Jabba: hybrid error correction for long sequencing reads

Background: Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. Results: In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is the use of a pseudo alignment approach with a seed-and-extend methodology, using maximal exact matches (MEMs) as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of MEMs in the context of third generation reads are presented. Conclusion: Jabba produces highly reliable corrected reads: almost all corrected reads align to the reference, and these alignments have a very high identity. Many of the aligned reads are error-free. Additionally, Jabba corrects reads using a very low amount of CPU time. From this we conclude that pseudo alignment with MEMs is a fast and reliable method to map long highly erroneous sequences on a de Bruijn graph

A molecular timetable for apical bud formation and dormancy induction in poplar

The growth of perennial plants in the temperate zone alternates with periods of dormancy that are typically initiated during bud development in autumn. In a systems biology approach to unravel the underlying molecular program of apical bud development in poplar (Populus tremula 3 Populus alba), combined transcript and metabolite profiling were applied to a high-resolution time course from short-day induction to complete dormancy. Metabolite and gene expression dynamics were used to reconstruct the temporal sequence of events during bud development. Importantly, bud development could be dissected into bud formation, acclimation to dehydration and cold, and dormancy. To each of these processes, specific sets of regulatory and marker genes and metabolites are associated and provide a reference frame for future functional studies. Light, ethylene, and abscisic acid signal transduction pathways consecutively control bud development by setting, modifying, or terminating these processes. Ethylene signal transduction is positioned temporally between light and abscisic acid signals and is putatively activated by transiently low hexose pools. The timing and place of cell proliferation arrest (related to dormancy) and of the accumulation of storage compounds (related to acclimation processes) were established within the bud by electron microscopy. Finally, the identification of a large set of genes commonly expressed during the growth-to-dormancy transitions in poplar apical buds, cambium, or Arabidopsis thaliana seeds suggests parallels in the underlying molecular mechanisms in different plant organs

Lignées divergentes pour la consommation alimentaire « résiduelle » des pondeuses: réponse des poussins à une inoculation par Eimeria acervulina et comparaison de paramètres biologiques

International audienc

A genome-wide function of THSC/TREX-2 at active genes prevents transcription–replication collisions

The THSC/TREX-2 complex of Saccharomyces cerevisiae mediates the anchoring of transcribed genes to the nuclear pore, linking transcription elongation with mRNA export and genome stability, as shown for specific reporters. However, it is still unknown whether the function of TREX-2 is global and the reason for its relevant role in genome integrity. Here, by studying two TREX-2 representative subunits, Thp1 and Sac3, we show that TREX-2 has a genome-wide role in gene expression. Both proteins show similar distributions along the genome, with a gradient disposition at active genes that increases towards the 3 end. Thp1 and Sac3 have a relevant impact on the expression of long, G+C-rich and highly transcribed genes. Interestingly, replication impairment detected by the genome-wide accumulation of the replicative Rrm3 helicase is increased preferentially at highly expressed genes in the thp1Δ and sac3Δ mutants analyzed. Therefore, our work provides evidence of a function of TREX-2 at the genome-wide level and suggests a role for TREX-2 in preventing transcription– replication conflicts, as a source of genome instability derived from a defective messenger ribonucleoprotein particle (mRNP) biogenesis.Spanish Ministry of Economy and Competitiveness [BFU2010-16372]; Junta de Andalucía [CVI4567 and P12/BIO-1238]; European Union (FEDER); and a JAE predoctoral training grant from the Spanish Research Council (CSIC) [to J.M.S-P.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BFU2010-16372].Peer reviewe

Taux de corticostérone plasmatique, variation de poids et de température corporelle de poules Leghorn blanches naines (dw) et normales (Dw+) en réponse à une privation d'aliment

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Endometriosis and the Coronavirus (COVID-19) Pandemic: Clinical Advice and Future Considerations

The COVID-19 pandemic has led to a dramatic shift in the clinical practice of women’s health and routine care for endometriosis has been severely disrupted. Endometriosis is defined as an inflammatory disease characterized by lesions of endometrial-like tissue outside the uterus that is associated with pelvic pain and/or infertility (1). It affects ∼10% of reproductive age women worldwide, is diagnosed by surgical visualization or by radiological imaging, and is managed with hormone treatments or by laparoscopic removal of lesions (2–4). At the time of writing, under the guidance of international gynecological organizations (5–7), many centers temporarily ceased offering outpatient appointments, diagnostic imaging for nonacute pelvic pain, surgery for endometriosis, and fertility treatments. In the absence of routine care pathways and uncertainty about when health services will be available again, endometriosis sufferers are likely to feel vulnerable and that resultant stress and anxiety may contribute to a worsening of symptoms. The pandemic poses several important questions for healthcare providers on how best to deliver care within these restrictions. Herein, we present clinical advice on the management of endometriosis during the COVID-19 pandemic and future considerations