Concurrent infall of satellites: Collective effects changing the overall picture

A variety of new physical processes have proven to play an important role in orbital decay of a satellite galaxy embedded inside a dark matter halo but this is not fully understood. Our goal is to assess if the orbital history of a satellite remains unchanged during a concurrent sinking. For this purpose we analyze the impact that the internal structure of the satellites and their spatial distribution inside the host halo may have on the concurrent sinking process due to both mass loss and the combined effect of self-friction, which have not been studied before for concurrent sinking. We set up a set of N-body simulations that include multiple satellites, sinking simultaneously in a host halo and we compare them with models including a single satellite. The main result of our work is that the satellite's accretion history differs from the classical isolated view when we consider the collective effects. The accretion history of each satellite strongly depends on the initial configuration, the number of satellites in the halo at the time of infall and the internal properties of each satellite. We observe that compact satellites in a flat configuration fall slower than extended satellites that have lost mass, showing a non-reported behavior of self-friction. We find that such effects are maximized when satellites are located in a flat configuration. We show that in a flat configuration similar to the Vast Polar Structure, deviations in the apocenters can be of about 30% with respect to the isolated case, and up to 50% on the eccentricities. We conclude that ignoring the collective effects produced by the concurrent sinking of satellite galaxies may lead to large errors in the determination of the merger progenitors properties, making it considerably more challenging to trace back the accretion event. Timing constrains on host density profile may be modified by the effects discussed here.Comment: A&A, Forthcoming article Received: 29 March 2022 / Accepted: 26 September 2022 6 pages, 6 figure

Assessing the Hierarchical Hamiltonian Splitting Integrator for Collisionless N-body Simulations

The N-body problem has become one of the hottest topics in the fields of computational dynamics and cosmology. The large dynamical range in some astrophysical problems led to the use of adaptive time steps to integrate particle trajectories, however, the search of optimal strategies is still challenging. We quantify the performance of the hierarchical time step integrator Hamiltonian Splitting (HamSp) for collisionless multistep simulations. We compare with the constant step Leap-Frog (LeapF) integrator and the adaptive one (AKDK). Additionally, we explore the impact of different time step assigning functions. There is a computational overhead in HamSp however there are two interesting advantages: choosing a convenient time-step function may compensate and even turn around the efficiency compared with AKDK. We test both reversibility and time symmetry. The symmetrized nature of the HamSp integration is able to provide time-reversible integration for medium time scales and overall deliver better energy conservation for long integration times, and the linear and angular momentum are preserved at machine precision. We address the impact of using different integrators in astrophysical systems. We found that in most situations both AKDK and HamSp are able to correctly simulate the problems. We conclude that HamSp is an attractive and competitive alternative to AKDK, with, in some cases, faster and with better energy and momentum conservation. The use of recently discussed Bridge splitting techniques with HamSp may allow to reach considerably high efficiency.Comment: 13 pages, 16 figure

Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves

Low temperature severely affects plant growth and development. To overcome this constraint, several plant species from regions having a cool season have evolved an adaptive response, called cold acclimation. We have studied this response in olive tree (Olea europaea L.) cv. Picual. Biochemical stress markers and cold-stress symptoms were detected after the first 24 h as sagging leaves. After 5 days, the plants were found to have completely recovered. Control and cold-stressed plants were sequenced by Illumina HiSeq 1000 paired-end technique. We also assembled a new olive transcriptome comprising 157,799 unigenes and found 6,309 unigenes differentially expressed in response to cold. Three types of response that led to cold acclimation were found: short-term transient response, early long-term response, and late long-term response. These subsets of unigenes were related to different biological processes. Early responses involved many cold-stress-responsive genes coding for, among many other things, C-repeat binding factor transcription factors, fatty acid desaturases, wax synthesis, and oligosaccharide metabolism. After long-term exposure to cold, a large proportion of gene down-regulation was found, including photosynthesis and plant growth genes. Up-regulated genes after long-term cold exposure were related to organelle fusion, nucleus organization, and DNA integration, including retrotransposons.This work was supported by grant AGR-5948 from Junta de Andalucía (Consejería de Economía, Innovación y Ciencia) and Ministerio de Ciencia e Innovación. Funding to pay the Open Access publication charges for this article was provided by the University of Jaén.Peer reviewe

Cold response in olive tree; A RNAseq study

Póster presentado en el COST TD801 StatSeq 5th Workshop, celebrado en Helsinki del 24 al 26 de abril de 2013.Low temperature severely affects plant growth and development. Several plant species have evolved an adaptive response, named cold acclimation. In order to study this response in olive tree (Olea europaea), we maintained twomonths- old vegetative propagated olive trees cv. Picual at low temperature (14h at 10ºC with light, 10h at 4ºC at the dark) for 15 days. Control plants were maintained in field growing conditions. Cold stress symptoms were observed after the first 24h as sagging leaf and biochemical stress markers. After 5 days the plants were observed completely recovered. We extracted RNA from leaves of three control plants and the same number from 24h and 10 days cold stressed plants. We pooled RNA and made two cDNA libraries for sequencing. We used Illumina HiSeq 1000 sequencer.Peer Reviewe

Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction

[EN] Understanding the nature of pathogen host interaction may help improve strawberry (Fragaria x anahassa) cultivars. Plant resistance to pathogenic agents usually operates through a complex network of defense mechanisms mediated by a diverse array of signaling molecules. In strawberry, resistance to a variety of pathogens has been reported to be mostly polygenic and quantitatively inherited, making it difficult to associate molecular markers with disease resistance genes. Colletotrichum acutaturn spp. is a major strawberry pathogen, and completely resistant cultivars have not been reported. Moreover, strawberry defense network components and mechanisms remain largely unknown and poorly understood. Assessment of the strawberry response to C. acutatum included a global transcript analysis, and acidic hormones SA and JA measurements were analyzed after challenge with the pathogen. Induction of transcripts corresponding to the SA and JA signaling pathways and key genes controlling major steps within these defense pathways was detected. Accordingly, SA and JA accumulated in strawberry after infection. Contrastingly, induction of several important SA, JA, and oxidative stress-responsive defense genes, including FaPR1-1, FaLOX2, FaJAR1, FaPDF1, and FaGST1, was not detected, which suggests that specific branches in these defense pathways (those leading to FaPR1-2, FaPR2-1, FaPR2-2, FaAOS, FaPR5, and FaPR10) were activated. Our results reveal that specific aspects in SA and JA dependent signaling pathways are activated in strawberry upon interaction with C. acutatum. Certain described defense-associated transcripts related to these two known signaling pathways do not increase in abundance following infection. This finding suggests new insight into a specific putative molecular strategy for defense against this pathogen.Authors are grateful to Dr. JM Lopez-Aranda (IFAPA-Centro de Churriana) for providing micropropagated strawberry plants and to Nicolas Garcia-Caparros for technical assistance. Authors also want to thank Kevin M. Folta for his insightful comments on the paper. This work was supported by Junta de Andalucia, Spain [Proyectos de Excelencia P07-AGR-02482/P12-AGR-2174, and grants to Grupo-BIO278].Amil-Ruiz, F.; Garrido-Gala, J.; Gadea Vacas, J.; Blanco-Portales, R.; Munoz-Merida, A.; Trelles, O.; De Los Santos, B.... (2016). Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction. Frontiers in Plant Science. 7(1036). https://doi.org/10.3389/fpls.2016.01036S71036Acosta, I. F., & Farmer, E. E. (2010). Jasmonates. The Arabidopsis Book, 8, e0129. doi:10.1199/tab.0129Al-Shahrour, F., Diaz-Uriarte, R., & Dopazo, J. (2004). 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ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

Abstract Background There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC) environment with a greatly extended data storage capacity. Results We designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM) and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA). The new editing option and the graphical user interface (GUI) provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets. Conclusions ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1) the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2) Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3) Support for both single PC and distributed cluster systems.</p

Principles of meiotic chromosome assembly revealed in S. cerevisiae

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process

Quality of Care in Humanitarian Surgery

Humanitarian surgical programs are set up de novo, within days or hours in emergency or disaster settings. In such circumstances, insuring quality of care is extremely challenging. Basic structural inputs such as a safe structure, electricity, clean water, a blood bank, sterilization equipment, a post-anesthesia recovery unit, appropriate medications should be established. Currently, no specific credentials are needed for surgeons to operate in a humanitarian setting; the training of more humanitarian surgeons is desperately needed. Standard perioperative protocols for the humanitarian setting after common procedures such as Cesarean section, burn care, open fractures, and amputations and antibiotic prophylaxis, and post-operative pain management must be developed. Outcome data, especially long-term outcomes, are difficult to collect as patients often do not return for follow-up and may be difficult to trace; standard databases for post-operative infections and mortality rates should be established. Checklists have recently received significant attention as an instrument to support the improvement of surgical quality; knowing which items are most applicable to humanitarian settings remains unknown. In conclusion, the quality of surgical services in humanitarian settings must be regulated. Many other core medical activities of humanitarian organizations such as therapeutic feeding, mass vaccination, and the treatment of infectious diseases, such as tuberculosis and human immunodeficiency virus, are subject to rigorous reporting of quality indicators. There is no reason why surgery should be exempted from quality oversight. The surgical humanitarian community should pull together before the next disaster strikes