near extirpation toward the end of the century as the Bering Sea became ice-free. Considerable uncertainty around parameter estimates for survival in years with minimal sea ice contributed to variation in stochastic projections of future population size, and this uncertainty could be reduced with additional survival data from low-ice winters.

The value of knowledge accumulation on climate sensitivity uncertainty: comparison between perfect information, single stage and act then learn decisions

In COP21 followed by the Paris Agreement, the world is now seriously planning actions to mitigate greenhouse gas emissions toward a "below 2 °C above preindustrial levels" future. Currently, we are still far from identifying the emission pathways to achieve this target because of the various uncertainties in both climate science and the human behavior. As a part of the ICA-RUS project, conducted by Dr. Seita Emori of the National Institute for Environmental Studies we have studied how these uncertainties are eliminated by the accumulation of scientific knowledge and the decision-making processes. We consider the following three questions: first, when and how will the uncertainty range on the global temperature rise be eliminated, second which global emission pathway should be chosen before we get the perfect information, and third how much expenditure is justified in reducing the climate uncertainties. The first question has been investigated by one of the authors. Shiogama et al. (Sci Rep 6:18903, 2016) developed the Allen-Stott-Kettleborough (ASK) method further to estimate how quickly and in what way the uncertainties in future global mean temperature changes can decline when the current observation network of surface air temperature is maintained. Fourteen global climate model results in CMIP5 (CMIP http://cmip-pcmdi.llnl.gov/, 2017) are used as virtual observations of surface air temperature. The purpose of this study is to answer the remaining two questions. Based on the ASK research outcomes, we apply the multi stage decision-making known as Act Then Learn (ATL) process to an integrated assessment model MARIA which includes energy technologies, economic activities, land use changes and a simple climate model block. We reveal how accumulating observations helps to mitigate economic losses by expanding the existing ATL method to deal with the uncertainty eliminating process by ASK. The primary findings are as follows. First, the value of information largely increases as the climate target policy is more stringent. Second, even if the uncertainties in the equilibrium climate sensitivity are not fully resolved, scientific knowledge is still valuable. In other words, the expenditure for scientific researches is rationalized when we really concern the global climate changes.

Immunologic and Virologic Mechanisms for Partial Protection from Intravenous Challenge by an Integration-Defective SIV Vaccine

The suppression of viral loads and identification of selection signatures in non-human primates after challenge are indicators for effective human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) vaccines. To mimic the protective immunity elicited by attenuated SIV vaccines, we developed an integration-defective SIV (idSIV) vaccine by inactivating integrase, mutating sequence motifs critical for integration, and inserting the cytomegalovirus (CMV) promoter for more efficient expression in the SIVmac239 genome. Chinese rhesus macaques were immunized with idSIV DNA and idSIV particles, and the cellular and humoral immune responses were measured. After the intravenous SIVmac239 challenge, viral loads were monitored and selection signatures in viral genomes from vaccinated monkeys were identified by single genome sequencing. T cell responses, heterologous neutralization against tier-1 viruses, and antibody-dependent cellular cytotoxicity (ADCC) were detected in idSIV-vaccinated macaques post immunization. After challenge, the median peak viral load in the vaccine group was significantly lower than that in the control group. However, this initial viral control did not last as viral set-points were similar between vaccinated and control animals. Selection signatures were identified in Nef, Gag, and Env proteins in vaccinated and control macaques, but these signatures were different, suggesting selection pressure on viruses from vaccine-induced immunity in the vaccinated animals. Our results showed that the idSIV vaccine exerted some pressure on the virus population early during the infection but future modifications are needed in order to induce more potent immune responses.

Influence of environmental temperature on risk of gestational diabetes

BACKGROUND

Cold-induced thermogenesis is known to improve insulin sensitivity, which may become increasingly relevant in the face of global warming. The aim of this study was to examine the relation between outdoor air temperature and the risk of gestational diabetes mellitus.

METHODS

We identified all births in the Greater Toronto Area from 2002 to 2014 using administrative health databases. Generalized estimating equations were used to examine the relation between the mean 30-day outdoor air temperature before the time of gestational diabetes mellitus screening and the likelihood of diagnosis of gestational diabetes mellitus based on a validated algorithm using hospital records and physician service claims.

RESULTS

Over the 12-year period, there were 555 911 births among 396 828 women. Prevalence of gestational diabetes mellitus was 4.6% among women exposed to extremely cold mean outdoor air temperatures (≤ -10°C) in the 30-day period before screening and increased to 7.7% among those exposed to hot mean 30-day temperatures (≥ 24°C). Each 10°C increase in mean 30-day temperature was associated with a 1.06 (95% confidence interval [CI] 1.04-1.07) times higher odds of gestational diabetes mellitus, after adjusting for maternal age, parity, neighbourhood income quintile, world region and year. A similar effect was seen for each 10°C rise in outdoor air temperature difference between 2 consecutive pregnancies for the same woman (adjusted odds ratio 1.06, 95% CI 1.03-1.08).

INTERPRETATION

In our setting, there was a direct relation between outdoor air temperature and the likelihood of gestational diabetes mellitus. Future climate patterns may substantially affect global variations in the prevalence of diabetes, which also has important implications for the prevention and treatment of gestational diabetes mellitus.

The anthroposphere as an anticipatory system: Open questions on steering the climate

Climate change research and action counteracting it affect everyone and would involve cross-societal transformations reshaping the anthroposphere in its entirety. Scrutinizing climate-related science and policies, we recognize attempts to steer the evolution of climate according to expected (or modelled) futures. Such attempts would turn the anthroposphere into a large "anticipatory system", in which human society seeks to anticipate and, possibly, to govern climate dynamics. The chief aim of this discussion paper is to open a critical debate on the climate change paradigm (CCP) drawing on a strategic and systemic framework grounded in the concept of anticipatory system sensu Rosen (1991). The proposed scheme is ambitiously intended to turn an intricate issue into a complex but structured problem that is to say, to make such complexity clear and manageable. This framework emerges from concepts borrowed from different scientific fields (including future studies and system dynamics) and its background lies in a simple quantitative literature overview, relying upon a broad level of analysis. The proposed framework will assist researchers and policy makers in thinking of CCP in terms of an anticipatory system, and in disentangling its interrelated (and sometimes intricate) aspects. In point of fact, several strategic questions related to CCP were not subjected to an adequate transdisciplinary discussion: what are the interplays between physical processes and social-political interventions, who is the observer (what he/she is looking for), and which paradigm is being used (or who defines the desirable future). The proposed scheme allows to structure such various topics in an arrangement which is easier to communicate, highlighting the linkages in between, and making them intelligible and open to verification and discussion. Furthermore, ideally developments will help scientists and policy makers address the strategic gaps between the evidence-based climatological assessments and the plurality of possible answers as applied to the geopolitical contingencies.

Collapse of Cytolytic Potential in SIV-Specific CD8+ T Cells Following Acute SIV Infection in Rhesus Macaques

Poor maintenance of cytotoxic factor expression among HIV-specific CD8+ T cells, in part caused by dysregulated expression of the transcription factor T-bet, is associated with HIV disease progression. However, the precise evolution and context in which CD8+ T cell cytotoxic functions become dysregulated in HIV infection remain unclear. Using the rhesus macaque (RM) SIV infection model, we evaluated the kinetics of SIV-specific CD8+ T cell cytolytic factor expression in peripheral blood, lymph node, spleen, and gut mucosa from early acute infection through chronic infection. We identified rapid acquisition of perforin and granzyme B expression in SIV-specific CD8+ T cells in blood, secondary lymphoid tissues and gut mucosa that collapsed rapidly during the transition to chronic infection. The evolution of this expression profile was linked to low expression of T-bet and occurred independent of epitope specificity, viral escape patterns and tissue origin. Importantly, during acute infection SIV-specific CD8+ T cells that maintained T-bet expression retained the ability to express granzyme B after stimulation, but this relationship was lost in chronic infection. Together, these data demonstrate the loss of cytolytic machinery in SIV-specific CD8+ T cells in blood and at tissue sites of viral reservoir and active replication during the transition from acute to chronic infection. This phenomenon occurs despite persistent high levels of viremia suggesting that an inability to maintain properly regulated cytotoxic T cell responses in all tissue sites enables HIV/SIV to avoid immune clearance, establish persistent viral reservoirs in lymphoid tissues and gut mucosa, and lead ultimately to immunopathogenesis and death.

Predicting future uncertainty constraints on global warming projections

Projections of global mean temperature changes (ΔT) in the future are associated with intrinsic uncertainties. Much climate policy discourse has been guided by “current knowledge” of the ΔTs uncertainty, ignoring the likely future reductions of the uncertainty, because a mechanism for predicting these reductions is lacking. By using simulations of Global Climate Models from the Coupled Model Intercomparison Project Phase 5 ensemble as pseudo past and future observations, we estimate how fast and in what way the uncertainties of ΔT can decline when the current observation network of surface air temperature is maintained. At least in the world of pseudo observations under the Representative Concentration Pathways (RCPs), we can drastically reduce more than 50% of the ΔTs uncertainty in the 2040 s by 2029, and more than 60% of the ΔTs uncertainty in the 2090 s by 2049. Under the highest forcing scenario of RCPs, we can predict the true timing of passing the 2 °C (3 °C) warming threshold 20 (30) years in advance with errors less than 10 years. These results demonstrate potential for sequential decision-making strategies to take advantage of future progress in understanding of anthropogenic climate change.

Weighting climate model projections using observational constraints

Projected climate change integrates the net response to multiple climate feedbacks. Whereas existing long-term climate change projections are typically based on unweighted individual climate model simulations, as observed climate change intensifies it is increasingly becoming possible to constrain the net response to feedbacks and hence projected warming directly from observed climate change. One approach scales simulated future warming based on a fit to observations over the historical period, but this approach is only accurate for near-term projections and for scenarios of continuously increasing radiative forcing. For this reason, the recent Fifth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC AR5) included such observationally constrained projections in its assessment of warming to 2035, but used raw model projections of longer term warming to 2100. Here a simple approach to weighting model projections based on an observational constraint is proposed which does not assume a linear relationship between past and future changes. This approach is used to weight model projections of warming in 2081-2100 relative to 1986-2005 under the Representative Concentration Pathway 4.5 forcing scenario, based on an observationally constrained estimate of the Transient Climate Response derived from a detection and attribution analysis. The resulting observationally constrained 5-95% warming range of 0.8-2.5 K is somewhat lower than the unweighted range of 1.1-2.6 K reported in the IPCC AR5.

The Relative Impact of Climate Change on the Extinction Risk of Tree Species in the Montane Tropical Andes

There are widespread concerns that anthropogenic climate change will become a major cause of global biodiversity loss. However, the potential impact of climate change on the extinction risk of species remains poorly understood, particularly in comparison to other current threats. The objective of this research was to examine the relative impact of climate change on extinction risk of upper montane tree species in the tropical Andes, an area of high biodiversity value that is particularly vulnerable to climate change impacts. The extinction risk of 129 tree species endemic to the region was evaluated according to the IUCN Red List criteria, both with and without the potential impacts of climate change. Evaluations were supported by development of species distribution models, using three methods (generalized additive models, recursive partitioning, and support vector machines), all of which produced similarly high AUC values when averaged across all species evaluated (0.82, 0.86, and 0.88, respectively). Inclusion of climate change increased the risk of extinction of 18–20% of the tree species evaluated, depending on the climate scenario. The relative impact of climate change was further illustrated by calculating the Red List Index, an indicator that shows changes in the overall extinction risk of sets of species over time. A 15% decline in the Red List Index was obtained when climate change was included in this evaluation. While these results suggest that climate change represents a significant threat to tree species in the tropical Andes, they contradict previous suggestions that climate change will become the most important cause of biodiversity loss in coming decades. Conservation strategies should therefore focus on addressing the multiple threatening processes currently affecting biodiversity, rather than focusing primarily on potential climate change impacts.

Development of a novel AIDS vaccine: the HIV-1 transactivator of transcription protein vaccine

INTRODUCTION

Classical approaches aimed at targeting the HIV-1 envelope as well as other structural viral proteins have largely failed. The HIV-1 transactivator of transcription (Tat) is a key HIV virulence factor, which plays pivotal roles in virus gene expression, replication, transmission and disease progression. Notably, anti-Tat Abs are uncommon in natural infection and, when present, correlate with the asymptomatic state and lead to lower or no disease progression. Hence, targeting Tat represents a pathogenesis-driven intervention.

AREAS COVERED

Here, we review the rationale and the translational development of a therapeutic vaccine targeting the Tat protein. Preclinical and Phase I studies, Phase II trials with Tat in anti-Tat Ab-negative, virologically suppressed highly active antiretroviral therapy-treated subjects in Italy and South Africa were conducted. The results indicate that Tat-induced immune responses are necessary to restore immune homeostasis, to block the replenishment and to reduce the size of the viral reservoir. Additionally, they may help in establishing key parameters for highly active antiretroviral therapy intensification and a functional cure.

EXPERT OPINION

We propose the therapeutic setting as the most feasible to speed up the testing and comparison of preventative vaccine candidates, as the distinction lies in the use of the vaccine in uninfected versus infected subjects and not in the vaccine formulation.

Selection pressure in CD8⁺ T-cell epitopes in the pol gene of HIV-1 infected individuals in Colombia. A bioinformatic approach

One of the main characteristics of the human immunodeficiency virus is its genetic variability and rapid adaptation to changing environmental conditions. This variability, resulting from the lack of proofreading activity of the viral reverse transcriptase, generates mutations that could be fixed either by random genetic drift or by positive selection. Among the forces driving positive selection are antiretroviral therapy and CD8+ T-cells, the most important immune mechanism involved in viral control. Here, we describe mutations induced by these selective forces acting on the pol gene of HIV in a group of infected individuals. We used Maximum Likelihood analyses of the ratio of non-synonymous to synonymous mutations per site (dN/dS) to study the extent of positive selection in the protease and the reverse transcriptase, using 614 viral sequences from Colombian patients. We also performed computational approaches, docking and algorithmic analyses, to assess whether the positively selected mutations affected binding to the HLA molecules. We found 19 positively-selected codons in drug resistance-associated sites and 22 located within CD8+ T-cell epitopes. A high percentage of mutations in these epitopes has not been previously reported. According to the docking analyses only one of those mutations affected HLA binding. However, algorithmic methods predicted a decrease in the affinity for the HLA molecule in seven mutated peptides. The bioinformatics strategies described here are useful to identify putative positively selected mutations associated with immune escape but should be complemented with an experimental approach to define the impact of these mutations on the functional profile of the CD8+ T-cells.

Characterization of CD8+ T cell differentiation following SIVΔnef vaccination by transcription factor expression profiling

The onset of protective immunity against pathogenic SIV challenge in SIVΔnef-vaccinated macaques is delayed for 15-20 weeks, a process that is related to qualitative changes in CD8⁺ T cell responses induced by SIVΔnef. As a novel approach to characterize cell differentiation following vaccination, we used multi-target qPCR to measure transcription factor expression in naïve and memory subsets of CD8+⁺ T cells, and in SIV-specific CD8⁺ T cells obtained from SIVΔnef-vaccinated or wild type SIVmac239-infected macaques. Unsupervised clustering of expression profiles organized naïve and memory CD8⁺ T cells into groups concordant with cell surface phenotype. Transcription factor expression patterns in SIV-specific CD8⁺ T cells in SIVΔnef-vaccinated animals were distinct from those observed in purified CD8⁺ T cell subsets obtained from naïve animals, and were intermediate to expression profiles of purified central memory and effector memory T cells. Expression of transcription factors elicited by SIVΔnef vaccination also varied over time: cells obtained at later time points, temporally associated with greater protection, appeared more central-memory like than cells obtained at earlier time points, which appeared more effector memory-like. Expression of transcription factors associated with effector differentiation, such as ID2 and RUNX3, were decreased over time, while expression of transcription factors associated with quiescence or memory differentiation, such as TCF7, BCOR and EOMES, increased. CD8⁺ T cells specific for a more conserved epitope expressed higher levels of TBX21 and BATF, and appeared more effector-like than cells specific for an escaped epitope, consistent with continued activation by replicating vaccine virus. These data suggest transcription factor expression profiling is a novel method that can provide additional data complementary to the analysis of memory cell differentiation based on classical phenotypic markers. Additionally, these data support the hypothesis that ongoing stimulation by SIVΔnef promotes a distinct protective balance of CD8⁺ T cell differentiation and activation states.

The live attenuated vaccine SIVΔnef can induce robust CD8⁺ T cell- mediated protection against infection with pathogenic SIV in macaques. Thus, there is substantial interest in characterizing these immune responses to inform HIV vaccine design. Animals challenged at 15–20 weeks post vaccination exhibit robust protection, whereas animals challenged at 5 weeks post-vaccination manifest little protection. Since the frequency of SIV-specific T cells decreases from week 5 to week 20, it is likely that the quality of the response to challenge changes as virus-specific cells differentiate. We applied a novel approach of transcription factor expression profiling to characterize the differences in SIV-specific cell function and phenotype at more protected and less protected time points. Using unsupervised clustering methods informed by expression profiles assessed in purified CD8⁺ T cell subsets, we show that SIV-specific cells display expression profiles different than any purified CD8⁺ T cell subset, and intermediate to sorted effector memory and central memory subsets. SIV-specific cells overall appear more effector memory-like at week 5 post-vaccination, and more central memory-like at week 20 post-vaccination. Distinct profiles of CD8⁺ T cells specific for different SIV epitopes having different immune escape kinetics suggests maturation is regulated by ongoing low-level replication of vaccine virus.

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial

The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or "signatures" and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.

Understanding HIV infection for the design of a therapeutic vaccine. Part II: Vaccination strategies for HIV

HIV infection leads to a gradual loss CD4(+) T lymphocytes comprising immune competence and progression to AIDS. Effective treatment with combined antiretroviral drugs (cART) decreases viral load below detectable levels but is not able to eliminate the virus from the body. The success of cART is frustrated by the requirement of expensive lifelong adherence, accumulating drug toxicities and chronic immune activation resulting in increased risk of several non-AIDS disorders, even when viral replication is suppressed. Therefore, there is a strong need for therapeutic strategies as an alternative to cART. Immunotherapy, or therapeutic vaccination, aims to increase existing immune responses against HIV or induce de novo immune responses. These immune responses should provide a functional cure by controlling viral replication and preventing disease progression in the absence of cART. The key difficulty in the development of an HIV vaccine is our ignorance of the immune responses that control of viral replication, and thus how these responses can be elicited and how they can be monitored. Part one of this review provides an extensive overview of the (patho-) physiology of HIV infection. It describes the structure and replication cycle of HIV, the epidemiology and pathogenesis of HIV infection and the innate and adaptive immune responses against HIV. Part two of this review discusses therapeutic options for HIV. Prevention modalities and antiretroviral therapy are briefly touched upon, after which an extensive overview on vaccination strategies for HIV is provided, including the choice of immunogens and delivery strategies.

Understanding HIV infection for the design of a therapeutic vaccine. Part I: Epidemiology and pathogenesis of HIV infection

HIV infection leads to a gradual loss CD4+ T lymphocytes comprising immune competence and progression to AIDS. Effective treatment with combined antiretroviral drugs (cART) decreases viral load below detectable levels but is not able to eliminate the virus from the body. The success of cART is frustrated by the requirement of expensive life-long adherence, accumulating drug toxicities and chronic immune activation resulting in increased risk of several non-AIDS disorders, even when viral replication is suppressed. Therefore there is a strong need for therapeutic strategies as an alternative to cART. Immunotherapy, or therapeutic vaccination, aims to increase existing immune responses against HIV or induce de novo immune responses. These immune responses should provide a functional cure by controlling viral replication and preventing disease progression in the absence of cART. The key difficulty in the development of an HIV vaccine is our ignorance of the immune responses that control of viral replication, and thus how these responses can be elicited and how they can be monitored. Part one of this review provides an extensive overview of the (patho-) physiology of HIV infection. It describes the structure and replication cycle of HIV, the epidemiology and pathogenesis of HIV infection and the innate and adaptive immune responses against HIV. Part two of this review discusses therapeutic options for HIV. Prevention modalities and antiretroviral therapy are briefly touched upon, after which an extensive overview on vaccination strategies for HIV is provided, including the choice of immunogens and delivery strategies.

Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments

Methods for identifying physiologically relevant CD8 T-cell epitopes are critically important not only for the development of T-cell-based vaccines but also for understanding host-pathogen interactions. As experimentally mapping an optimal CD8 T-cell epitope is a tedious procedure, many bioinformatic tools have been developed that predict which peptides bind to a given MHC molecule. We assessed the ability of the CD8 T-cell epitope prediction tools syfpeithi, ctlpred and iedb to foretell nine experimentally mapped optimal HIV-specific epitopes. Randomly - for any of the subjects' HLA type and with any matching score - the optimal epitope was predicted in seven of nine epitopes using syfpeithi, in three of nine epitopes using ctlpred and in all nine of nine epitopes using iedb. The optimal epitope within the three highest ranks was given in four of nine epitopes applying syfpeithi, in two of nine epitopes applying ctlpred and in seven of nine epitopes applying iedb when screening for all of the subjects' HLA types. Knowing the HLA restriction of the peptide of interest improved the ranking of the optimal epitope within the predicted results. Epitopes restricted by common HLA alleles were more likely to be predicted than those restricted by uncommon HLA alleles. Epitopes with aberrant lengths compared with the usual HLA-class I nonamers were most likely not predicted. Application of epitope prediction tools together with literature searches for already described optimal epitopes narrows down the possibilities of optimal epitopes within a screening peptide of interest. However, in our opinion, the actual fine-mapping of a CD8 T-cell epitope cannot yet be replaced.

Microdevices for examining immunological responses of single cells to HIV

More than 60 million people in the world have been diagnosed with HIV infections since the virus was recognized as the causative agent of AIDS in the 1980s. Even though more than half of the infected patients have died, effective disease treatment and prevention measures have not been established. ART (antiretroviral therapy) is the only proven HIV treatment that sustains the suppression of patient viraemia. Current routine approaches to treat HIV infections are targeted at developing vaccines that will induce humoral or cell memory immune responses. However, developing an effective vaccine has been challenging because the HIV mutates rapidly, which allows the virus to evade immune surveillances established against the previous strain. In addition, the virus is able to quickly establish a reservoir and treatment is difficult because of the general lack of knowledge about HIV immune response mechanisms. This review introduces common disease symptoms and the progression of HIV infection with a brief summary of the current treatment approaches. Different cellular immune responses against HIV are also discussed, with emphasis on a nanotechnology research that has focused on probing T-cell response to HIV infection. Furthermore, we discuss recent noteworthy nanotechnology updates on T-cell response screening that is focused on HIV infection. Finally, we review potential future treatment strategies based on the correlations between T-cell response and HIV infection.

Rates of CTL killing in persistent viral infection in vivo

The CD8⁺ cytotoxic T lymphocyte (CTL) response is an important defence against viral invasion. Although CTL-mediated cytotoxicity has been widely studied for many years, the rate at which virus-infected cells are killed in vivo by the CTL response is poorly understood. To date the rate of CTL killing in vivo has been estimated for three virus infections but the estimates differ considerably, and killing of HIV-1-infected cells was unexpectedly low. This raises questions about the typical anti-viral capability of CTL and whether CTL killing is abnormally low in HIV-1. We estimated the rate of killing of infected cells by CD8⁺ T cells in two distinct persistent virus infections: sheep infected with Bovine Leukemia Virus (BLV) and humans infected with Human T Lymphotropic Virus type 1 (HTLV-1) which together with existing data allows us to study a total of five viruses in parallel. Although both BLV and HTLV-1 infection are characterised by large expansions of chronically activated CTL with immediate effector function ex vivo and no evidence of overt immune suppression, our estimates are at the lower end of the reported range. This enables us to put current estimates into perspective and shows that CTL killing of HIV-infected cells may not be atypically low. The estimates at the higher end of the range are obtained in more manipulated systems and may thus represent the potential rather than the realised CTL efficiency.

Virus replication is countered by a range of innate and adaptive host defences. One important and widely studied adaptive defence is the CD8⁺ cytotoxic T lymphocyte (CTL) response. Quantification of the in vivo lytic capability of CTLs is essential for a detailed understanding of the immune response. This includes understanding the balance between viral replication and viral clearance, understanding the rate limiting steps in CTL killing and thus how killing can be increased and understanding the failure of CTL vaccines. However, the typical rate at which virus-infected cells are killed by the CTL response in vivo is poorly understood. Current estimates differ considerably and are especially low for HIV-1-infection. We estimated the rate of killing of infected cells by CD8⁺ T cells in two distinct persistent virus infections which enables us to put current estimates into perspective. We show that CTL killing of HIV-infected cells may not be atypically low. The estimates at the higher end of the range are obtained in more manipulated systems and may thus represent the potential rather than the realised CTL efficiency.

Spatial and temporal dynamics of fucoid populations (Ascophyllum nodosum and Fucus serratus): a comparison between central and range edge populations

Persistence of populations at range edges relies on local population dynamics and fitness, in the case of geographically isolated populations of species with low dispersal potential. Focusing on spatial variations in demography helps to predict the long-term capability for persistence of populations across the geographical range of species' distribution. The demography of two ecological and phylogenetically close macroalgal species with different life history characteristics was investigated by using stochastic, stage-based matrix models. Populations of Ascophyllum nodosum and Fucus serratus were sampled for up to 4 years at central locations in France and at their southern range limits in Portugal. The stochastic population growth rate (λ(s)) of A. nodosum was lower and more variable in central than in southern sites whilst for F. serratus this trend was reversed with λ(s) much lower and more variable in southern than in central populations. Individuals were larger in central than in southern populations for both species, which was reflected in the lower transition probabilities of individuals to larger size classes and higher probability of shrinkage in the southern populations. In both central and southern populations elasticity analysis (proportional sensitivity) of population growth rate showed that fertility elements had a small contribution to λ(s) that was more sensitive to changes in matrix transitions corresponding to survival. The highest elasticities were found for loop transitions in A. nodosum and for growth to larger size classes in F. serratus. Sensitivity analysis showed high selective pressure on individual growth for both species at both locations. The results of this study highlight the deterministic role of species-specific life-history traits in population demography across the geographical range of species. Additionally, this study demonstrates that individuals' life-transitions differ in vulnerability to environmental variability and shows the importance of vegetative compared to reproductive stages for the long-term persistence of populations.

Mucosal immunology of HIV infection

Recent advances in the immunology, pathogenesis, and prevention of human immunodeficiency virus (HIV) infection continue to reveal clues to the mechanisms involved in the progressive immunodeficiency attributed to infection, but more importantly have shed light on the correlates of immunity to infection and disease progression. HIV selectively infects, eliminates, and/or dysregulates several key cells of the human immune system, thwarting multiple arms of the host immune response, and inflicting severe damage to mucosal barriers, resulting in tissue infiltration of 'symbiotic' intestinal bacteria and viruses that essentially become opportunistic infections promoting systemic immune activation. This leads to activation and recruitment or more target cells for perpetuating HIV infection, resulting in persistent, high-level viral replication in lymphoid tissues, rapid evolution of resistant strains, and continued evasion of immune responses. However, vaccine studies and studies of spontaneous controllers are finally providing correlates of immunity from protection and disease progression, including virus-specific CD4(+) T-cell responses, binding anti-bodies, innate immune responses, and generation of antibodies with potent antibody-dependent cell-mediated cytotoxicity activity. Emerging correlates of immunity indicate that prevention of HIV infection may be possible through effective vaccine strategies that protect and stimulate key regulatory cells and immune responses in susceptible hosts. Furthermore, immune therapies specifically directed toward boosting specific aspects of the immune system may eventually lead to a cure for HIV-infected patients.

HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in gag

Expression of HLA-B*57 and the closely related HLA-B*58:01 are associated with prolonged survival after HIV-1 infection. However, large differences in disease course are observed among HLA-B*57/58:01 patients. Escape mutations in CTL epitopes restricted by these HLA alleles come at a fitness cost and particularly the T242N mutation in the TW10 CTL epitope in Gag has been demonstrated to decrease the viral replication capacity. Additional mutations within or flanking this CTL epitope can partially restore replication fitness of CTL escape variants. Five HLA-B*57/58:01 progressors and 5 HLA-B*57/58:01 long-term nonprogressors (LTNPs) were followed longitudinally and we studied which compensatory mutations were involved in the restoration of the viral fitness of variants that escaped from HLA-B*57/58:01-restricted CTL pressure. The Sequence Harmony algorithm was used to detect homology in amino acid composition by comparing longitudinal Gag sequences obtained from HIV-1 patients positive and negative for HLA-B*57/58:01 and from HLA-B*57/58:01 progressors and LTNPs. Although virus isolates from HLA-B*57/58:01 individuals contained multiple CTL escape mutations, these escape mutations were not associated with disease progression. In sequences from HLA-B*57/58:01 progressors, 5 additional mutations in Gag were observed: S126N, L215T, H219Q, M228I and N252H. The combination of these mutations restored the replication fitness of CTL escape HIV-1 variants. Furthermore, we observed a positive correlation between the number of escape and compensatory mutations in Gag and the replication fitness of biological HIV-1 variants isolated from HLA-B*57/58:01 patients, suggesting that the replication fitness of HLA-B*57/58:01 escape variants is restored by accumulation of compensatory mutations.

Adaptation of CD8 T cell responses to changing HIV-1 sequences in a cohort of HIV-1 infected individuals not selected for a certain HLA allele

HIV evades CD8 T cell mediated pressure by viral escape mutations in targeted CD8 T cell epitopes. A viral escape mutation can lead to a decline of the respective CD8 T cell response. Our question was what happened after the decline of a CD8 T cell response and - in the case of viral escape – if a new CD8 T cell response towards the mutated antigen could be generated in a population not selected for certain HLA alleles. We studied 19 antiretroviral-naïve HIV-1 infected individuals with different disease courses longitudinally. A median number of 12 (range 2-24) CD8 T cell responses towards Gag and Nef were detected per study subject. A total of 30 declining CD8 T cell responses were studied in detail and viral sequence analyses showed amino acid changes in 25 (83%) of these. Peptide titration assays and definition of optimal CD8 T cell epitopes revealed 12 viral escape mutations with one de-novo response (8%). The de-novo response, however, showed less effector functions than the original CD8 T cell response. In addition we identified 4 shifts in immunodominance. For one further shift in immunodominance, the mutations occurred outside the optimal epitope and might represent processing changes. Interestingly, four adaptations to the virus (the de-novo response and 3 shifts in immunodominance) occurred in the group of chronically infected progressors. None of the subjects with adaptation to the changing virus carried the HLA alleles B57, B*58:01 or B27. Our results show that CD8 T cell responses adapt to the mutations of HIV. However it was limited to only 20% (5 out of 25) of the epitopes with viral sequence changes in a cohort not expressing protective HLA alleles.

Impact of derived global weather data on simulated crop yields

Crop simulation models can be used to estimate impact of current and future climates on crop yields and food security, but require long-term historical daily weather data to obtain robust simulations. In many regions where crops are grown, daily weather data are not available. Alternatively, gridded weather databases (GWD) with complete terrestrial coverage are available, typically derived from: (i) global circulation computer models; (ii) interpolated weather station data; or (iii) remotely sensed surface data from satellites. The present study's objective is to evaluate capacity of GWDs to simulate crop yield potential (Yp) or water-limited yield potential (Yw), which can serve as benchmarks to assess impact of climate change scenarios on crop productivity and land use change. Three GWDs (CRU, NCEP/DOE, and NASA POWER data) were evaluated for their ability to simulate Yp and Yw of rice in China, USA maize, and wheat in Germany. Simulations of Yp and Yw based on recorded daily data from well-maintained weather stations were taken as the control weather data (CWD). Agreement between simulations of Yp or Yw based on CWD and those based on GWD was poor with the latter having strong bias and large root mean square errors (RMSEs) that were 26-72% of absolute mean yield across locations and years. In contrast, simulated Yp or Yw using observed daily weather data from stations in the NOAA database combined with solar radiation from the NASA-POWER database were in much better agreement with Yp and Yw simulated with CWD (i.e. little bias and an RMSE of 12-19% of the absolute mean). We conclude that results from studies that rely on GWD to simulate agricultural productivity in current and future climates are highly uncertain. An alternative approach would impose a climate scenario on location-specific observed daily weather databases combined with an appropriate upscaling method.

Vaccine-induced gag-specific T cells are associated with reduced viremia after HIV-1 infection

The contribution of host T-cell immunity and HLA class I alleles to the control of human immunodeficiency virus (HIV-1) replication in natural infection is widely recognized. We assessed whether vaccine-induced T-cell immunity, or expression of certain HLA alleles, impacted HIV-1 control after infection in the Step MRKAd5/HIV-1 gag/pol/nef study. Vaccine-induced T cells were associated with reduced plasma viremia, with subjects targeting ≥3 gag peptides presenting with half-log lower mean viral loads than subjects without Gag responses. This effect was stronger in participants infected proximal to vaccination and was independent of our observed association of HLA-B*27, -B*57 and -B*58:01 alleles with lower HIV-1 viremia. These findings support the ability of vaccine-induced T-cell responses to influence postinfection outcome and provide a rationale for the generation of T-cell responses by vaccination to reduce viremia if protection from acquisition is not achieved. Clinical trials identifier: NCT00095576.

CD8(+) T-cell effector function and transcriptional regulation during HIV pathogenesis

A detailed understanding of the immune response to human immunodeficiency virus (HIV) infection is needed to inform prevention and therapeutic strategies that aim to contain the acquired immunodeficiency syndrome (AIDS) pandemic. The cellular immune response plays a critical role in controlling viral replication during HIV infection and will likely need to be a part of any vaccine approach. The qualitative feature of the cellular response most closely associated with immunological control of HIV infection is CD8(+) T-cell cytotoxic potential, which is responsible for mediating the elimination of infected CD4(+) T cells. Understanding the underlying mechanisms involved in regulating the elicitation and maintenance of this kind of effector response can provide guidance for vaccine design. In this review, we discuss the evidence for CD8(+) T cells as correlates of protection, the means by which their antiviral capacity is evaluated, and transcription factors responsible for their function, or dysfunction, during HIV infection.

Updating beliefs and combining evidence in adaptive forest management under climate change: a case study of Norway spruce (Picea abies L. Karst) in the Black Forest, Germany

We study climate uncertainty and how managers' beliefs about climate change develop and influence their decisions. We develop an approach for updating knowledge and beliefs based on the observation of forest and climate variables and illustrate its application for the adaptive management of an even-aged Norway spruce (Picea abies L. Karst) forest in the Black Forest, Germany. We simulated forest development under a range of climate change scenarios and forest management alternatives. Our analysis used Bayesian updating and Dempster's rule of combination to simulate how observations of climate and forest variables may influence a decision maker's beliefs about climate development and thereby management decisions. While forest managers may be inclined to rely on observed forest variables to infer climate change and impacts, we found that observation of climate state, e.g. temperature or precipitation is superior for updating beliefs and supporting decision-making. However, with little conflict among information sources, the strongest evidence would be offered by a combination of at least two informative variables, e.g., temperature and precipitation. The success of adaptive forest management depends on when managers switch to forward-looking management schemes. Thus, robust climate adaptation policies may depend crucially on a better understanding of what factors influence managers' belief in climate change.

Immunogenicity of seven new recombinant yellow fever viruses 17D expressing fragments of SIVmac239 Gag, Nef, and Vif in Indian rhesus macaques

An effective vaccine remains the best solution to stop the spread of human immunodeficiency virus (HIV). Cellular immune responses have been repeatedly associated with control of viral replication and thus may be an important element of the immune response that must be evoked by an efficacious vaccine. Recombinant viral vectors can induce potent T-cell responses. Although several viral vectors have been developed to deliver HIV genes, only a few have been advanced for clinical trials. The live-attenuated yellow fever vaccine virus 17D (YF17D) has many properties that make it an attractive vector for AIDS vaccine regimens. YF17D is well tolerated in humans and vaccination induces robust T-cell responses that persist for years. Additionally, methods to manipulate the YF17D genome have been established, enabling the generation of recombinant (r)YF17D vectors carrying genes from unrelated pathogens. Here, we report the generation of seven new rYF17D viruses expressing fragments of simian immunodeficiency virus (SIV)mac239 Gag, Nef, and Vif. Studies in Indian rhesus macaques demonstrated that these live-attenuated vectors replicated in vivo, but only elicited low levels of SIV-specific cellular responses. Boosting with recombinant Adenovirus type-5 (rAd5) vectors resulted in robust expansion of SIV-specific CD8⁺ T-cell responses, particularly those targeting Vif. Priming with rYF17D also increased the frequency of CD4⁺ cellular responses in rYF17D/rAd5-immunized macaques compared to animals that received rAd5 only. The effect of the rYF17D prime on the breadth of SIV-specific T-cell responses was limited and we also found evidence that some rYF17D vectors were more effective than others at priming SIV-specific T-cell responses. Together, our data suggest that YF17D – a clinically relevant vaccine vector – can be used to prime AIDS virus-specific T-cell responses in heterologous prime boost regimens. However, it will be important to optimize rYF17D-based vaccine regimens to ensure maximum delivery of all immunogens in a multivalent vaccine.

Antibody selection and amino acid reversions

Pathogens adapt to antibody surveillance through amino acid replacements in targeted protein regions, or epitopes, that interfere with antibody binding. However, such escape mutations may exact a fitness cost due to impaired protein function. Here, it is hypothesized that the recurring generation of specific neutralizing antibodies to an epitope region as it evolves in response to antibody selection will cause amino acid reversions by releasing early escape mutations from immune selection. The plausibility of this hypothesis was tested with stochastic simulation of adaptation at the molecular sequence level in finite populations. Under the conditions of strong selection and weak mutation, the rates of allele fixation and amino acid reversion increased with population size and selection coefficients. These rates decreased with population size, however, if mutation became strong, because clonal interference reduced the rate of adaptation. The model successfully predicts the rate of reversion per allele fixation for an important human immunodeficiency virus type 1 (HIV-1) antibody epitope region. Therefore, antibody selection may generate complex adaptive dynamics.

Improved composting of poultry feces via supplementation with ammonia oxidizing archaea

Ammonia-oxidizing archaea (AOA) play an important role in the oxidation of ammonia. However, the participation of AOA in the composting process has not been established. The addition of AOA to a compost mix was able to speed up both the onset of the hyperthermic phase and the composting time. The composition of the microflora and the relative abundance were determined by using denaturing gradient gel electrophoresis and quantitative real-time PCR, based on the presence of the archaeal amoA genes. The amplicon profiles allowed some of the major AOA species present in the final compost to be identified, and their relative abundance to be estimated from their amplification intensity. The lower pH during the lower temperature phase of compost served to enhance the nitrogen content of the final compost. The addition of AOA resulted in the expanding diversity of microflora species than that of the natural colonization.

Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland Honeyeater (Phylidonyris novaehollandiae)

Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits - shorter, deeper bills, longer tarsi, and longer wings - would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale.

Global air quality and climate

Emissions of air pollutants and their precursors determine regional air quality and can alter climate. Climate change can perturb the long-range transport, chemical processing, and local meteorology that influence air pollution. We review the implications of projected changes in methane (CH(4)), ozone precursors (O(3)), and aerosols for climate (expressed in terms of the radiative forcing metric or changes in global surface temperature) and hemispheric-to-continental scale air quality. Reducing the O(3) precursor CH(4) would slow near-term warming by decreasing both CH(4) and tropospheric O(3). Uncertainty remains as to the net climate forcing from anthropogenic nitrogen oxide (NO(x)) emissions, which increase tropospheric O(3) (warming) but also increase aerosols and decrease CH(4) (both cooling). Anthropogenic emissions of carbon monoxide (CO) and non-CH(4) volatile organic compounds (NMVOC) warm by increasing both O(3) and CH(4). Radiative impacts from secondary organic aerosols (SOA) are poorly understood. Black carbon emission controls, by reducing the absorption of sunlight in the atmosphere and on snow and ice, have the potential to slow near-term warming, but uncertainties in coincident emissions of reflective (cooling) aerosols and poorly constrained cloud indirect effects confound robust estimates of net climate impacts. Reducing sulfate and nitrate aerosols would improve air quality and lessen interference with the hydrologic cycle, but lead to warming. A holistic and balanced view is thus needed to assess how air pollution controls influence climate; a first step towards this goal involves estimating net climate impacts from individual emission sectors. Modeling and observational analyses suggest a warming climate degrades air quality (increasing surface O(3) and particulate matter) in many populated regions, including during pollution episodes. Prior Intergovernmental Panel on Climate Change (IPCC) scenarios (SRES) allowed unconstrained growth, whereas the Representative Concentration Pathway (RCP) scenarios assume uniformly an aggressive reduction, of air pollutant emissions. New estimates from the current generation of chemistry-climate models with RCP emissions thus project improved air quality over the next century relative to those using the IPCC SRES scenarios. These two sets of projections likely bracket possible futures. We find that uncertainty in emission-driven changes in air quality is generally greater than uncertainty in climate-driven changes. Confidence in air quality projections is limited by the reliability of anthropogenic emission trajectories and the uncertainties in regional climate responses, feedbacks with the terrestrial biosphere, and oxidation pathways affecting O(3) and SOA.