Evolution of Daily Gene Co-expression Patterns from Algae to Plants

Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions

A Classification of Countable Lower 1-transitive Linear Orders

This paper contains a classification of countable lower 1-transitive linear orders. This is the first step in the classification of countable 1-transitive trees given in Chicot and Truss (2009): the notion of lower 1-transitivity generalises that of 1-transitivity for linear orders, and it is essential for the structure theory of 1-transitive trees. The classification is given in terms of coding trees, which describe how a linear order is fabricated from simpler pieces using concatenations, lexicographic products and other kinds of construction. We define coding trees and show that a coding tree can be constructed from a lower 1-transitive linear order (X,≤) by examining all the invariant partitions on X. Then we show that a lower 1-transitive linear order can be recovered from a coding tree up to isomorphism

Probabilistic Guarded P Systems, A New Formal Modelling Framework

Multienvironment P systems constitute a general, formal framework for modelling the dynamics of population biology, which consists of two main approaches: stochastic and probabilistic. The framework has been successfully used to model biologic systems at both micro (e.g. bacteria colony) and macro (e.g. real ecosystems) levels, respectively. In this paper, we extend the general framework in order to include a new case study related to P. Oleracea species. The extension is made by a new variant within the probabilistic approach, called Probabilistic Guarded P systems (in short, PGP systems). We provide a formal definition, a simulation algorithm to capture the dynamics, and a survey of the associated software.Ministerio de Economía y Competitividad TIN2012- 37434Junta de Andalucía P08-TIC-0420

An evolutionarily conserved DOF-CONSTANS module controls plant photoperiodic signaling

© 2015 American Society of Plant Biologists. All Rights Reserved. The response to daylength is a crucial process that evolved very early in plant evolution, entitling the early green eukaryote to predict seasonal variability and attune its physiological responses to the environment. The photoperiod responses evolved into the complex signaling pathways that govern the angiosperm floral transition today. The Chlamydomonas reinhardtii DNA-Binding with One Finger (CrDOF) gene controls transcription in a photoperiod-dependent manner, and its misexpression influences algal growth and viability. In short days, CrDOF enhances CrCO expression, a homolog of plant CONSTANS (CO), by direct binding to its promoter, while it reduces the expression of cell division genes in long days independently of CrCO. In Arabidopsis (Arabidopsis thaliana), transgenic plants overexpressing CrDOF show floral delay and reduced expression of the photoperiodic genes CO and FLOWERING LOCUS T. The conservation of the DOF-CO module during plant evolution could be an important clue to understanding diversification by the inheritance of conserved gene toolkits in key developmental programs.Peer Reviewe

Isolation of Sarcocystis neurona from an opossum (Didelphis albiventris) in Argentina

Sarcocystis neurona is an Apicomplexan parasite which affects awide range of animal hosts. This protozoan is the main cause ofequine protozoal myeloecephalitis (EPM) inWestern Hemispherehorses. The parasite reproduces sexually in the intestine ofdefinitive hosts (DH) and asexually in tissues of intermediate andaberrant hosts. The geographical distribution of S. neurona isrelated with the distribution its definitive hosts, the opossumsDidelphis virginiana and D. albiventris. A recent serological studyconducted in Argentinean horses using S. neurona antigenrevealed an overall seroprevalence of 26.1%. However, the parasitehas not been isolated in Argentina. Tissues from an opossum (D.albiventris) hunted by dogs in a farm from the central region ofBuenos Aires province were collected. Horses raised in the farmshowed a 50% (10/20) S. neurona seroprevalence. One seropositivehorse developed neurological signs and evidenced clinicalimprovement after a 2 month treatment with Ponazuril. A completenecropsy of the opossum was conducted and the intestinalmucosal scraping was subjected to a parasitological study withsucrose solution. A high amount of Sarcocystis spp. oocysts/sporocystswere observed (Fig. 1). DNA was extracted from concentratedoocysts with a commercial kit (ZR Fecal DNA, ZymoResearch). The sample was identified as S. neurona by specificPCR-restriction fragment length polymorphism (RFLP) and bysequencing of a fragment of the 18S rRNA gene. Approximately 5 x105 oocysts were subjected to a pepsin-HCl digestion followed bya physical disruption. Released sporozoites were used to infectfresh BM cell cultures, maintained by 3 passages during 2 monthsand further preserved in liquid nitrogen. This study represents thefirst isolation of S. neurona in Argentina. Further studies will beconducted in order to identify antigen expression as well as tocompare genetic characteristics between the isolated strain andreference strains.Fil: Moré, Gastón Andrés. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Epizootiología y Salud Pública. Laboratorio de Inmunoparasitología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Rambead, M.. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Epizootiología y Salud Pública. Laboratorio de Inmunoparasitología; ArgentinaFil: Braun, F.. No especifíca;Fil: Campero, Lucía María. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Epizootiología y Salud Pública. Laboratorio de Inmunoparasitología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Walkosksi, A.. No especifíca;Fil: Venturini, M. C.. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Epizootiología y Salud Pública. Laboratorio de Inmunoparasitología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina10th International Equine Infectious Diseases ConferenceCiudad Autónoma de Buenos AiresArgentinathe Equine Infectious Disease Conferenc

Deterministic and stochastic P systems for modelling cellular processes

This paper presents two approaches based on metabolic and stochastic P systems, together with their associated analysis methods, for modelling biological sys- tems and illustrates their use through two case studies.Kingdom's Engineering and Physical Sciences Research Council EP/ E017215/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/D019613/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/F01855X/

The Arabidopsis Polycomb Repressive Complex 1 (PRC1) components AtBMI1A, B and C impact gene networks throughout all stages of plant development.

Polycomb Group regulation in Arabidopsis (Arabidopsis thaliana) is required to maintain cell differentiation and allow developmental phase transitions. This is achieved by the activity of three PcG repressive complex 2s (PRC2s) and the participation of a yet poorly defined PRC1. Previous results showed that apparent PRC1 components perform discrete roles during plant development, suggesting the existence of PRC1 variants; however, it is not clear in how many processes these components participate. We show that AtBMI1 proteins are required to promote all developmental phase transitions and to control cell proliferation during organ growth and development, expanding their proposed range of action. While AtBMI1 function during germination is closely linked to B3 domain transcription factors VAL1/2 possibly in combination with GT-box binding factors, other AtBMI1 regulatory networks require participation of different factor combinations. Conversely, EMF1 and LHP1 bind many H3K27me3 positive genes up-regulated in atbmi1a/b/c mutants; however, loss of their function affects expression of a different subset, suggesting that even if EMF1, LHP1, and AtBMI1 exist in a common PRC1 variant, their role in repression depends on the functional context

Cellular modelling using P systems and process algebra.

In this paper various molecular chemical interactions are modelled under different computational paradigms. P systems and -calculus are used to describe intra-cellular reactions like protein-protein interactions and gene regulation control

ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage

Background Chlamydomonas reinhardtii is the model organism that serves as a reference for studies in algal genomics and physiology. It is of special interest in the study of the evolution of regulatory pathways from algae to higher plants. Additionally, it has recently gained attention as a potential source for bio-fuel and bio-hydrogen production. The genome of Chlamydomonas is available, facilitating the analysis of its transcriptome by RNA-seq data. This has produced a massive amount of data that remains fragmented making necessary the application of integrative approaches based on molecular systems biology. Results We constructed a gene co-expression network based on RNA-seq data and developed a web-based tool, ChlamyNET, for the exploration of the Chlamydomonas transcriptome. ChlamyNET exhibits a scale-free and small world topology. Applying clustering techniques, we identified nine gene clusters that capture the structure of the transcriptome under the analyzed conditions. One of the most central clusters was shown to be involved in carbon/nitrogen metabolism and signalling, whereas one of the most peripheral clusters was involved in DNA replication and cell cycle regulation. The transcription factors and regulators in the Chlamydomonas genome have been identified in ChlamyNET. The biological processes potentially regulated by them as well as their putative transcription factor binding sites were determined. The putative light regulated transcription factors and regulators in the Chlamydomonas genome were analyzed in order to provide a case study on the use of ChlamyNET. Finally, we used an independent data set to cross-validate the predictive power of ChlamyNET. Conclusions The topological properties of ChlamyNET suggest that the Chlamydomonas transcriptome posseses important characteristics related to error tolerance, vulnerability and information propagation. The central part of ChlamyNET constitutes the core of the transcriptome where most authoritative hub genes are located interconnecting key biological processes such as light response with carbon and nitrogen metabolism. Our study reveals that key elements in the regulation of carbon and nitrogen metabolism, light response and cell cycle identified in higher plants were already established in Chlamydomonas. These conserved elements are not only limited to transcription factors, regulators and their targets, but also include the cis-regulatory elements recognized by them.España, Ministerio de Economía y Competitividad CSD2007-00057España, Ministerio de Economía y Competitividad BIO2011-28847-C02-00España, Ministerio de Economía y Competitividad BIO2014-52425-