QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing

Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying additional minor QTLs that are relevant for the phenotypic difference between the original parents

Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering

Background: The production of bioethanol from lignocellulose hydrolysates requires a robust, D-xylose-fermenting and inhibitor-tolerant microorganism as catalyst. The purpose of the present work was to develop such a strain from a prime industrial yeast strain, Ethanol Red, used for bioethanol production. Results: An expression cassette containing 13 genes including Clostridium phytofermentans XylA, encoding D-xylose isomerase (XI), and enzymes of the pentose phosphate pathway was inserted in two copies in the genome of Ethanol Red. Subsequent EMS mutagenesis, genome shuffling and selection in D-xylose-enriched lignocellulose hydrolysate, followed by multiple rounds of evolutionary engineering in complex medium with D-xylose, gradually established efficient D-xylose fermentation. The best-performing strain, GS1.11-26, showed a maximum specific D-xylose consumption rate of 1.1 g/g DW/h in synthetic medium, with complete attenuation of 35 g/L D-xylose in about 17 h. In separate hydrolysis and fermentation of lignocellulose hydrolysates of Arundo donax (giant reed), spruce and a wheat straw/hay mixture, the maximum specific D-xylose consumption rate was 0.36, 0.23 and 1.1 g/g DW inoculum/h, and the final ethanol titer was 4.2, 3.9 and 5.8% (v/v), respectively. In simultaneous saccharification and fermentation of Arundo hydrolysate, GS1.11-26 produced 32% more ethanol than the parent strain Ethanol Red, due to efficient D-xylose utilization. The high D-xylose fermentation capacity was stable after extended growth in glucose. Cell extracts of strain GS1.11-26 displayed 17-fold higher XI activity compared to the parent strain, but overexpression of XI alone was not enough to establish D-xylose fermentation. The high D-xylose consumption rate was due to synergistic interaction between the high XI activity and one or more mutations in the genome. The GS1.11-26 had a partial respiratory defect causing a reduced aerobic growth rate. Conclusions: An industrial yeast strain for bioethanol production with lignocellulose hydrolysates has been developed in the genetic background of a strain widely used for commercial bioethanol production. The strain uses glucose and D-xylose with high consumption rates and partial cofermentation in various lignocellulose hydrolysates with very high ethanol yield. The GS1.11-26 strain shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates

On the Number of Zeros of Abelian Integrals: A Constructive Solution of the Infinitesimal Hilbert Sixteenth Problem

We prove that the number of limit cycles generated by a small non-conservative perturbation of a Hamiltonian polynomial vector field on the plane, is bounded by a double exponential of the degree of the fields. This solves the long-standing tangential Hilbert 16th problem. The proof uses only the fact that Abelian integrals of a given degree are horizontal sections of a regular flat meromorphic connection (Gauss-Manin connection) with a quasiunipotent monodromy group.Comment: Final revisio

RelB-Dependent Stromal Cells Promote T-Cell Leukemogenesis

BACKGROUND: The Rel/NF-kappaB transcription factors are often activated in solid or hematological malignancies. In most cases, NF-kappaB activation is found in malignant cells and results from activation of the canonical NF-kappaB pathway, leading to RelA and/or c-Rel activation. Recently, NF-kappaB activity in inflammatory cells infiltrating solid tumors has been shown to contribute to solid tumor initiation and progression. Noncanonical NF-kappaB activation, which leads to RelB activation, has also been reported in breast carcinoma, prostate cancer, and lymphoid leukemia. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a novel role for RelB in stromal cells that promote T-cell leukemogenesis. RelB deficiency delayed leukemia onset in the TEL-JAK2 transgenic mouse model of human T acute lymphoblastic leukemia. Bone marrow chimeric mouse experiments showed that RelB is not required in the hematopoietic compartment. In contrast, RelB plays a role in radio-resistant stromal cells to accelerate leukemia onset and increase disease severity. CONCLUSIONS/SIGNIFICANCE: The present results are the first to uncover a role for RelB in the crosstalk between non-hematopoietic stromal cells and leukemic cells. Thus, besides its previously reported role intrinsic to specific cancer cells, the noncanonical NF-kappaB pathway may also play a pro-oncogenic role in cancer microenvironmental cells

Valorisation of lignocellulose waste streams

Although second generation bioethanol starts being produced at industrial scale, considerable improvement is still required for commercial viability. Up to now, the substrates that can be used are very limited. Most interesting substrates (e.g. wood or cellulose containing waste products) cannot be used because: 1) The process of pretreatment and hydrolysis (to liberate fermentable sugars) is too expensive or inefficient 2) The fermentable hydrolysate contains too many inhibitors. In a TETRA project, a grant programme to stimulate innovation in Flemish companies through technology transfer, we are comparing several pretreatment and hydrolysis conditions of lignocellulosic waste and energy crops. When a hydrolysate is obtained with at least 5% fermentable sugars, fermentation experiments are performed. A range of Saccharomyces cerevisiae strains is being tested and pre-culture and fermentation conditions are modified in order to find the best combination. From our first series of experiments it is clear that: 1) With some substrates it is very difficult to obtain a hydrolysate that contains sufficient fermentable sugars 2) Even with a mild treatment, the hydrolysate still contains inhibitory compounds 3) The different yeast strains tested with flax hydrolysate exhibited a very different fermentation pattern. Most strains were able to ferment the sugars to the same extend, but the rate of fermentation strongly depended on the strain 4) Pre-culture of the yeast (shaking flasks) in the presence of flax hydrolysate did not affect the yield of the pre-culture, but had a clear effect on the subsequent fermentation. Conclusion: from our first results it is clear that by screening a collection of different substrates, evaluating different pretreatment methods, screening a large set of yeast strains and optimizing the pre-culture and fermentation conditions, we may be able to produce second generation bioethanol from different substrates in an economically viable way

Les pratiques des enseignants de mathématiques en classe de seconde. Rapport sur le projet de recherche 97-98 (appel d'offres de l'IUFM de Versailles)

International audienceUne comparaison de 2x4 séances dans 4 classes de seconde différentes d'un même établissement "ordinaire" est proposée dans ce texte. La première séance, moins analysée que la deuxième, est consacrée au cours sur les fonctions ; pour la deuxième séance, les 4 enseignants s'étaient mis d'accord sur un texte de problème, écrit, permettant d'étudier le maximum d'une fonction (du second degré) obtenue à partir d'un calcul d'aire d'une figure donnée.Sont étudiés successivement les scénarios (notamment pour la deuxième séance respect ou non du texte initial), les discours de l'enseignant pendant la séance (une étude du vocabulaire utilisé est tentée), et dans la mesure du possible des réactions d'élèves, y compris au moyen d'entretiens après les séances. Il s'avère que les séances se déroulent très différemment ; trois types de variables se dégagent : le niveau de mise en fonctionnement des connaissances auquel les enseignants font appel dans leurs interventions, la gestion temporelle de la séance (accélération ou pas), l'âge du savoir sur lequel portent les interventions (ancien, nouveau)

Les pratiques des enseignants de mathématiques en classe de seconde. Rapport sur le projet de recherche 97-98 (appel d'offres de l'IUFM de Versailles)

International audienceUne comparaison de 2x4 séances dans 4 classes de seconde différentes d'un même établissement "ordinaire" est proposée dans ce texte. La première séance, moins analysée que la deuxième, est consacrée au cours sur les fonctions ; pour la deuxième séance, les 4 enseignants s'étaient mis d'accord sur un texte de problème, écrit, permettant d'étudier le maximum d'une fonction (du second degré) obtenue à partir d'un calcul d'aire d'une figure donnée.Sont étudiés successivement les scénarios (notamment pour la deuxième séance respect ou non du texte initial), les discours de l'enseignant pendant la séance (une étude du vocabulaire utilisé est tentée), et dans la mesure du possible des réactions d'élèves, y compris au moyen d'entretiens après les séances. Il s'avère que les séances se déroulent très différemment ; trois types de variables se dégagent : le niveau de mise en fonctionnement des connaissances auquel les enseignants font appel dans leurs interventions, la gestion temporelle de la séance (accélération ou pas), l'âge du savoir sur lequel portent les interventions (ancien, nouveau)

Les pratiques des enseignants de mathématiques en classe de seconde. Rapport sur le projet de recherche 97-98 (appel d'offres de l'IUFM de Versailles)

International audienceUne comparaison de 2x4 séances dans 4 classes de seconde différentes d'un même établissement "ordinaire" est proposée dans ce texte. La première séance, moins analysée que la deuxième, est consacrée au cours sur les fonctions ; pour la deuxième séance, les 4 enseignants s'étaient mis d'accord sur un texte de problème, écrit, permettant d'étudier le maximum d'une fonction (du second degré) obtenue à partir d'un calcul d'aire d'une figure donnée.Sont étudiés successivement les scénarios (notamment pour la deuxième séance respect ou non du texte initial), les discours de l'enseignant pendant la séance (une étude du vocabulaire utilisé est tentée), et dans la mesure du possible des réactions d'élèves, y compris au moyen d'entretiens après les séances. Il s'avère que les séances se déroulent très différemment ; trois types de variables se dégagent : le niveau de mise en fonctionnement des connaissances auquel les enseignants font appel dans leurs interventions, la gestion temporelle de la séance (accélération ou pas), l'âge du savoir sur lequel portent les interventions (ancien, nouveau)