From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).

We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal, and largely repetitive, genomes of conifers. Synthetic long read technologies have existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine subhaploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation. When combined with inexpensive light shotgun sequencing, the resulting data can be used to scaffold large genomes. The protocol is efficient enough to consider routinely for even the largest genomes. Conifers represent the largest reference genome projects executed to date. The largest of these is that of the conifer Pinus lambertiana (sugar pine), with a genome size of 31 billion bp. In this paper, we report on the molecular and computational protocols for scaffolding the P. lambertiana genome using the library technology from 10× Genomics. At 247,000 bp, the NG50 of the existing reference sequence is the highest scaffold contiguity among the currently published conifer assemblies; this new assembly's NG50 is 1.94 million bp, an eightfold increase

Predispositions and symptoms of Agrilus borer attack in declining oak trees

International audienceThis paper presents results of a semi-quantitative study on the role of Agrilus biguttatus F. in oak decline in Belgium. Larvae of this insect breed in living subcortical tissues of European oak. Several factors favouring attacks are discussed, among which the overall health condition and the local physical and biochemical status of the host tree. Larvae, feeding galleries, pupae, imago and D-shaped emergence-holes of A. biguttatus were observed exclusively in declining and recently dead oaks. Attacks start in the south-facing, sun-exposed parts of the subcrown stem, with a preference for thicker-barked trees or similar areas within declining trees. The feeding of early larval stages induces subcortical necrosis and longitudinal bark cracking. The more destructive tunnelling of advanced larval stages cuts functional vessels and phloem elements, which enhances the decline. In conclusion, effects on wood quality and suitable control options are discussed.Prédispositions et symptômes d'attaques d'Agrilus dans des chênes dépérissants. Nous présentons les résultats d'une étude semi-quantitative portant sur le rôle du Coléoptère Agrilus biguttatus F. dans le dépérissement de chênes en Belgique. Les larves de cet insecte s'attaquent au xylème et au phloème vivants. Plusieurs facteurs favorisant les attaques sont discutés. Parmi ces facteurs, la santé générale et les états physiques et biochimiques locaux de l'arbre hôte semblent être décisifs pour permettre sa colonisation. Des larves, des galeries sous-corticales, des nymphes, des adultes et des trous d'émergence en forme de D d'A. biguttatus ont été trouvés uniquement dans des chênes dépérissants ou morts récemment. Les attaques commencent dans les parties ensoleillées de l'arbre situées en dessous de la couronne et exposées vers le sud, avec une préférence pour des arbres ou des zones de l'arbre qui sont affaiblis et qui ont une écorce épaisse. Les larves juvéniles endommagent le cambium vasculaire et provoquent ainsi une fissuration longitudinale dans l'écorce. Les galeries des stades larvaires plus avancés coupent des éléments de xylème et de phloème fonctionnels et stimulent ainsi le dépérissement. Pour conclure, les effets sur la qualité du bois et des mesures de contrôle adéquates sont discutés

End-use related physical and mechanical properties of selected fast-growing poplar hybrids (Populus trichocarpa x P-deltoides)

This study focused on physical and mechanical properties of fast-growing poplar clones in relation to potential end uses with high added value. A total of 14 trees from three different clones, all P. trichocarpa x deltoides (T x D) hybrids, were felled in a poplar plantation in Lille (Belgium): six 'Beaupre', four 'Hazendans' and four 'Hoogvorst'. Growth rate was found to have no significant influence on the physical mechanical properties. Although the investigated clones are genetically closely related, important variations in physical and mechanical properties were observed. Specific features such as spatial distribution of tension wood and dimensional stability are the main quality factors. It was concluded that 'Beaupre' is suitable for a wide range of high value added applications, such as plywood or construction wood. 'Hazendans' and 'Hoogvorst' will need adapted technology in processing. Further research is needed to characterize clonally induced variation in properties and to assess adequate processing strategies for multiclonal poplar stands

Metacognition for spelling in higher etudents with dyslexia: is there evidence for the dual burden hypothesis?

We examined whether academic and professional bachelor students with dyslexia are able to compensate for their spelling deficits with metacognitive experience. Previous research suggested that students with dyslexia may suffer from a dual burden. Not only do they perform worse on spelling but in addition they are not as fully aware of their difficulties as their peers without dyslexia. According to some authors, this is the result of a worse feeling of confidence, which can be considered as a form of metacognition (metacognitive experience). We tried to isolate this metacognitive experience by asking 100 students with dyslexia and 100 matched control students to rate their feeling of confidence in a word spelling task and a proofreading task. Next, we used Signal Detection Analysis to disentangle the effects of proficiency and criterion setting. We found that students with dyslexia showed lower proficiencies but not suboptimal response biases. They were as good at deciding when they could be confident or not as their peers without dyslexia. They just had more cases in which their spelling was wrong. We conclude that the feeling of confidence in our students with dyslexia is as good as in their peers without dyslexia. These findings go against the Dual Burden theory (Kruger & Dunning, 1999), which assumes that people with a skills problem suffer twice as a result of insufficiently developed metacognitive competence. As a result, there is no gain to be expected from extra training of this metacognitive experience in higher education students with dyslexia

New collision attacks on SHA-1 based on optimal joint local-collision analysis

The main contributions of this paper are two-fold. Firstly, we present a novel direction in the cryptanalysis of the cryptographic hash function {\SHA}. Our work builds on previous cryptanalytic efforts on {\SHA} based on combinations of local collisions. Due to dependencies, previous approaches used heuristic corrections when combining the success probabilities and message conditions of the individual local collisions. Although this leads to success probabilities that are seemingly sufficient for feasible collision attacks, this approach most often does not lead to the maximum success probability possible as desired. We introduce novel techniques that enable us to determine the theoretical maximum success probability for a given set of (dependent) local collisions, as well as the smallest set of message conditions that attains this probability. We apply our new techniques and present an implemented open-source near-collision attack on {\SHA} with a complexity equivalent to $2^{57.5}$ {\SHA} compressions. Secondly, we present an identical-prefix collision attack and a chosen-prefix collision attack on {\SHA} with complexities equivalent to approximately $2^{61}$ and $2^{77.1}$ {\SHA} compressions, respectively