A review of iguanian and anguimorph lizard genitalia (Squamata: Chamaeleonidae; Varanoidea, Shinisauridae, Xenosauridae, Anguidae) and their phylogenetic significance: comparisons with molecular data sets

We compare phylogenetic hypotheses for iguanian (chameleonids) and anguimorph lizard groups (varanoids, xenosauroids, anguids) which were generated from analyses of genital (hemipenial) morphology, with recent molecular phylogenetic approaches towards the same groups. Taxa with infraspecific communication by means of visible, sexually dimorphic epigamic characters usually have less diverse genital structures than taxa with less developed visible epigamic characters but with a more highly developed chemical intersexual communication. Generally, it turned out in the cases considered here, that phylogenetic hypotheses based on hemipenial characters coincide much better with molecular-genetic phylogenies than with earlier concepts based solely on external morphology. It seems that genital morphological characters are phylogenetically more informative – on both the species and the supraspecific level – than external morphological characters at least in these examples, because the former seem not to be affected by environmental selective pressures but seem to be only subject to sexual selection. Our data suggest that sexual selective pressure on genital structural diversity is higher the less sexually dimorphic, optical cues for infraspecific communication have evolved. They further suggest a correlation with the mating system (single versus multiple matings).     

Effect of stand age on greenhouse gas fluxes from a Sitka spruce [Picea sitchensis (Bong.) Carr.] chronosequence on a peaty gley soil

The influence of forest stand age in a Picea sitchensis plantation on (1) soil fluxes of three greenhouse gases (GHGs – CO₂, CH₄ and N₂O) and (2) overall net ecosystem global warming potential (GWP), was investigated in a 2‐year study. The objective was to isolate the effect of forest stand age on soil edaphic characteristics (temperature, water table and volumetric moisture) and the consequent influence of these characteristics on the GHG fluxes. Fluxes were measured in a chronosequence in Harwood, England, with sites comprising 30‐ and 20‐year‐old second rotation forest and a site clearfelled (CF) some 18 months before measurement. Adjoining unforested grassland (UN) acted as a control. Comparisons were made between flux data, soil temperature and moisture data and, at the 30‐year‐old and CF sites, eddy covariance data for net ecosystem carbon (C) exchange (NEE). The main findings were: firstly, integrated CO₂ efflux was the dominant influence on the GHG budget, contributing 93–94% of the total GHG flux across the chronosequence compared with 6–7% from CH₄ and N₂O combined. Secondly, there were clear links between the trends in edaphic factors as the forest matured, or after clearfelling, and the emission of GHGs. In the chronosequence sites, annual fluxes of CO₂ were lower at the 20‐year‐old (20y) site than at the 30‐year‐old (30y) and CF sites, with soil temperature the dominant control. CH₄ efflux was highest at the CF site, with peak flux 491±54.5 μg m⁻² h⁻¹ and maximum annual flux 18.0±1.1 kg CH₄ ha⁻¹ yr⁻¹. No consistent uptake of CH₄ was noted at any site. A linear relationship was found between log CH₄ flux and the closeness of the water table to the soil surface across all sites. N₂O efflux was highest in the 30y site, reaching 108±38.3 μg N₂O‐N m⁻² h⁻¹ (171 μg N₂O m⁻² h⁻¹) in midsummer and a maximum annual flux of 4.7±1.2 kg N₂O ha⁻¹ yr⁻¹ in 2001. Automatic chamber data showed a positive exponential relationship between N₂O flux and soil temperature at this site. The relationship between N₂O emission and soil volumetric moisture indicated an optimum moisture content for N₂O flux of 40–50% by volume. The relationship between C : N ratio data and integrated N₂O flux was consistent with a pattern previously noted across temperate and boreal forest soils.     

The problems of sustainable water use in the Mediterranean and research requirements for agriculture

This study addresses the sustainable use of water resources in the Mediterranean basin, particularly in the Southern and Eastern parts of the region, and the many problems generated by water scarcity and misuse. Water economy in the region is beset by two specific problems: high irrigation needs and changes in consumer demands (especially after population shifts from rural to urban areas and because of increasing tourism and industrialisation). The challenges presented by the water crisis are even greater because of growing populations and estimated future climatic changes in the region. The integrated management of limited water resources in the Southern and Eastern parts of the Mediterranean involves several areas of research. Those most directly related with agriculture concern improving water (and nutrient) use in agriculture through the management and breeding of irrigated and rain-fed crops. However, these fields of research address only one face of a multi-factorial equation that affects water sustainability in the region. Thus, other research fields include the design of comprehensive water policies and integrated planning, and technologies for advanced water treatment and re-use. Moreover, local problems and socio-economic aspects must be considered when addressing research issues.     

ITMSQ: A software tool for N‐ and C‐terminal fragment ion pairs based isobaric tandem mass spectrometry quantification

Tandem MS (MS2) quantification using the series of N‐ and C‐terminal fragment ion pairs generated from isobaric‐labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64 and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solutionfor N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantitative methods.     

A slide down a slippery slope – alpine ecosystem responses to nitrogen deposition

Background: Nitrogen (N) deposition in the Front Range of the southern Rocky Mountains has been increasing for several decades, and has exceeded the critical load for several ecological metrics.

Aims: Our objective was to predict potential future ecological changes in alpine zones in response to anthropogenic N deposition based on a review of research from Niwot Ridge, Colorado.

Results: Empirical observations and experimental studies indicate that plant, algal and soil microbe species compositions are changing in response to N deposition, with nitrophilic species increasing in abundance. Biotic sequestration of N deposition is insufficient to compensate for greater nitrate production, leading to the potential for acidification and base cation loss.

Conclusions: Changes in biotic composition in both terrestrial and aquatic ecosystems have important impacts on ecosystem functioning, including a lower capacity to take up and neutralise the acidifying effect of anthropogenic N, increasing phosphorus limitation of production in terrestrial and aquatic systems, and shifts in rates of N and carbon cycling. Continued elevated N deposition rates coupled with ongoing climate change, including warmer summer temperatures and lower snow cover of shorter duration, will influence the ecological thresholds for biotic and functional changes. We suggest that these thresholds will occur at lower inputs of N deposition under future climate change, meriting reconsideration of current N critical loads to protect sensitive alpine ecosystems.     

Influence of soil texture and crop management on the productivity of miscanthus (Miscanthus × giganteus Greef et Deu.) in the Mediterranean

Biomass productivity is the main favorable trait of candidate bioenergy crops. Miscanthus × giganteus is a promising species, due to its high‐yield potential and positive traits including low nutrient requirements and potential for C sequestration in soils. However, miscanthus productivity appears to be mostly related to water availability in the soil. This is important, particularly in Mediterranean regions where the risk of summer droughts is high. To date, there have been no studies on miscanthus responses under different soil conditions, while only a few have investigated the role of different crop managements, such as irrigation and nitrogen fertilization, in the Mediterranean. Therefore, the effects of contrasting soil textures (i.e. silty‐clay‐loam vs. sandy‐loam) and alternative agricultural intensification regimes (i.e. rainfed vs. irrigated and 0, 50, 100 kg ha^?1 nitrogen fertilization), on miscanthus productivity were evaluated at three different harvest times for two consecutive years. Our results confirmed the importance of water availability in determining satisfactory yields in Mediterranean environments, and how soil and site characteristics strongly affect biomass production. We found that the aboveground dry yields varied between 5 Mg ha^?1 up to 29 Mg ha^?1. Conversely, nitrogen fertilization played only a minor role on crop productivity, and high fertilization levels were relatively inefficient. Finally, a marked decrease, of up to ?40%, in the aboveground yield occurred when the harvest time was delayed from autumn to winter. Overall, our results highlighted the importance of determining crop responses on a site‐by‐site basis, and that decisions on the optimal harvest time should be driven by the biomass end use and other long‐term considerations, such as yield stability and the maintenance of soil fertility.     

Enhanced extraction of proteins using cholinium‐based ionic liquids as phase‐forming components of aqueous biphasic systems

Aqueous biphasic systems (ABS) composed of ionic liquids (ILs) are promising platforms for the extraction and purification of proteins. In this work, a series of alternative and biocompatible ABS composed of cholinium‐based ILs and polypropylene glycol were investigated. The respective ternary phase diagrams, tie‐lines, tie‐line lengths and critical points were determined at 25°C. The extraction performance of these systems for commercial bovine serum albumin (BSA) was then evaluated. The stability of BSA at the IL‐rich phase was ascertained by size exclusion high‐performance liquid chromatography and Fourier transform infrared spectroscopy. Appropriate ILs lead to the complete extraction of BSA for the IL‐rich phase, in a single step, while maintaining the protein's native conformation. Furthermore, to evaluate the performance of these systems when applied to real matrices, the extraction of BSA from bovine serum was additionally carried out, revealing that the complete extraction of BSA was maintained and achieved in a single step. The remarkable extraction efficiencies obtained are far superior to those observed with typical polymer‐based ABS. Therefore, the proposed ABS may be envisaged as a more effective and biocompatible approach for the separation and purification of other value‐added proteins.     

Soil carbon balance following conversion of grassland to oil palm

Oil palm (Elaeis guineensis Jacq.) crops are expanding rapidly in the tropics, with implications for the global carbon cycle. Little is currently known about soil organic carbon (SOC) dynamics following conversion to oil palm and virtually nothing for conversion of grassland. We measured changes in SOC stocks following conversion of tropical grassland to oil palm plantations in Papua New Guinea using a chronosequence of plantations planted over a 25‐year period. We further used carbon isotopes to quantify the loss of grassland‐derived and gain in oil palm‐derived SOC over this period. The grassland and oil palm soils had average SOC stocks of 10.7 and 12.0 kg m^?2, respectively, across all the study sites, to a depth of 1.5 m. In the 0–0.05 m depth interval, 0.79 kg m^?2 of SOC was gained from oil palm inputs over 25 years and approximately the same amount of the original grass‐derived SOC was lost. For the whole soil profile (0–1.5 m), 3.4 kg m^?2 of SOC was gained from oil palm inputs with no significant losses of grass‐derived SOC. The grass‐derived SOC stocks were more resistant to decrease than SOC reported in other studies. Black carbon produced in grassfires could partially but not fully account for the persistence of the original SOC stocks. Oil palm‐derived SOC accumulated more slowly where soil nitrogen contents where high. Forest soils in the same region had smaller carbon stocks than the grasslands. In the majority of cases, conversion of grassland to oil palm plantations in this region resulted in net sequestration of soil organic carbon.