Qualité biologique de l’eau de mer évaluée in situ par le test embryo-larvaire de Crassostrea gigas et Mytilus galloprovincialis = In situ monitoring of sea water quality with the embryo-larval bioassay of Crassostrea gigas and Mytilus galloprovincialis

Embryos and larvae of bivalves are frequently used in marine ecotoxicology for the purpose of assessing seawater quality, because they are very sensitive to pollutants and provide rapid responses. Laboratory studies, however, cannot accurately simulate natural conditions. We conducted bivalve embryo-larval studies in situ at the marina of Arcachon (southwest French Atlantic coast), in order to assess ‘biological quality’ of the water. One experiment conducted in winter 1999 (temperatures of 10 °C) with embryos of the Mediterranean mussel, Mytilus galloprovincialis, has shown that such tests are practicable in winter at low temperatures. This study did not show any deterioration in ‘biological quality’ of the water. Four series of experiments were subsequently performed during summer 2000 (ambient water temperatures of 19 to 22.4 °C) with embryos of the Japanese oyster, Crassostrea gigas. The results show that the ‘sea water biological quality’ deteriorates from the port entrance towards its inner part. To our knowledge, this is the first investigation of the marine environment in which bivalve embryos have been used in situ. They are very suitable for this type of study, because bivalve embryos and larvae are more sensitive to pollutants than the adults, and also because they belong to euryhaline species and the embryos tolerate summer temperatures (both species) as well as winter temperatures (mussels), allowing biomonitoring to be conducted all over the year

Modeling of the plasma jet of a stationary plasma thruster

We have developed a two-dimensional hybrid fluid – particle-in-cell Monte Carlo collisions (PIC- MCC) model to study the plume of a stationary plasma thruster. The model is based on a fluid description of the electrons (the electron density follows a Boltzmann distribution) and a particle description of the ion and neutral transport. Collisions between heavy species are taken into account with a Monte Carlo method. The electric field is obtained from Poisson's equation or from the quasineutrality assumption. We first show that the results from the PIC-MCC model are close to the results of a more time-consuming direct simulation Monte Carlo approach. We then compare the model predictions of the plume density and ion energy distribution with experimental measurements. Finally, we present a brief discussion on the assumptions of the model and on its ability to give reliable predictions on important issues such as the flux of ions backscattered to the satellite. © 2002 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70320/2/JAPIAU-91-12-9521-1.pd

Analysis of TerraSAR-X data and their sensitivity to soil surface parameters over bare agricultural fields

International audienceCette recherche a pour objectif de mettre en évidence la contribution des capteurs haute résolution pour une meilleure caractérisation de la surface du sol et pour analyser les effets de la polarisation et de l'angle d'incidence radar. L'objectif de cet article est d'analyser la sensibilité des données haute résolution Terrassar-X sur des sols sans couverture végétale et d'étudier la variabilité spatiale. Les relations entre le coefficient de rétrodiffusion et les paramètres du sol seront étudiés grâce aux images (TerraSAR, Ikonos, SPOT) ainsi que grâce aux mesures de terrain recueillies pendant plusieurs campagnes de terrain en hiver et printemps 2008-2009. Ce travail a été mené sur le bassin de l'Orgeval (France). / Our research aims to show the contribution of high resolution spatial sensors for a better characterization of soil surface, and to analyze polarization effects and radar incidence angle. The objective of this paper is to analyze the sensitivity of very high resolution TerraSAR-X radar data taken over bare soils, and to study the spatial variability. The relationship between backscattering coefficient and soil's parameters (moisture, surface roughness, and texture) will be examined by means of satellite images (TerraSAR, Ikonos, SPOT), as well as ground truth measurements, recorded during several field campaigns in the winter and spring of 2008 and 2009. This study is carried out on Orgeval catchment (France)

CRISPR/Cas9 facilitates rapid generation of constitutive forms of transcription factors in Aspergillus niger through specific on-site genomic mutations resulting in increased saccharification of plant biomass

The CRISPR/Cas9 system has been successfully applied for gene editing in filamentous fungi. Previous studies reported that single stranded oligonucleotides can be used as repair templates to induce point mutations in some filamentous fungi belonging to genus Aspergillus. In Aspergillus niger, extensive research has been performed on regulation of plant biomass degradation, addressing transcription factors such as XlnR or GaaR, involved in (hemi-)cellulose and pectin utilization, respectively. Single nucleotide mutations leading to constitutively active forms of XlnR and GaaR have been previously reported. However, the mutations were performed by the introduction of versions obtained through site-directed or UV-mutagenesis into the genome. Here we report a more time- and cost-efficient approach to obtaining constitutively active versions by application of the CRISPR/Cas9 system to generate the desired mutation on-site in the A. niger genome. This was also achieved using only 60-mer single stranded oligonucleotides, shorter than the previously reported 90-mer strands. In this study, we show that CRISPR/Cas9 can also be used to efficiently change functional properties of the proteins encoded by the target gene by on-site genomic mutations in A. niger. The obtained strains with constitutively active XlnR and GaaR versions resulted in increased production of plant biomass degrading enzymes and improved release of D-xylose and L-arabinose from wheat bran, and D-galacturonic acid from sugar beet pulp.Peer reviewe

Heterologous protein production in filamentous fungi

Abstract: Filamentous fungi are able to produce a wide range of valuable proteins and enzymes for many industrial applications. Recent advances in fungal genomics and experimental technologies are rapidly changing the approaches for the development and use of filamentous fungi as hosts for the production of both homologous and heterologous proteins. In this review, we highlight the benefits and challenges of using filamentous fungi for the production of heterologous proteins. We review various techniques commonly employed to improve the heterologous protein production in filamentous fungi, such as strong and inducible promoters, codon optimization, more efficient signal peptides for secretion, carrier proteins, engineering of glycosylation sites, regulation of the unfolded protein response and endoplasmic reticulum associated protein degradation, optimization of the intracellular transport process, regulation of unconventional protein secretion, and construction of protease-deficient strains. Key points: • This review updates the knowledge on heterologous protein production in filamentous fungi. • Several fungal cell factories and potential candidates are discussed. • Insights into improving heterologous gene expression are given

One Dimensional Hybrid-Vlasov Simulation of a Hall Thruster

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97103/1/AIAA2012-4313.pd

Practical formulas for the refraction coefficient

Knowledge of the actual refraction coefficient is essential in leveling surveys and precise electromagnetic distance measurement reduction. The most common method followed by the surveyor for its determination is based on the use of simultaneous reciprocal zenith observations. The commonly used formula is only an approximation valid for approximately horizontal sightings, whereas the exact geometric solution turns out to be very complicated so that an iterative computation procedure is suggested instead. In the present paper, the goal is to derive a compact formula from the complete solution that is easy to implement and retains the necessary accuracy for horizontal and slanted sightings. In addition, the paper will also focus on the common situation for the surveyor where isolated observations have to be done and no partially compensating procedures—e.g., leap-frog or middle point—are possible. If temperature vertical profiles are unknown then the refraction coefficient cannot be reliably determined. Some surveyors may customarily use then an average value, e.g., k 5 0:13, perhaps being unaware of the risks involved in such simplistic assumption. In the present paper, it is also a goal to present a useful and simple formula for approximately estimating the refraction coefficient in terms of easily accessible parameters to correct the bulk of the refraction effect in single observations, always bearing in mind that determination of the refraction coefficient by means of a model may turn out to be somewhat inaccurate, but still better than the blind use of a universal k.The authors are grateful to the editor and the anonymous reviewers for their valuable suggestions, corrections, and comments that helped improve the original manuscript. This research is funded by the Spanish Ministry of Science and Innovation (Grant No. AYA2011-23232).Baselga Moreno, S.; García-Asenjo Villamayor, L.; Garrigues Talens, P. (2014). Practical formulas for the refraction coefficient. Journal of Surveying Engineering. 140(2):1-5. https://doi.org/10.1061/(ASCE)SU.1943-5428.0000124S15140

Strategies for the Development of Industrial Fungal Producing Strains

The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed

Relationship between aerodynamic roughness length and bulk sedge leaf area index in a mixed-species boreal mire complex

Leaf area index (LAI) is an important parameter in natural ecosystems, representing the seasonal development of vegetation and photosynthetic potential. However, direct measurement techniques require labor-intensive field campaigns that are usually limited in time, while remote sensing approaches often do not yield reliable estimates. Here we propose that the bulk LAI of sedges (LAI(s)) can be estimated alternatively from a micrometeorological parameter, the aerodynamic roughness length for momentum (z(0)). z(0) can be readily calculated from high-response turbulence and other meteorological data, typically measured continuously and routinely available at ecosystem research sites. The regressions of LAI versus z(0) were obtained using the data from two Finnish natural sites representative of boreal fen and bog ecosystems. LAI(s) was found to be well correlated with z(0) and sedge canopy height. Superior method performance was demonstrated in the fen ecosystem where the sedges make a bigger contribution to overall surface roughness than in bogs.Peer reviewe

Non-homologous end-joining-deficient filamentous fungal strains mitigate the impact of off-target mutations during the application of CRISPR/Cas9

CRISPR/Cas9 genome editing technology has been implemented in almost all living organisms. Its editing precision appears to be very high and therefore could represent a big change from conventional genetic engineering approaches. However, guide RNA binding to nucleotides similar to the target site could result in undesired off-target mutations. Despite this, evaluating whether mutations occur is rarely performed in genome editing studies. In this study, we generated CRISPR/Cas9-derived filamentous fungal strains and analyzed them for the occurrence of mutations, and to which extent genome stability affects their occurrence. As a test case, we deleted the (hemi-)cellulolytic regulator-encoding gene xlnR in two Aspergillus niger strains: a wild type (WT) and a non-homologous end-joining (NHEJ)-deficient strain ΔkusA. Initial phenotypic analysis suggested a much higher prevalence of mutations in the WT compared to NHEJ-deficient strains, which was confirmed and quantified by whole-genome sequencing analysis. Our results clearly demonstrate that CRISPR/Cas9 applied to an NHEJ-deficient strain is an efficient strategy to avoid unwanted mutations. IMPORTANCE Filamentous fungi are commonly used biofactories for the production of industrially relevant proteins and metabolites. Often, fungal biofactories undergo genetic development (genetic engineering, genome editing, etc.) aimed at improving production yields. In this context, CRISPR/Cas9 has gained much attention as a genome editing strategy due to its simplicity, versatility, and precision. However, despite the high level of accuracy reported for CRISPR/Cas9, in some cases unintentional cleavages in non-targeted loci-known as off-target mutations-could arise. While biosafety should be a central feature of emerging biotechnologies to minimize unintended consequences, few studies quantitatively evaluate the risk of off-target mutations. This study demonstrates that the use of non-homologous end-joining-deficient fungal strains drastically reduces the number of unintended genomic mutations, ensuring that CRISPR/Cas9 can be safely applied for strain development