Functional assessment of genetic variants of α1-Antitrypsin

Summary The specific activity of thirteen genetic variants of the protease inhibitor ₁-antitrypsin (₁-AT) has been determined. Elastase inhibitor activity was assayed using protein substrates (elastin and gelatin) and the synthetic substrate N-tert-butoxycarbonyl-l-alanine p-nitrophenyl ester. The synthetic substrate -N-benzoyl-dl-arginine p-nitroanilide HCl was used to assay trypsin inhibitor activity. The specific activity of ₁-AT was expressed as serum inhibition/immunological concentration of ₁-AT. Sera of PI type FM had reduced specific activity with elastase, but not with trypsin. With the possible exception of MP, no other variants showed significant differences in specific activity when compared with normal PI type M.This research was supported by the Medical Research Council of Canada (No. MA 5426)     

Quantitative assessment of organism–environment couplings

The evolutionary implications of environmental change due to organismic action remain a controversial issue, after a decades—long debate on the subject. Much of this debate has been conducted in qualitative fashion, despite the availability of mathematical models for organism–environment interactions, and for gene frequencies when allele fitness can be related to exploitation of a particular environmental resource. In this article we focus on representative models dealing with niche construction, ecosystem engineering, the Gaia Hypothesis and community interactions of Lotka–Volterra type, and show that their quantitative character helps bring into sharper focus the similarities and differences among their respective theoretical contexts.     

Validation of biomarkers of food intake—critical assessment of candidate biomarkers

Biomarkers of food intake (BFIs) are a promising tool for limiting misclassification in nutrition research where more subjective dietary assessment instruments are used. They may also be used to assess compliance to dietary guidelines or to a dietary intervention. Biomarkers therefore hold promise for direct and objective measurement of food intake. However, the number of comprehensively validated biomarkers of food intake is limited to just a few. Many new candidate biomarkers emerge from metabolic profiling studies and from advances in food chemistry. Furthermore, candidate food intake biomarkers may also be identified based on extensive literature reviews such as described in the guidelines for Biomarker of Food Intake Reviews (BFIRev). To systematically and critically assess the validity of candidate biomarkers of food intake, it is necessary to outline and streamline an optimal and reproducible validation process. A consensus-based procedure was used to provide and evaluate a set of the most important criteria for systematic validation of BFIs. As a result, a validation procedure was developed including eight criteria, plausibility, dose-response, time-response, robustness, reliability, stability, analytical performance, and inter-laboratory reproducibility. The validation has a dual purpose: (1) to estimate the current level of validation of candidate biomarkers of food intake based on an objective and systematic approach and (2) to pinpoint which additional studies are needed to provide full validation of each candidate biomarker of food intake. This position paper on biomarker of food intake validation outlines the second step of the BFIRev procedure but may also be used as such for validation of new candidate biomarkers identified, e.g., in food metabolomic studies.     

Life cycle assessment of aquaculture systems—a review of methodologies

Purpose  

As capture fishery production has reached its limits and global demand for aquatic products is still increasing, aquaculture has become the world’s fastest growing animal production sector. In attempts to evaluate the environmental consequences of this rapid expansion, life cycle assessment (LCA) has become a frequently used method. The present review of current peer-reviewed literature focusing on LCA of aquaculture systems is intended to clarify the methodological choices made, identify possible data gaps, and provide recommendations for future development within this field of research. The results of this review will also serve as a start-up activity of the EU FP7 SEAT (Sustaining Ethical Aquaculture Trade) project, which aims to perform several LCA studies on aquaculture systems in Asia over the next few years.     

Precision nutrition — review of methods for point-of-care assessment of nutritional status

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Allergenicity assessment of genetically modified crops--what makes sense?

GM crops have great potential to improve food quality, increase harvest yields and decrease dependency on certain chemical pesticides. Before entering the market their safety needs to be scrutinized. This includes a detailed analysis of allergenic risks, as the safety of allergic consumers has high priority. However, not all tests currently being applied to assessing allergenicity have a sound scientific basis. Recent events with transgenic crops reveal the fallacy of applying such tests to GM crops.     

Phylogenetic assessment of filoviruses: how many lineages of Marburg virus?

Filoviruses have to date been considered as consisting of one diverse genus (Ebola viruses) and one undifferentiated genus (Marburg virus). We reconsider this idea by means of detailed phylogenetic analyses of sequence data available for the Filoviridae: using coalescent simulations, we ascertain that two Marburg isolates (termed the "RAVN" strain) represent a quite-distinct lineage that should be considered in studies of biogeography and host associations, and may merit recognition at the level of species. In contrast, filovirus isolates recently obtained from bat tissues are not distinct from previously known strains, and should be considered as drawn from the same population. Implications for understanding the transmission geography and host associations of these viruses are discussed.     

Risk assessment of GM plants: avoiding gridlock?

Cultivation of genetically modified crops is presently based largely on four crops containing few transgenes and grown in four countries. This will soon change and pose new challenges for risk assessment. A more structured approach that is as generic as possible is advocated to study consequences of gene flow. Hazards should be precisely defined and prioritized, with emphasis on quantifying elements of exposure. This requires coordinated effort between large, multidisciplinary research teams.     

Quantitative assessment of the association of the α-I fragment of spectrin with oligomers of intact spectrin

• 1.1. The α-I fragment of human spectrin that carries the binding site on the α-chain of spectrin for the β -chain has been purified from limited trypsin digests of spectrin by means of FPLC.
• 2.2. The self-association of spectrin and the binding of the α-I fragment to spectrin heterodimers and to tetramers have been quantified through the use of gel electrophoresis, staining with Coomassie Blue, and quantification of the bound dye following elution with pyridine.
• 3.3. The parameters of self-association were found to be consistent with those estimated from sedimentation equilibrium analysis.
• 4.4. The data were consistent with a model in which both self-association and the binding of the α-I fragment are considered to occur through an intermediate in which the α-β interface is initially dissociated. The α-β interface in the heterodimer was found to be less stable than that of higher oligomers by approx. 3 kJ/mol.

     

Social aspects for sustainability assessment of technologies—challenges for social life cycle assessment (SLCA)

Purpose

Technologies can contribute to sustainable development (e.g., improving living conditions) and at the same time cause sustainability problems (e.g., emissions). Decisions on alternative technologies should thus ideally be based on the principle to minimize the latter. Analyzing environmental, economic, and social aspects related to technologies supports decisions by identifying the “more sustainable” technology. This paper focuses on social issues. First, it discusses the applicability of the social life cycle assessment (SLCA) guidelines for a comparative technology analysis, taking the example of two case studies in developing countries. Indicating technologies as “sustainable” also means that they are indeed operated over the expected lifetime, which, in development projects, is often not guaranteed. Consequently, social aspects related to implementation conditions should be considered in an SLCA study as well. Thus, a second focus is laid on identifying appropriate indicators to address these aspects.

Methods

First, the SLCA guidelines were examined with regard to applying this product-related approach to two real case studies (analysis of technologies/plants for water supply and for decentralized fuel production) for a comparative technology analysis. Suitable indicators are proposed. To address the second focus, a literature research on technology assessment and implementation in developing countries was conducted. Moreover, socioeconomic studies in the investigation areas of the case studies were consulted. Based on this, indicators addressing implementation conditions were identified from the SLCA guidelines and additional literature.

Results and discussion

The study shows social issues and indicators found in the SLCA guidelines and considered suitable for a comparative technology analysis in the case studies. However, for a sustainability assessment of technologies, especially in developing countries, further indicators are required to address technology implementation conditions. A set of additional social indicators like reported trust in institutions or fluctuation of personnel is proposed. Though these indicators were derived based on specific case studies, they can also be suggested to other technologies and are not necessarily limited to developing countries.

Conclusions

The study pointed out that an application of the SLCA guidelines considering the whole life cycle was not (yet) feasible for the case studies considered. This is mainly due to the lack of data. Regarding technology implementation, it was examined which indicators are available in this SLCA approach and which could additionally be integrated and applied. This is relevant as a potential contribution of technologies to sustainable development can only be achieved when the technologies are successfully implemented.     

Aquatic plants–based risk model for assessment of ecological safety of rivers

In order to ensure the ecological safety in river beds, each project affecting it must be subjected to an evaluation in terms of its implementation results on the river habitats. Technical activities in the river beds can cause irreversible changes in their biocenosis. However, due to the lack of a method that allows us to predict these changes, the decisions made by designers and contractors can be evaluated only after completing the investment. Therefore, it is necessary to elaborate a method to evaluate the environmental safety in regulated and maintenanced rivers. This article presents a model that allows us to predict the changes in vascular aquatic plant communities, which result from technical interference in the river bed. The model was elaborated based on the results of the study performed in 2007–2011 in natural and transformed lowland watercourses from Lower Silesia area (Poland). It takes into account the elements of the watercourse bed ecosystem, which significantly affect the magnitude of the changes in plant communities. Based on this model, it is possible to evaluate the level of ecological risk associated with the execution of maintenance and regulatory works.     

Characteristics of a nickel–albumin binding assay for assessment of myocardial ischaemia

Background: The aim of this study was to describe a method to measure ischaemia-induced alterations of the binding capacity of serum albumin to exogenous nickel.

Methods: We measured the levels of cardiac troponin I (cTnI), serum albumin, ischaemia-modified albumin (IMA) measured by a cobalt–albumin binding assay (CABA), and a nickel–albumin binding assay (NABA) in the following groups: myocardial infarction (n?=?32) and non-ischaemic chest pain (n?=?64).

Results: IMA, cTnI and NABA levels were higher in the myocardial infarction group. NABA presented a higher ability to discriminate myocardial ischaemia than CABA.

Conclusions: Patients with myocardial infarction have reduced nickel binding to human serum albumin, and NABA may have an important role as an early marker of myocardial ischaemia.     

Precautionary risk assessment of Bt maize: what uncertainties?

GM crops have become a test case for the conflicting slogans of 'the precautionary principle' versus 'sound science.' The issues can be illustrated by developments in regulatory science for Bt maize in the European Union. As this case study suggests, risk assessment is always framed by some account of the relevant uncertainties. These in turn depend upon how the environment is valued and how scientific questions are posed about cause-effect pathways of potential harm. The slogan of 'sound science' hides such judgements, by representing ignorance or value-judgements as 'science.' By contrast, precaution can challenge such judgements, identify new unknowns, generate different criteria for evidence, open up new scientific questions, and make these judgements more transparent. It is doubtful whether these complexities have been fully acknowledged by specialists, and thus whether the continued risk debate is due solely to a public misunderstanding of science.     

Computational methods for evaluation of cell-based data assessment—Bioconductor

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Highlights► Bioconductor proposes more than 20 R packages for FCM analysis. ► Data infrastructure proposed by flowCore has become the standard for many packages. ► Automated gating is improving but remains an intensive field of research.     

Telomere length assessment: biomarker of chronic oxidative stress?

Telomeres are nucleoprotein structures, located at the ends of chromosomes and are subject to shortening at each cycle of cell division. They prevent chromosomal ends from being recognized as double strand breaks and protect them from end to end fusion and degradation. Telomeres consist of stretches of repetitive DNA with a high G-C content and are reported to be highly sensitive to damage induced by oxidative stress. The resulting DNA strand breaks can be formed either directly or as an intermediate step during the repair of oxidative bases. In contrast to the majority of genomic DNA, there is evidence that telomeric DNA is deficient in the repair of single strand breaks. Since chronic oxidative stress plays a major role in the pathophysiology of several chronic inflammatory diseases, it is hypothesized that telomere length is reducing at a faster rate during oxidative stress. Therefore, assessment of telomere length might be a useful biomarker of disease progression. In this review several features of telomere length regulation, their relation with oxidative stress, and the potential application of measurement of telomere length as biomarker of chronic oxidative stress, will be discussed.     

Ecological assessment of groundwater ecosystems – Vision or illusion?

Environmental policy and in particular the European water legislation, in the framework of the EU Groundwater Directive, has started to consider groundwater not only as a resource but as a living ecosystem. A precondition for comprehensive groundwater protection is thus the assessment of the biological and ecological state. The assessment of ecosystems requires consideration of ecological criteria, which so far are not available for groundwater systems. In the framework of a national project, the German Federal Environment Agency (UBA) supports a consortium of scientists and stakeholders from water boards and regional environmental authorities to develop a first concept for an ecological assessment scheme for groundwater ecosystems. The attempts towards an integrative concept include the following steps: (i) selection of appropriate biological and ecological parameters, (ii) typology of groundwater ecosystems, (iii) derivation of a reference status (Leitbild) and natural background values for biological variables, (iv) identification of potential bioindicators and definition of threshold values, and (v) development of an assessment model. These proposed steps are discussed on the basis of a data set from two groundwater landscapes in Southern Germany. Investigations considered three different spatial units, i.e. the habitat unit at the local scale, and the aquifer type unit as well as the landscape unit at the regional scale. Fauna as well as bacterial communities could provide valuable ecological information on the ecosystems status. The paper reviews ‘state of the art’ knowledge and evaluates the near future perspectives for the development and implementation of groundwater ecosystems assessment programmes.     

Application of RAPD markers for characterization of γ-ray-induced rose mutants and assessment of genetic diversity

Six parent and their 12 gamma ray-induced somatic flower colour mutants of garden rose were characterized to discriminate the mutants from their respective parents and understanding the genetic diversity using Random amplification of polymorphic DNA (RAPD) markers. Out of 20 primers screened, 14 primers yielded completely identical fragments patterns. The other 7 primers gave highly polymorphic banding patterns among the radiomutants. All the cultivars were identified by using only 7 primers. Moreover, individual mutants were also distinguished by unique RAPD marker bands. Based on the presence or absence of the 48 polymorphic bands, the genetic variations within and among the 18 cultivars were measured. Genetic distance between all 18 cultivars varied from 0.40 to 0.91, as revealed by Jaccard’s coefficient matrix. A dendrogram was constructed based on the similarity matrix using the Neighbor Joining Tree method showed three main clusters. The present RAPD analysis can be used not only for estimating genetic diversity present in gamma ray-induced mutants but also for correct identification of mutant/new varieties for their legal protection under plant variety rights.     

Analysis of informativeness of immunohistochemical and flow cytometric methods for estrogen receptor α assessment

Informative capacity analysis of immunohistochemistry (IHC) and flow cytometry (FCM) in the assessment of estrogen receptor α (ERα) expression in breast cancer tissue was performed. Similar frequencies of expression were shown by both methods: 27% of ERα-negative and 73% ERα-positive cases. However, IHC evaluation detected low levels in only 20% of ERα-positive cases, whereas low levels of ERα detected by FCM were 2 times more often (48%). Moreover, FCM revealed positive expression (23–60%) in 33% of IHC ERα-negative cases. Among IHC ER-positive cases, zero ERα expression was detected by FCM in 12.5%. The approaches to minimize errors in routine clinical determination of the estrogen receptor status were proposed.     

Power of counter movement jumps with external load – coherence of three assessment methods

Background

The purpose of this study was to evaluate the coherence between three different methods assessing the power driven from a counter movement jump (CMJ); the Powertimer 300-series contact mat (C-mat), the MuscleLab 4010 infrared mat (IR-mat) and the MuscleLab 4010 linear encoder (M-encoder), and to evaluate the test-retest reliability of the M-encoder.

Methods

Twenty-two males and 29 female, elite athletes performed two test sessions with three days in between. Each test session included counter movement jumps (CMJ) performed on a Smith-machine with external loads of 40 kg. Jump height and flight time were assessed with C-mat and IR-mat, and power was additionally assessed with C-mat. Variables analyzed from the M-encoder were average power (AP), average force (AV), average velocity (AV), and distance (D).

Results

The results from the C-mat were systematically higher than the ones obtained from the M-encoder and IR-mat. The correlation between the C-mat, M-encoder and the IR-mat was strong (r_p?=?0.95-0.98). The results showed a high test-retest reliability for all indices assessed with the M-encoder, AP (r_p?=?0.97, p?<?0.001; TE%?=?3.9%), AF (r_p?=?0.99, p?<?0.001; TE%?=?1.4%). Furthermore, the AV had high values (r_p?=?0.94, p?<?0.001; TE%?=?2.9%) as well as D (r_p?=?0.87, p?<?0.001; TE%?=?5.4%).

Conclusion

It is important to use the same equipment in both pre- and post-testing, since all three methods were reliable, coherent but not interchangeable to each other.