Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for a residual postglacial founder effect in a highly dispersive freshwater invertebrate

In the northern hemisphere, glacial periods have had profound and lasting effects on the population genetics of numerous species, with founder effects often persisting for many generations in formerly glaciated regions. We found an unusual example of this in the freshwater bryozoan Cristatella mucedo, which showed regional differences in haplotype diversity with relatively low levels of haplotype diversity in northern Europe compared to central/southern Europe despite previous evidence for frequent dispersal between C. mucedo populations. Such contradictions between high dispersal and low gene flow have now been reported in several other freshwater taxa and may be attributed to persistent founder effects following colonization of sites by a few individuals whose efficient reproduction leads to rapid population growth. Alternatively, selection may determine which genotypes can thrive in northerly locations, or it may be that C. mucedo has undergone cryptic speciation. Future work on adaptive genomic regions is required before we can understand how gene flow, local adaptation, and speciation influence the current distribution patterns of bryozoans and other freshwater invertebrates.
Applying next generation sequencing to skeletal development and disease

Next Generation Sequencing (NGS) technologies have dramatically increased the throughput and lowered the cost of DNA sequencing. In this thesis, I apply these technologies to unresolved questions in skeletal development and disease. Firstly, I use targeted re-sequencing of genomic DNA to identify the genetic cause of the cartilage tumor syndrome, metachondromatosis (MC). I show that the majority of MC patients carry heterozygous loss-of-function mutations in the PTPN11 gene, which encodes a phosphatase, SHP2, involved in many signaling pathways. Furthermore, I show that cartilage lesions in MC patients likely arise following somatic second-hit mutations in PTPN11. Secondly, I use RNA-seq to identify gene expression changes that occur following genetic inactivation of Ptpn11 in mouse chondrocyte cultures. I show that chondrocytes lacking Ptpn11 fail to properly undergo terminal differentiation and instead continue to express genes associated with earlier stages of chondrocyte maturation. I validate these findings in vivo by examining markers of specific chondrocyte maturation stages in the vertebral growth plates of mice following postnatal mosaic inactivation of Ptpn11. Together, my results provide insight into the molecular mechanisms underlying the initiation and growth of cartilage tumors. In the third component of my thesis, I develop a method to map and clone zebrafish mutations by performing whole genome sequencing on pooled DNA. I apply this method to zebrafish mutants identified in a mutagenesis screen for adult phenotypes, including skeletal phenotypes, and determine that a nonsense mutation in bmp1a underlies the craniofacial phenotype in the wdd mutant. In summary, I show that NGS technologies can be successfully utilized to firstly identify the genetic cause of a human skeletal disorder, secondly investigate the molecular mechanisms regulating the maturation of skeletal cells, and thirdly expedite the process of mapping and cloning zebrafish mutants with skeletal phenotypes. Altogether, my research provides insight into the pathways and processes regulating skeletal development and disease.
A Taxonomic Revision of Podalyria (Fabaceae)

Abstract A revision of the generic and infrageneric taxonomy of Podalyria (Fabaceae, Podalyrieae) is presented. The genus comprises 17 species, of which 16 are endemic to the Cape Floristic Region of South Africa and one extends eastwards to southern KwaZulu-Natal. Morphological, cytological and chemical characters are briefly discussed. A cladistic analysis of 19 morphological characters and one chemical character resulted in a partially resolved topology with two main clades. These two groups are described as sections, namely Villosae and Podalyria. Two new species are described: P. leipoldtii and P. variabilis, and one new combination P. rotundifolia is made. Historically, the application of names in Podalyria has been variable and unreliable, so that considerable effort was required to unravel the intricate nomenclature, synonymy, and typification of the species. This revision (the first since 1862) also includes full descriptions, diagnostic characters, photographs, illustrations, and distribution maps. The red data list status of five of the threatened species is given.
Perdas fermentativas e composição bromatológica da entrecasca de palmito pupunha ensilada com aditivos químicos

Feeding animals with agro-residues may reduce costs and environmental concerns. The agroindustrial wastes used as ruminant feeding are an alternative for ambient problems caused by it accumulation. This study aimed to evaluate chemical additives on the ensilage of residues of pupunha palm (Bactris gasipaes, Kunth) production. Experimental silos (20 L buckets) were used equipped with meters to determine gas and effluent DM losses. The experimental treatments were: control (no additives); urea (1% - wet basis) and calcium oxide (1% WB). After 70 days storage, the silos were weighed, opened and sampled. Effluent and gas DM losses increased with the application of calcium oxide at ensiling. Total DM losses were 15.1, 14.4 and 26.6% for the Control, Urea and Calcium oxide treatments, respectively. In all the treatments there was reduction in the NDF and increase in ADF increasing rates, that showed hemicellulose disappearance. The Ca:P ratio increased dramatically after calcium oxide addition, from 4.1:1 to 15.6:1. The residue from pupunha heart of palm extraction can be classified as a medium quality foodstuff with high moisture content. The additive applied at ensiling are not effective in reducing fermentative losses during the conservation process.
The relevance of molecular biology to pure and applied entomology

Article de reflexion et de synthese sur l'interet des outils de la biologie moleculaire dans la recherche fondamentale et appliquee en entomologie (genetique moleculaire, genie genetique, cytochimie, immunochimie, histochimie)
Influence of Environmental Factors on Seed Germination and Emergence of Asia Minor Bluegrass (Polypogon fugax)

Asia minor bluegrass (AmB) is a major weed impacting rapeseed production in Dongting Lake District, China. Growth chamber experiments were conducted to determine the influence of environmental factors on germination and emergence of AmB. The optimum constant temperature for germination was around 20 C. Seeds showed germination percentages above 60% under 22/15 and 24/19 C day/night temperature regimes. Seeds could germinate in the dark, but light exposure significantly enhanced the germination percentage. More than 50% of seeds germinated over a pH range between 4 and 10. Seeds were highly sensitive to osmotic stress, and germination was completely inhibited at an osmotic potential of −0.4 MPa, indicating that it was favored by a moist environment. Increasing salinity reduced germination of AmB seeds from 58% at 0 mM to 13% at 80 mM NaCl. The highest seedling emergence (62%) was observed when seeds were placed on the soil surface, and no seedlings emerged from seeds placed at a depth of 5 cm. This work shows that the climate and soil conditions in Dongting Lake District are suitable for AmB seed germination and that no-till fields, where seeds remain on the soil surface, promote the successful establishment of the weed. Nomenclature: Asia minor bluegrass, Polypogon fugax Nees ex Steud. ; rapeseed, Brassica napus L. Polypogon fugax (AmB) es una maleza importante que impacta la producción de colza en el distrito Lago Dongting, China. Se realizaron experimentos en cámaras de crecimiento para determinar la influencia de factores ambientales en la germinación y emergencia de AmB. La temperatura constante óptima para la germinación fue alrededor de 20 C. Las semillas mostraron porcentajes de germinación superiores a 60% con regímenes de temperatura de 22/15 y 24/19 C día/noche. Las semillas pudieron germinar en la oscuridad, pero la exposición a la luz mejoró significativamente el porcentaje de germinación. Más del 50% de las semillas germinaron en un rango de pH entre 4 y 10. Las semillas fueron muy sensibles al estrés osmótico y la germinación fue completamente inhibida a un potencial osmótico de −0.4 MPa, indicando que la germinación fue favorecida en un ambiente húmedo. El aumentar la salinidad redujo la germinación de las semillas de AmB desde 58% con 0mM a 13% con 80 mM NaCl. La mayor emergencia de plántulas (62%) fue observada cuando las semillas fueron puestas sobre la superficie del suelo, y ninguna plántula emergió cuando las semillas fueron puestas a una profundidad de 5 cm. Este trabajo muestra que el clima y las condiciones de suelo en el distrito Lago Dongting son favorables para la germinación de semillas de AmB y que los campos con labranza cero, donde la semilla permanece sobre la superficie del suelo, promueven el establecimiento exitoso de esta maleza.
Inhibition of Nitrogen Fixation in Soybean Plants Supplied with Nitrate III. Kinetics of the Formation of Nitrosylleghemoglobin and of the Inhibition of Formation of Oxyleghemoglobin

(.) The decrease, by nitrite, in the oxygen-binding capacity of leghemoglobin was caused by the increase in levels of LbNO formed from ferrous leghemoglobin. In this case, the oxygen-binding site of leghemoglobin was competitively occupied by nitric oxide produced from nitrite. (.)
SREBP: A Key Effector of mTORC1 Signaling in Metabolism and Cancer

The mammalian target of rapamycin complex 1 (mTORC1), a master regulator of cell growth and proliferation, is aberrantly activated in cancer, genetic tumor syndromes and obesity. Much progress has been made to understand the upstream pathways that regulate mTORC1, most of which converge upon its negative regulator, the Tuberous Sclerosis Complex (TSC) 1-TSC2 complex. However, the cell intrinsic consequences of aberrant mTORC1 activation remain poorly characterized. Using systems in which mTORC1 is constitutively activated by genetic loss of TSC1 or TSC2 and pharmacologically inhibited by treatment with an mTORC1-specific inhibitor rapamycin, we have identified that mTORC1 controls specific aspects of cellular metabolism, including glycolysis, the pentose phosphate pathway, and de novo lipogenesis. Induction of the pentose phosphate pathway and de novo lipogenesis is achieved by activation of a transcriptional program affecting metabolic gene targets of sterol regulatory elementbinding protein (SREBP). We have demonstrated that mTORC1 stimulates the accumulation of processed, active SREBP, although details of the molecular mechanism remain to be elucidated. To understand the physiological and pathological relevance of mTORC1dependent activation of SREBPs and lipogenesis, we explored these findings in the liver and in cancer. While we find that the induction of hepatic SREBP1c and lipogenesis by insulin requires mTORC1, mTORC1 activation is not sufficient to stimulate hepatic SREBP1c in the absence of Akt signaling, revealing the existence of an additional downstream pathway also required for this induction. We demonstrate that this
CO2‐fluxes in different plant communities of a high‐Arctic tundra watershed (Western Spitsbergen)

There is little information on (1) whether the net carbon balance is positive or negative in different habitats in high Arctic ecosystems such as Spitsbergen today, and (2) what effect a cloudier, cooler summer could have on carbon balance. To provide data on this subject CO2-flux measure- ments in different plant communities were made in the high- Arctic coastal tundra of Spitsbergen, using a mobile macro- cuvette system based on infrared gas analysis. The study area was situated on the exposed west coast, where westerly winds produce precipitation daily in the form of rain, drizzle and fog. During the cold and cloudy measurement period in 1996, light and surface temperatures were limiting for primary producers, resulting in low size and low physiological activity of the plants. Net CO2-flux measurements showed carbon fluxes from soil to atmosphere in most of the communities even during the brightest hours of the day, when mean photon flux density was 325 mmol m-2 s-1. Calculations based on spatial distribution of the plant communities and soils in the water- shed combined with C-flux measurements revealed informa- tion on daily carbon loss. For instance, the Drepanocladus community, covering 21 % of the catchment area, was respon- sible for 42.6 % of the catchment carbon loss. Only two of nine investigated plant communities, the Racomitrium and a Salix- Saxifraga community on debris, both adapted to frequent fog situations, were able to compensate for respiratory CO2-losses under the prevailing low light conditions during daytime. Since there were no significant sunny periods in this area in the summer of 1996, the habitats of the investigated coastal tundra finished the season with a marked carbon loss due to increased cloudiness.
Characterization of microsatellite loci in the African fig Ficus sycomorus L. (Moraceae)

Microsatellite loci were characterized in the African fig tree Ficus sycomorus in order to investigate patterns of pollination and gene flow in this species. The loci characterized included new loci isolated from F. sycomorus and a single locus originally developed in Ficus carica. In total 12 loci were polymorphic when tested in between eight and 79 Namibian F. sycomorus individuals. Three of the new F. sycomorus loci were found to be polymorphic in cultivars of the edible fig F. carica suggesting a selection of these loci will be useful for population studies in other fig species.
Regions at the carboxyl end of bacteriophage ø29 protein p6 required for DNA binding and activity in ø29 DNA replication

Series of deletions corresponding to the carboxyl end of the phage phi 29 protein p6 have been constructed and their activity in the initiation of phi 29 DNA replication and their capacity to interact with the phi 29 DNA ends have been studied. Determination of the activity of the deletion mutants in phi 29 DNA replication indicated the dispensability of the 14 carboxy-terminal amino acids of the protein. The activity of protein p6 decreased with deletions from 23 to 39 amino acids and was undetectable when 44 amino acids were removed. A similar behaviour was obtained when the interaction of the mutant proteins with the phi 29 DNA ends was analyzed. These results indicate that the stimulation of phi 29 DNA replication by protein p6 requires a specific binding to the phi 29 DNA ends.
Reactive sucrose derivatives

De nouveaux esters et ethers du sucrose avec des groupes fonctionnels presentant des groupes hydroxiles de reactivites differentes sont etudies: les esters methacryliques de sucrose; les gels hydrophiles de methacrylate de sucrose pour l'immobilisation des reactifs; les derives du sucrose avec des groupes amides de l'acide carbonique ou des groupes amides N-methyloles; des derives du sucrose avec des groupes photoactifs pour la preparation de composes photoresistants; des derives du sucrose avec des groupes primaires amines et les amides derivees de leurs acides gras; des derives du sucrose hydrosolubles avec des groupes biologiquement actifs
Preliminary assessment of oestrogenic activity in water sources in Rietvlei Nature Reserve, Gauteng, South Africa

A preliminary assessment was made of oestrogenic activity in water sources in the Rietvlei Nature Reserve, from which water is supplied to the metropolitan area of Pretoria. Single samples were extracted from seven sites using a solid phase C18 cartridge and the extracts assessed for oestrogenic activity using the Recombinant Yeast Screen bio-assay. Estradiol equivalents ranged from 0.31–2.1 ng l−1, which are comparable to those reported for rivers near Paris (1.0–32 ng l−1) and for environmental water in Korea (0.5 pg l−1 and 7.4 ng l−1). The oestrogenic activity found in Rietvlei water samples is supported by a report of intersex in catfish, Clarias gariepinus, in the reserve. Further studies are required to determine whether this phenomenon is consistent, to determine the chemical(s) responsible for this activity and to characterise the potential effects on human, aquatic, and wildlife health in the area.
The Composition of Northern Pike (Esox lucius L.) Populations in Four Shallow Waters in the Netherlands, with Special Reference to Factors Influencing 0+ Pike Biomass

The composition and abundance of Northern pike (Esox lucius L.) populations in four shallow waters was monitored during a 4–5 year period, using mark-recapture methods. In general, the populations were sampled by using a combination of fishing gear but pike that completed their first growing season (0+ pike) are captured quantitatively by electrofishing (3 kw, DC) exclusively. Within the length range of 0–54 cm fork length, the biomasses of 0+ pike appeared to be negatively correlated with those of larger pike. It is suggested that intraspecific predation is mainly responsible for these relations. The standing stock of <54-cm pike was found to be determined by the amount of aquatic vegetation and more especially so if the different habitat preference of 0+ pike, 0+ < pike < 41 cm and 41 cm ≤ pike < 54 cm was taken into account.
Suitability of Arabidopsis thaliana as a model for host plant–Plutella xylostella–Cotesia plutellae interactions

Successful pest management is often hindered by the inherent complexity of the interactions of a pest with its environment. The use of genetically characterized model plants can allow investigation of chosen aspects of these interactions by limiting the number of variables during experimentation. However, it is important to study the generic nature of these model systems if the data generated are to be assessed in a wider context, for instance, with those systems of commercial significance. This study assesses the suitability of Arabidopsis thaliana (L.) Heynh. (Brassicaceae) as a model host plant to investigate plant–herbivore–natural enemy interactions, with Plutella xylostella (L.) (Lepidoptera: Plutellidae), the diamondback moth, and Cotesia plutellae (Kurdjumov) (Hymenoptera: Braconidae), a parasitoid of P. xylostella. The growth and development of P. xylostella and C. plutellae on an A. thaliana host plant (Columbia type) were compared to that on Brassica rapa var. pekinensis (L.) (Brassicaceae), a host crop that is widely cultivated and also commonly used as a laboratory host for P. xylostella rearing. The second part of the study investigated the potential effect of the different A. thaliana background lines, Columbia and Landsberg (used in wider scientific studies), on growth and development of P. xylostella and C. plutellae. Plutella xylostella life history parameters were found generally to be similar between the host plants investigated. However, C. plutellae were more affected by the differences in host plant. Fewer adult parasitoids resulted from development on A. thaliana compared to B. rapa, and those that did emerge were significantly smaller. Adult male C. plutellae developing on Columbia were also significantly smaller than those on Landsberg A. thaliana.
Distribution of β-Lactamases in Actinomycetes

ABSTRACT The distribution of β-lactamase activities in a collection of actinomycete strains was surveyed. Six of 127 strains were found to produce β-lactamase. This low frequency was in contrast to the case with Streptomyces species. The producing strains were not related phylogenetically. MICs of benzylpenicillin did not correlate with β-lactamase production.
Effects of silver nitrate on shoot regeneration of Artemisia annua L.

In order to further increase the shoot regeneration frequency of Artemisia annua L. , the effects of silver nitrate on this process was investigated in this study. Different concentration of silver nitrate was added to the shoot induction medium, which was MS basic medium containing 1.0 mg l −1 6-benzyladenine (6-BA) and 0.05 mg l −1 α -napthaleneacetic acid (NAA). When 2 mg l −1 silver nitrate was added to the shoot induction medium, the shoot induction frequency and shoot number per explants was significantly higher than that of the control (without silver nitrate). In addition, silver nitrate at all the tested concentrations could significantly reduce callus formation of the explants. Silver nitrate had also positive influence on shoot elongation in the first 20 days. Furthermore, silver nitrate did not affect the sensitivity of A. annua shoots to Kanamycin (KM); therefore, silver nitrate could be used to improve shoot regeneration capacity and frequency in A. annua genetic transformation.
Stability of Adult-plant Resistance to Septoria tritici blotch in 24 European Winter Wheat Varieties Across Nine Field Environments

Septoria tritici blotch (STB) is one of the most important leaf diseases in wheat worldwide. Objectives of this study were (i) to compare inoculation and natural infection ; (ii) to evaluate the level of adult-plant resistance to STB using four isolates; and (iii) to analyse environmental stability of 24 winter wheat (Triticum aestivum L.) varieties in inoculated vs. non-inoculated field trials across 3 years including nine environments (location x year combinations). Field trials were sown in split-plot design inoculated with four aggressive isolates of S. tritici plus one non-inoculated variant as main factor and 24 wheat varieties as subfactor. Septoria tritici blotch severity was visually scored as percentage flag leaves covered with lesions bearing pycnidia. Overall STB rating ranged from 8% (Solitar) to 63% (Rubens) flag leaf area affected, resulting in significant (P < 0.01) genotypic variance. Variance of genotype x environment interaction amounted to approximately 50% of the genotypic variance. Genotype x isolate interaction variance was significant too (P < 0.01) but of minor importance. Therefore, environmental stability of varieties should be a major breeding goal. The varieties Solitar, History and Florett were most resistant and stable as revealed by a regression approach, and the susceptible varieties were generally unstable. Hence, STB resistance and stability are correlated (P < 0.01), but there were some exceptions (Tuareg, Ambition). Promising candidates for an environmentally stable, effective adult-plant resistance have been identified.
Selection of indicators by machine learning: application to estimate permanent grassland plant richness.

Indicator based on key species or other data from field observation are very useful to manage permanent grasslands or to control result-oriented agri-environment schemes. These indicators must generally fulfil the following features: purpose relevance (i.e. optimize forage quality, maximize biodiversity, etc), minimization of the acquisition cost (time and money), stability in time and space, low specialized knowledge requirement, sensitivity. Permanent grasslands are complex ecosystems based on multispecific swards and multiple agronomic and ecological functions. Adequate methodologies are thus required to determine simple indicators. We tested the regression tree methodology coming from machine learning techniques (artificial intelligence) to predict the plant richness of mountain and lowland permanent grasslands in France. Four potential indicators were considered (alone or combined): species, genus, families, and colours of flowers. Each indicator was associated to its easiness of observation, and the prediction quality of the models was estimated by several criteria (coefficient of determination, relative absolute error). A combination of plant genus and colour of flowers was found as the best compromise in order to estimate permanent grassland plant richness.