Contemplating the future: Acting now on long‐term monitoring to answer 2050's questions

In 2050, which aspects of ecosystem change will we regret not having measured? Long‐term monitoring plays a crucial part in managing Australia's natural environment because time is a key factor underpinning changes in ecosystems. It is critical to start measuring key attributes of ecosystems – and the human and natural process affecting them – now, so that we can track the trajectory of change over time. This will facilitate informed choices about how to manage ecological changes (including interventions where they are required) and promote better understanding by 2050 of how particular ecosystems have been shaped over time. There will be considerable value in building on existing long‐term monitoring programmes because this can add significantly to the temporal depth of information. The economic and social processes driving change in ecosystems are not identical in all ecosystems, so much of what is monitored (and the means by which it is monitored) will most likely target specific ecosystems or groups of ecosystems. To best understand the effects of ecosystem‐specific threats and drivers, monitoring also will need to address the economic and social factors underpinning ecosystem‐specific change. Therefore, robust assessments of the state of Australia's environment will be best achieved by reporting on the ecological performance of a representative sample of ecosystems over time. Political, policy and financial support to implement appropriate ecosystem‐specific monitoring is a perennial problem. We suggest that the value of ecological monitoring will be demonstrable, when plot‐based monitoring data make a unique and crucial contribution to Australia's ability to produce environmental accounts, environmental reports (e.g. the State of the Environment, State of the Forests) and to fulfilling reporting obligations under international agreements, such as the Convention on Biological Diversity. This paper suggests what must be done to meet Australia's ecological information needs by 2050.     

Effects of residual hydrocarbons on the reed community after 10 years of oil extraction and the effectiveness of different biological indicators for the long-term risk assessments

The selection of certain indicators is critical to undertake ecological risk assessments of long-term oil pollution and other environmental changes. The indicators should be easily and routinely monitored, be sensitive to pollution, respond to pollution in a predictable manner, and match the spatial and temporal scales of investigations. To compare the effectiveness of indicators for the long-term risk assessments, this study investigated the multiple ecological effects of chronic oil pollution on the plant community dominated by reed (Phragmites australis). The physiology, growth and reproduction of reed, together with the composition and productivity of the reed community, were measured around oil wells that have operated for approximately 10 years in the Yellow River Delta, eastern China. The predictive power of each indicator was evaluated using the coefficients of determination (R²) of linear regression models established for each indicator and soil Total Petroleum Hydrocarbons (TPH) concentration. The sensitivities of indicators were evaluated by comparing slopes of new established regression lines using standardized data. The top three indicators in terms of predictive power were leaf length, width and number, followed by the Shannon–Wiener index, Pielou evenness index and Simpson's diversity index. Community aboveground biomass, foliar projective coverage and species richness showed predictive power lower than those of the three diversity indexes, but higher than those of leaf net photosynthetic rate, reed height, aboveground biomass and vertical projective coverage of reed plants. Leaf transpiration, chlorophyll concentration and reed stem density showed no significant linear response to elevated soil TPH concentration. In terms of sensitivity, the top three biological indicators were Pielou evenness index, Simpson's diversity index and Shannon–Wiener index, followed by community vertical projective coverage, community aboveground biomass, and species richness. Leaf number, length and width were moderately sensitive, followed by reed coverage, aboveground biomass and height. The sensitivity of net photosynthetic rate was the lowest. The predictive power and sensitivities of indicators were compared in terms of their spatial and temporal scales. In conclusion, scale can be used to facilitate the selection of indicators, and the combination of different indicators may yield improved understanding of the various effects of elevated soil TPH concentration at the different biological levels.     

Development of a Flooded Forest Anthropization Index (FFAI) applied to Amazonian areas under pressure from different human activities

The floodplain forests in the Amazon basin suffer from the continued exploitation of natural resources and, after being disturbed, show slow and sometimes irreversible recovery. Our goal was to create an index that could be used to assess the relative level of human disturbance in floodplain forests and determine the relative importance of different types of disturbance on a given site and between sites. The index proposed here (Flooded Forest Anthropization Index – FFAI) assesses human disturbance on a local scale and is composed by 15 indicators divided into three groups that represent different levels of impact: (1) simplification of ecosystems and reduction of local diversity; (2) ecosystem replacement/destruction; (3) disturbances with the potential to impact the ecosystem in both ways. The FFAI proved to be robust and revealed a wide range of values in the evaluated landscapes. The sites classified a priori as more anthropogenic showed significantly higher FFAI values than the less anthropogenic ones (0.14 ± 0.05 and 0.08 ± 0.02, respectively, F = 18.9, df = 19, p < 0.0001). The FFAI enabled a comprehensive assessment of human disturbance on a local scale in Amazonian floodplain forests and can be a useful tool for decision makers in choosing priority areas for interventions and for targeting the type of intervention that must be carried out. Although specific to floodplains, the index can be adjusted to be used in other ecosystems.     

Mass spectrometry meets the challenge of understanding the complexity of the lipoproteome: recent findings regarding proteins involved in dyslipidemia and cardiovascular disease

Despite the fact that link between dyslipidemia and atherosclerosis was made over 100 years ago, atherosclerosis remains a major cause of morbidity and mortality worldwide. Major efforts focus towards understanding lipid metabolism, particularly by studying its particle compartments in circulation: the lipoproteins. In recent years, mass spectrometry has played an integral role in the deep sequencing of the lipoproteome and in metabolism studies conducted in vivo. This review highlights the path of lipoprotein research towards state-of-the-art mass spectrometry with special emphasis on the method of selected reaction monitoring and its impact on apolipoprotein metabolism studies. Also presented is what is expected for the lipoprotein field with the recent advent of high resolution/accurate mass parallel reaction monitoring mass spectrometry. The benefits of high resolution/accurate mass measurements are demonstrated by example instrument workflows and by detailing a novel method to quantify very low levels of circulating proprotein convertase subtilisin-kexin type 9 in rabbit. It is anticipated that future clinical studies or clinical trials aimed to treat dyslipidemia by manipulating key regulatory proteins will benefit from the new and exciting opportunities afforded by the latest technologies in mass spectrometry.     

Advances in high-resolution quantitative proteomics: implications for clinical applications

The advances in high-resolution mass spectrometry instrumentation, capable of accurate mass measurement and fast acquisition, have enabled new approaches for targeted quantitative proteomics. More specifically, analyses performed on quadrupole-orbitrap mass spectrometers operated in parallel reaction monitoring (PRM) mode leverage the intrinsic high resolving power and trapping capabilities. The PRM technique offers unmatched degrees of selectivity and analytical sensitivity, typically required to analyze peptides in complex samples, such as those encountered in biomedical research or clinical studies. The features of PRM have provoked a paradigm change in targeted experiments, by decoupling acquisition and data processing. It has resulted in a new analytical workflow comprising distinct methods for each step, thus enabling much larger flexibility. The PRM technique was further enhanced by a new data acquisition scheme, allowing dynamic parameter settings. The potential of the technique may radically impact future quantitative proteomics studies.     

Proteomics for the detection of indirect markers of steroids treatment in bovine muscle

Despite the ban by the European Union, anabolic steroids might still be illicitly employed in bovine meat production. The surveillance of misuse of such potentially harmful molecules is necessary to guarantee consumers’ health. Analytical methods for drug residue control are based on LC‐MS/MS, but their efficacy can be hindered due to undetectable residual concentrations as a result of low‐dosage treatments. Screening methods based on the recognition of indirect biological effects of growth promoters’ administration, such as the alteration of protein expression, can improve the efficacy of surveillance. The present study was aimed at identifying modifications in the muscle protein expression pattern between bulls treated with an ear implant (Revalor‐XS®) containing trenbolone acetate (200 mg) and estradiol (40 mg), and untreated animals. The analysis of skeletal muscle was carried out using a tandem mass tags shotgun proteomics approach. We defined 28 candidate protein markers with a significantly altered expression induced by steroids administration. A subset of 18 candidate markers was validated by SRM and allowed to build a predictive model based on partial least square discriminant analysis. Our findings confirm the effectiveness of the proteomics approach as potential tool to overcome analytical limitations of drug residue monitoring.     

On‐line yeast propagation process monitoring and control using an intelligent automatic control system

The monitoring and control of bioprocesses is a challenging task. This applies particularly if the actions to the process have to be carried out in real‐time. This work presents a system for on‐line monitoring and control of batch yeast propagation under limiting conditions based on a virtual plant operator, which uses the concept of intelligent control algorithms by means of fuzzy logic theory. Process information is provided on‐line using a sensor array comprising the measurement of OD, operating temperature, pressure, density, dissolved oxygen, and pH value. In this context practical problems arising through on‐line sensing and signal processing are addressed. The preprocessed sensor data are fed to a neural network for on‐line biomass estimation. The root mean squared error of prediction is 4 × 10⁶ cells/mL. The proposed system then triggers temperature and aeration by usage of a temperature dependent metabolic growth model and sensor data. The deviation of the predicted biomass from that of the reference trajectory as modeled by the metabolic growth model and its temporal derivative are used as inputs for the fuzzy temperature controller. The inputs used by the fuzzy aeration controller are the deviation of measured extract from that of the reference trajectory, the predicted cell count, and the dissolved oxygen concentration. The fuzzy‐based expert system allows to provide the desired yeast cell concentration of 100–120 × 10⁶ cells/mL at a minimum residual extract limit of 6.0 g/100 g at the required point of time. Thus, a dynamic adjustment of the propagation process to the overall production schedule is possible in order to produce the required amount of biomass at the right time.     

Real‐time monitoring of incision profile during laser surgery using shock wave detection

Lack of sensory feedback during laser surgery prevents surgeons from discerning the exact location of the incision, which increases duration and complexity of the treatment. In this study we demonstrate a new method for monitoring of laser ablation procedures. Real‐time tracking of the exact three dimensional (3D) lesion profile is accomplished by detection of shock waves emanating from the ablation spot and subsequent reconstruction of the incision location using time‐of‐flight data obtained from multiple acoustic detectors. Here, incisions of up to 9 mm in depth, created by pulsed laser ablation of fresh bovine tissue samples, were successfully monitored in real time. It was further observed that, by utilizing as little as 12 detection elements, the incision profile can be characterized with accuracy below 0.5 mm in all three dimensions and in good agreement with histological examinations. The proposed method holds therefore promise for delivering high precision real‐time feedback during laser surgeries. (© 2013 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Indicators of restoration success in riparian tropical forests using multiple reference ecosystems

Forest restoration by planting trees often accelerates succession, but the trajectories toward reference ecosystems have rarely been evaluated. Using a chronosequence (4–53 years) of 26 riparian forest undergoing restoration in the Brazilian Atlantic Forest, we modeled how the variables representing forest structure, tree species richness and composition, and the proportion of plant functional guilds change through time. We also estimated the time required for these variables to reach different types of reference ecosystems: old‐growth forest (OGF), degraded forest, and secondary forest. Among the attributes which follow a predictable trajectory over time are: the basal area, canopy cover, density and tree species richness, as well as proportions of shade tolerant and slow growing species or individuals. Most of the variation in density of pteridophythes, lianas, shrubs and phorophythes, proportion of animal‐dispersed individuals, rarefied richness and floristic similarity with reference ecosystems remain unexplained. Estimated time to reach the reference ecosystems is, in general, shorter for structural attributes than for species composition or proportion of functional guilds. The length of this time varies among the three types of reference ecosystems for most attributes. For instance, tree species richness and proportion of shade tolerant or slow growing individuals become similar to secondary forests in about 40 years, but is estimated to take 70 years or more to reach the OGF. Of all the variables considered, canopy cover, basal area, density, and richness of the understory—by their ecological relevance and predictability—are recommended as ecological indicators for monitoring tropical forest restoration success.     

If we build – they mostly come: partial functional recovery but persistent compositional differences in wetland beetle community restoration

There is growing evidence of restoration success for wetland plant communities. However, little research has been done on the associated invertebrate community. We test whether restoring plant communities after peat extraction is sufficient for restoring the taxonomic and functional composition of beetle communities. We monitored taxonomic and trait‐based community metrics for beetle assemblages on restoration islands that were up to 13 years old and compared these with the adjacent “target” undisturbed peat bog. Recovery of beetle abundance, species richness, and trophic structure on the islands was remarkably rapid (i.e. within a decade) and converged on that of the undisturbed peat bog within 13 years after restoration commenced. In contrast, small, native, and poor‐dispersing taxa were persistently less abundant on the islands than in the undisturbed peat bog, causing persistent differences in species composition, even on the oldest islands. These poor‐dispersers probably need assistance to reach the islands and possibly ongoing intervention to allow them to survive there. Our findings emphasize the potential for functional trait analysis to reveal barriers to full restoration of insect community composition.