Photosynthetic responses of young cashew plants to varying environmental conditions

The aim of this study was to characterize gas exchange responses of young cashew plants to varying photosynthetic photon flux density (PPFD), temperature, vapor-pressure deficit (VPD), and intercellular CO2 concentration (Ci), under controlled conditions. Daily courses of gas exchange and chlorophyll a fluorescence parameters were measured under natural conditions. Maximum CO2 assimilation rates, under optimal controlled conditions, were about 13 mmol m-2 s-1 , with light saturation around 1,000 mmol m-2 s-1. Leaf temperatures between 25ºC and 35ºC were optimal for photosynthesis. Stomata showed sensitivity to CO2, and a closing response with increasing Ci. Increasing VPD had a small effect on CO2 assimilation rates, with a small decrease above 2.5 kPa. Stomata, however, were strongly affected by VPD, exhibiting gradual closure above 1.5 kPa. The reduced stomatal conductances at high VPD were efficient in restricting water losses by transpiration, demonstrating the species adaptability to dry environments. Under natural irradiance, CO2 assimilation rates were saturated in early morning, following thereafter the PPFD changes. Transient Fv/Fm decreases were registered around 11h, indicating the occurrence of photoinhibition. Decreases of excitation capture efficiency, decreases of effective quantum yield of photosystem II, and increases in non-photochemical quenching were consistent with the occurrence of photoprotection under excessive irradiance levels.

Are niche-based species distribution models transferable in space?

Aim To assess the geographical transferability of niche-based species distribution models fitted with two modelling techniques. Location Two distinct geographical study areas in Switzerland and Austria, in the subalpine and alpine belts. Methods Generalized linear and generalized additive models (GLM and GAM) with a binomial probability distribution and a logit link were fitted for 54 plant species, based on topoclimatic predictor variables. These models were then evaluated quantitatively and used for spatially explicit predictions within (internal evaluation and prediction) and between (external evaluation and prediction) the two regions. Comparisons of evaluations and spatial predictions between regions and models were conducted in order to test if species and methods meet the criteria of full transferability. By full transferability, we mean that: (1) the internal evaluation of models fitted in region A and B must be similar; (2) a model fitted in region A must at least retain a comparable external evaluation when projected into region B, and vice-versa; and (3) internal and external spatial predictions have to match within both regions. Results The measures of model fit are, on average, 24% higher for GAMs than for GLMs in both regions. However, the differences between internal and external evaluations (AUC coefficient) are also higher for GAMs than for GLMs (a difference of 30% for models fitted in Switzerland and 54% for models fitted in Austria). Transferability, as measured with the AUC evaluation, fails for 68% of the species in Switzerland and 55% in Austria for GLMs (respectively for 67% and 53% of the species for GAMs). For both GAMs and GLMs, the agreement between internal and external predictions is rather weak on average (Kulczynski's coefficient in the range 0.3-0.4), but varies widely among individual species. The dominant pattern is an asymmetrical transferability between the two study regions (a mean decrease of 20% for the AUC coefficient when the models are transferred from Switzerland and 13% when they are transferred from Austria). Main conclusions The large inter-specific variability observed among the 54 study species underlines the need to consider more than a few species to test properly the transferability of species distribution models. The pronounced asymmetry in transferability between the two study regions may be due to peculiarities of these regions, such as differences in the ranges of environmental predictors or the varied impact of land-use history, or to species-specific reasons like differential phenotypic plasticity, existence of ecotypes or varied dependence on biotic interactions that are not properly incorporated into niche-based models. The lower variation between internal and external evaluation of GLMs compared to GAMs further suggests that overfitting may reduce transferability. Overall, a limited geographical transferability calls for caution when projecting niche-based models for assessing the fate of species in future environments.

Machine learning for spatial environmental data. Theory, applications and software

The book presents the state of the art in machine learning algorithms (artificial neural networks of different architectures, support vector machines, etc.) as applied to the classification and mapping of spatially distributed environmental data. Basic geostatistical algorithms are presented as well. New trends in machine learning and their application to spatial data are given, and real case studies based on environmental and pollution data are carried out. The book provides a CD-ROM with the Machine Learning Office software, including sample sets of data, that will allow both students and researchers to put the concepts rapidly to practice.

Determining Pu-241 in environmental samples: case studies in alpine soils

A procedure was developed for determining Pu-241 activity in environmental samples. This beta emitter isotope of plutonium was measured by ultra low level liquid scintillation, after several separation and purification steps that involved the use of a highly selective extraction chromatographic resin (Eichrom-TEVA). Due to the lack of reference material for Pu-241, the method was nevertheless validated using four IAEA reference sediments with information values for Pu-241. Next, the method was used to determine the Pu-241 activity in alpine soils of Switzerland and France. The Pu-241/Pu-239,Pu-240 and Pu-238/Pu-239,Pu-240 activity ratios confirmed that Pu contamination in the tested alpine soils originated mainly from global fallout from nuclear weapon tests conducted in the fifties and sixties. Estimation of the date of the contamination, using the Pu-241/Am-241 age-dating method, further confirmed this origin. However, the Pu-241/Am-241 dating method was limited to samples where Pu-Am fractionation was insignificant. If any, the contribution of the Chernobyl accident is negligible.

Evolutionary fate of retroposed gene copies in the human genome.

Given that retroposed copies of genes are presumed to lack the regulatory elements required for their expression, retroposition has long been considered a mechanism without functional relevance. However, through an in silico assay for transcriptional activity, we identify here >1,000 transcribed retrocopies in the human genome, of which at least approximately 120 have evolved into bona fide genes. Among these, approximately 50 retrogenes have evolved functions in testes, more than half of which were recruited as functional autosomal counterparts of X-linked genes during spermatogenesis. Generally, retrogenes emerge "out of the testis," because they are often initially transcribed in testis and later evolve stronger and sometimes more diverse spatial expression patterns. We find a significant excess of transcribed retrocopies close to other genes or within introns, suggesting that retrocopies can exploit the regulatory elements and/or open chromatin of neighboring genes to become transcribed. In direct support of this hypothesis, we identify 36 retrocopy-host gene fusions, including primate-specific chimeric genes. Strikingly, 27 intergenic retrogenes have acquired untranslated exons de novo during evolution to achieve high expression levels. Notably, our screen for highly transcribed retrocopies also uncovered a retrogene linked to a human recessive disorder, gelatinous drop-like corneal dystrophy, a form of blindness. These functional implications for retroposition notwithstanding, we find that the insertion of retrocopies into genes is generally deleterious, because it may interfere with the transcription of host genes. Our results demonstrate that natural selection has been fundamental in shaping the retrocopy repertoire of the human genome.

The environmental roots of non-communicable diseases (NCDs) and the epigenetic impacts of globalization

BACKGROUND: Non-communicable diseases (NCDs) are increasing worldwide. We hypothesize that environmental factors (including social adversity, diet, lack of physical activity and pollution) can become "embedded" in the biology of humans. We also hypothesize that the "embedding" partly occurs because of epigenetic changes, i.e., durable changes in gene expression patterns. Our concern is that once such factors have a foundation in human biology, they can affect human health (including NCDs) over a long period of time and across generations. OBJECTIVES: To analyze how worldwide changes in movements of goods, persons and lifestyles (globalization) may affect the "epigenetic landscape" of populations and through this have an impact on NCDs. We provide examples of such changes and effects by discussing the potential epigenetic impact of socio-economic status, migration, and diet, as well as the impact of environmental factors influencing trends in age at puberty. DISCUSSION: The study of durable changes in epigenetic patterns has the potential to influence policy and practice; for example, by enabling stratification of populations into those who could particularly benefit from early interventions to prevent NCDs, or by demonstrating mechanisms through which environmental factors influence disease risk, thus providing compelling evidence for policy makers, companies and the civil society at large. The current debate on the '25 × 25 strategy', a goal of 25% reduction in relative mortality from NCDs by 2025, makes the proposed approach even more timely. CONCLUSIONS: Epigenetic modifications related to globalization may crucially contribute to explain current and future patterns of NCDs, and thus deserve attention from environmental researchers, public health experts, policy makers, and concerned citizens.

The enterprise face to the environmental challenge: straddling the fence between social responsibility and penal responsibility

This contribution aims to analyse how to incur companies' criminal liability when they violate environmental protection globally. In Switzerland, companies' criminal liability has already been provided for to fight against money launder- ing (Article 102 CP). Could a similar liability be incurred, in Switzerland, for companies that infringe environmental protection? This is what our contribution is all about. Since the company is at the heart of our subject, the point is to see to what extent criminal liability could be transposed to cases of violation by companies of the environmental principles promoted by the CSR concept.

The fate and persistence of Leishmania major in mice of different genetic backgrounds: an example of exploitation of the immune system by intracellular parasites.

Leishmania spp. are intracellular protozoan parasites that are delivered within the dermis of their vertebrate hosts. Within this peripheral tissue and the draining lymph node, they find and/or rapidly create dynamic microenvironments that determine their ultimate fate, namely their more or less successful expansion, and favour their transmission to another vertebrate host though a blood-feeding vector. Depending on their genetic characteristics as well as the genetic make-up of their hosts, once within the dermis Leishmania spp. very rapidly drive and maintain sustained T cell-dependent immune responses that arbitrate their ultimate fate within their hosts. The analysis of the parasitism exerted by Leishmania major in mice of different genetic backgrounds has allowed us to recognize some of the early and late mechanisms driven by this parasite that lead to either uncontrolled or restricted parasitism. Uncontrolled parasitism by Leishmania major characterizing mice from a few inbred strains (e.g. BALB/c) is associated with the expansion of parasite reactive Th2 CD4 lymphocytes and results from their rapid and sustained activity. In contrast, restricted parasitism characteristic of mice from the majority of inbred strains results from the development of a polarized parasite-specific Th1 CD4 response. This murine model of infection has already been and will continue to be particularly instrumental in dissecting the rules controlling the pathway of differentiation of T cells in vivo. In the long run, the understanding of these rules should contribute to the rational development of novel immunotherapeutic interventions against severe infectious diseases.

A comparison of alpha and gamma spectrometry for environmental natural radioactivity surveys.

An alpha-spectrometry, using automated borate fusion and sequential extraction and exchange chromatography, was used to determine the uranium and thorium based on environmental radioactivity of 20 soil samples. The same set of the samples was analysed using gamma-spectrometry with an HPGe detector. The two data sets were checked for coherence using Z-score and chi2 statistical tests. We show that gamma-spectrometry is a valid alternative to time-consuming alpha-spectrometry for the determination of natural uranium and thorium activity in soil (activity range: 12.5-58.2 Bq/kg). The measured activities were compared with the theoretical activities to ensure secular equilibrium in the 238U and 232Th series. For 226Ra, a special study was made on deconvolution of the 186 keV multiplet with the Levenberg-Marquardt algorithm. Finally, the combined use of Z-score and chi2-tests was found to be a powerful tool for comparing the results obtained with two different methods.

Genetic variation and environmental effects on beta-conglycinin and glycinin content in Brazilian soybean cultivars

The objective of this work was to determine genetic and environmental effects on beta-conglycinin and glycinin content in Brazilian soybean cultivars. The concentrations of these protein fractions were analyzed by scanning densitometry after electrophoresis, in 90 Brazilian soybean cultivars sown in Ponta Grossa, PR, in 2001. The effects of the sowing location were determined in the cultivar MG/BR 46 (Conquista), sown in 16 locations of Goiás and Minas Gerais states (Central Brazil), and in the cultivar IAS 5, sown in 12 locations of Paraná and São Paulo states (Southern Brazil), in 2002 soybean season. A significant variability for beta-conglycinin (7S) and glycinin (11S) protein fractions ratio was observed among the 90 Brazilian soybean cultivars. 'MS/BRS 169' (Bacuri) and 'BR-8' (Pelotas) presented the highest and the lowest 11S/7S ratios (2.76 and 1.17, respectively). Beta-conglycinin protein fractions presented more variability than glycinin protein fractions. Grouping test classified 7S proteins in seven groups, 11S proteins in four groups, and protein fraction ratios (11S/7S) in nine groups. Significant effect of sowing locations was also observed on protein fractions contents. There is a good possibility of breeding for individual protein fractions, and their subunits, without affecting protein content.