A simplified procedure for terminal restriction fragment length polymorphism analysis of the soil bacterial community to study the effects of pesticides on the soil microflora using 4,6-dinitroorthocresol as a test case

We have studied the structural effects of application to the soil of a potentially detrimental herbicide, 4,6-dinitroorthocresol (DNOC) by analysing amplified ribosomal DNA restriction analysis (ARDRA) and terminal restriction fragment length polymorphism (T-RFLP) signatures of 16S rDNA fragments of culturable bacterial communities isolated from diluted soil suspensions. This approach has the potential to reveal changes induced by stressing the soil microflora with DNOC. This paper shows that, whereas only few changes of the ARDRA and T-RFLP profiles result from ageing of the soil, treatment of the soil with DNOC induces major modifications of these profiles. Therefore, for the practical purpose of pesticide registration, ARDRA and T-RFLP analysis performed on the dominant culturable fraction of the soil bacteria, implemented using conventional gel electrophoresis, offers the means of a routine, simple and meaningful test for detecting some of the changes affecting the structure of the soil microflora in response to pesticide application.     

Isolation of Gardnerella vaginalis from the reproductive tract of four mares

A gram-variable pleomorphic bacillus was isolated from the reproductive tracts of 4 mares during routine prebreeding soundness examinations. Using a commercial bacterial identification system, these organisms were identified as Streptococcus acidominimus. However, colonial and Gram-staining characteristics did not support this identification. Subsequent testing indicated the organism was similar to Gardnerella vaginalis. Additional growth and biochemical analysis performed in our laboratory and at the Michigan Department of Public Health and by the Center for Disease Control, Atlanta, Georgia, confirmed the identification of G. vaginalis.     

Chronically starved horses: predicting survival, economic, and ethical considerations

Nine of 45 horses subjected to prolonged malnutrition died subsequent to being placed with a responsible caregiver and being provided an appropriate diet. Initial extreme poor body condition score tended to be associated with death, although individual response to refeeding varied. The financial costs of stabilizing the group of horses significantly exceeded their free market price. Responsible management of chronically starved commercial animals should include options for immediate euthanasia.     

Predictive Factors of Sensitivity to Elisidepsin,a Novel Kahalalide F-Derived Marine Compound

Elisidepsin (PM02734, Irvalec^®) is a synthetic marine-derived cyclic peptide of the Kahalalide F family currently in phase II clinical development. Elisidepsin was shown to induce rapid oncosis in ErbB3-expressing cells. Other predictive factors of elisidepsin sensitivity remained unknown. A panel of 23 cancer cell lines of different origin was assessed for elisidepsin cytotoxicity and correlated with mutational state, mRNA and protein expression of selected genes. Elisidepsin showed potent and broad cytotoxic effects in our cancer cell line panel, being active at concentrations ranging from 0.4 to 2 μM that may be relevant for clinical settings. We have shown that elisidepsin is more active in cells harboring epithelial phenotype with high E-cadherin and low vimentin expression. In addition, high ErbB3 and Muc1 expression was correlated with sensitivity to elisidepsin, whereas the presence of KRAS activating mutations was associated with resistance. In DU-PM cells with acquired resistance to elisidepsin, ErbB3 expression was decreased, while Bcl2 was increased. DU-PM cells displayed higher sensitivity to ErbB1-inhibitors suggesting possible cross-talk of ErbB1 and ErbB3 signaling pathways. Combinations of elisidepsin with lapatinib and several chemotherapies including 5-FU and oxaliplatin resulted in synergistic effects that offer the potential of clinical use of elisidepsin in combination settings.     

Climate data challenges in the 21st century

Climate data are dramatically increasing in volume and complexity, just as the users of these data in the scientific community and the public are rapidly increasing in number. A new paradigm of more open, user-friendly data access is needed to ensure that society can reduce vulnerability to climate variability and change, while at the same time exploiting opportunities that will occur.     

GIS Coop: networks of silvicultural trials for supporting forest management under changing environment

Key message

The diversity of forest management systems and the contrasted competition level treatments applied make the experimental networks of the GIS Coop, a nationwide testing program in the field of emerging forestry topics within the framework of the ongoing global changes.

Context

To understand the dynamics of forest management systems and build adapted growth models for new forestry practices, long-term experiment networks remain more crucial than ever.

Aims

Two principles are at the basis of the experimental design of the networks of the Scientific Interest Group Cooperative for data on forest tree and stand growth (GIS Coop): contrasted and extreme silvicultural treatments in diverse pedoclimatic contexts.

Methods

Various forest management systems are under study: regular and even-aged stands of Douglas fir, sessile and pedunculate oaks, Maritime and Laricio pines, mixed stands of sessile oak, European silver fir, and Douglas fir combined with other species. Highly contrasted stand density regimes, from open growth to self-thinning, are formalized quantitatively.

Results

One hundred and eighty-five sites representing a total of 1206 plots have been set up in the last 20 years, where trees are measured regularly (every 3 to 10 years). The major outputs of these networks for research and management are the calibration/validation of growth and yield models and the drawing up of forest management guides.

Conclusion

The GIS Coop adapts its networks so that they can contribute to develop growth models that explicitly integrate pedoclimatic factors and thus also contribute to research on the sustainability of ecosystems under environmental and socio-economic changes.

     

Atomic-level characterization of the structural dynamics of proteins

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.     

Cardinal temperatures variability within a tropical japonica rice diversity panel

Air temperature is one of the most critical climatic factors controlling rice growth, development, and production in current and future climatic scenarii predicting increasingly frequent situations of extreme and/or fluctuating temperatures. With its large spectrum of geographical origins and cropping areas, one can credit tropical japonica rice subspecies of a probable genetic diversity of its response to air temperature, which is of major interest for the breeding of better adapted rice varieties. A panel of 195 rice accessions (175 japonica plus 20 reference cultivars) was studied in controlled environment to estimate cardinal (base, optimum, and maximum) temperatures based on the monitoring of the elongation rate (LERmax) of the sixth leaf on the main stem in response to six fixed thermal treatments ranging from 16 to 35 °C. A dedicated statistical framework was elaborated for estimating LERmax, cardinal temperature and related uncertainties. Developed statistical framework enhanced the precision of cardinal temperatures estimated compared to previously reported methods, especially for base temperature. Maximum temperature was trickier to estimate and will require further studies. A significant genotypic variability for base and optimal temperature was pointed out, suggesting tropical japonica subspecies represents a relevant genetic pool to breed for rice genotypes adapted to various thermal situations. These results also suggested that using genotype-dependent cardinal temperature values should enhance the way crop growth models account for genotype?×?environment interactions hence their predictive value in current and future climatic conditions.