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

Precision of readout at the hunchback gene: analyzing short transcription time traces in living fly embryos

The simultaneous expression of the hunchback gene in the numerous nuclei of the developing fly embryo gives us a unique opportunity to study how transcription is regulated in living organisms. A recently developed MS2-MCP technique for imaging nascent messenger RNA in living Drosophila embryos allows us to quantify the dynamics of the developmental transcription process. The initial measurement of the morphogens by the hunchback promoter takes place during very short cell cycles, not only giving each nucleus little time for a precise readout, but also resulting in short time traces of transcription. Additionally, the relationship between the measured signal and the promoter state depends on the molecular design of the reporting probe. We develop an analysis approach based on tailor made autocorrelation functions that overcomes the short trace problems and quantifies the dynamics of transcription initiation. Based on live imaging data, we identify signatures of bursty transcription initiation from the hunchback promoter. We show that the precision of the expression of the hunchback gene to measure its position along the anterior-posterior axis is low both at the boundary and in the anterior even at cycle 13, suggesting additional post-transcriptional averaging mechanisms to provide the precision observed in fixed embryos

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-

A contribution to the study of plant development evolution based on gene co-expression networks

Phototrophic eukaryotes are among the most successful organisms on Earth due to their unparalleled efficiency at capturing light energy and fixing carbon dioxide to produce organic molecules. A conserved and efficient network of light-dependent regulatory modules could be at the bases of this success. This regulatory system conferred early advantages to phototrophic eukaryotes that allowed for specialization, complex developmental processes and modern plant characteristics. We have studied light-dependent gene regulatory modules from algae to plants employing integrative-omics approaches based on gene co-expression networks. Our study reveals some remarkably conserved ways in which eukaryotic phototrophs deal with day length and light signaling. Here we describe how a family of Arabidopsis transcription factors involved in photoperiod response has evolved from a single algal gene according to the innovation, amplification and divergence theory of gene evolution by duplication. These modifications of the gene co-expression networks from the ancient unicellular green algae Chlamydomonas reinhardtii to the modern brassica Arabidopsis thaliana may hint on the evolution and specialization of plants and other organisms.España Ministerio de Economía y Competitividad CSD2007-00057España Ministerio de Economía y Competitividad BIO2011-28847-C02-0

O direito de morar no campo : o direito à moradia na zona rural, a partir da comunidade de caçador, no Vale do Ribeira - PR

Orientador: Vera Karam de ChueiriMonografia (graduação) - Universidade Federal do Paraná, Setor de Ciências Jurídicas, Curso de Graduação em DireitoPensar sobre o direito à moradia normalmente conduz a refletir sobre as ocupações irregulares urbanas e o déficit habitacional das grandes cidades. No entanto, sem de forma alguma retirar a indiscutível importância desse enfoque, busca-se, através deste estudo, refletir acerca do direito à moradia aplicado à realidade agrário-camponesa. Para tanto, toma-se para análise a pequena comunidade rural de Caçador, no Município de Itaperuçu, Região do Vale do Ribeira. Com um paralelo traçado entre as previsões normativo-constitucionais de um direito à moradia em conformidade com os princípios constitucionais, e a realidade do direito à moradia em Caçador, pretende-se verificar as condições de efetivação deste direito humano e fundamental naquele contexto rural específico. Desse modo, a indissociabilidade entre teoria e prática constitui um paradigma metodológico para este trabalho

O direito de morar no campo

Pensar sobre o direito à moradia normalmente conduz a refletir sobre as ocupações irregulares urbanas e o déficit habitacional das grandes cidades. No entanto, sem de forma alguma retirar a indiscutível importância desse enfoque, busca-se, através deste estudo, refletir acerca do direito à moradia aplicado à realidade agrário-camponesa. Para tanto, toma-se para análise a pequena comunidade rural de Caçador, no Município de Itaperuçu, Região do Vale do Ribeira. Com um paralelo traçado entre as previsões normativo-constitucionais de um direito à moradia em conformidade com os princípios constitucionais, e a realidade do direito à moradia em Caçador, pretende-se verificar as condições de efetivação deste direito humano e fundamental naquele contexto rural específico. Desse modo, a indissociabilidade entre teoria e prática constitui um paradigma metodológico para este trabalho

Synchronous firing of dorsal horn neurons at the origin of dorsal root reflexes in naïve and paw-inflamed mice

Spinal interneurons located in the dorsal horn induce primary afferent depolarization (PAD) controlling the excitability of the afferent?s terminals. Following inflammation, PAD may reach firing threshold contributing to maintain inflammation and pain. Our aim was to study the collective behavior of dorsal horn neurons, its relation to backfiring of primary afferents and the effects of a peripheral inflammation in this system. Experiments were performed on slices of spinal cord obtained from naïve adult mice or mice that had suffered an inflammatory pretreatment. Simultaneous recordings from groups of dorsal horn neurons and primary afferents were obtained and machine-learning methodology was used to analyze effective connectivity between them. Dorsal horn recordings showed grouping of spontaneous action potentials from different neurons in ?population bursts.? These occurred at irregular intervals and were formed by action potentials from all classes of neurons recorded. Compared to naïve, population bursts from treated animals concentrated more action potentials, had a faster onset and a slower decay. Population bursts were disrupted by perfusion of picrotoxin and held a strong temporal correlation with backfiring of afferents. Effective connectivity analysis allowed pinpointing specific neurons holding pre- or post-synaptic relation to the afferents. Many of these neurons had an irregular fast bursting pattern of spontaneous firing. We conclude that population bursts contain action potentials from neurons presynaptic to the afferents which are likely to control their excitability. Peripheral inflammation may enhance synchrony in these neurons, increasing the chance of triggering action potentials in primary afferents and contributing toward central sensitization.Ministerio de Ciencia e InnovaciónUniversidad de Alcal

Role of central terminals of primary afferents in the maintenance of coordinated spontaneous activity of dorsal horn neurons [Póster]

11th IBRO Word Congress of Neuroscience, 9-13 september 2023, Granada, Spain , , 09/09/2023-13/09/2023, Granada, EspañaMinisterio de Ciencia e Innovació