scholarly journals Characterization of eyes, photoreceptors and opsins in developmental stages of the chaetognath Spadella cephaloptera

2019 ◽  
Author(s):  
Tim Wollesen ◽  
Sonia Victoria Rodríguez Monje ◽  
Adam Phillip Oel ◽  
Detlev Arendt
Keyword(s):  
Regulatory Networks ◽  
Developmental Stages ◽  
Photoreceptor Cells ◽  
Phylogenetic Position ◽  
Developmental Studies ◽  
Head Region ◽  
Platynereis Dumerilii ◽  
Spadella Cephaloptera ◽  
Gene Regulatory

AbstractThe phylogenetic position of chaetognaths has been debated for decades, however recently they have been grouped into the Gnathifera, sister taxon to the Lophotrochozoa. Chaetognaths possess photoreceptor cells that are anatomically unique and arranged remarkably different in the eyes of the various species. Studies investigating eye development and underlying gene regulatory networks are so far missing.In order to gain insights into the development and the molecular toolkit of chaetognath photoreceptors and eyes a new transcriptome of the epibenthic species Spadella cephaloptera was searched for opsins. Our screen revealed single-copies of xenopsin and peropsin and gene expression analyses demonstrated that only xenopsin is expressed in photoreceptor cells of the developing lateral eyes. Adults likewise exhibit two xenopsin+ photoreceptor cells in each of their lateral eyes. Beyond that, a single cryptochrome gene was uncovered and found co-expressed with xenopsin in some photoreceptor cells of the lateral developing eye. In addition, it is co-expressed with peropsin in the cerebral ganglia, a condition reminiscent of a non-visual photoreceptive zone in the apical nervous system of the annelid Platynereis dumerilii that performs circadian entrainment and melatonin release. Cryptochrome expression was also detected in cells of the corona ciliata, a circular organ in the posterior dorsal head region that has been attributed several functions arguing for an involvement of this organ in circadian entrainment. Our study demonstrates the importance to investigate representatives of the Gnathifera, a clade that has been neglected with respect to developmental studies and that might contribute to unravel the evolution of spiralian and bilaterian body plans.

scholarly journals Integration of a Computational Pipeline for Dynamic Inference of Gene Regulatory Networks in Single Cells

2019 ◽  
Author(s):  
Kyung Dae Ko ◽  
Stefania Dell’Orso ◽  
Aster H. Juan ◽  
Vittorio Sartorelli
Keyword(s):  
Prior Knowledge ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Developmental Stages ◽  
Individual Cell ◽  
Single Cells ◽  
Rna Seq ◽  
Gene Regulatory ◽  
Molecular Expression

SUMMARYSingle-cell RNA-seq permits the characterization of the molecular expression states of individual cells. Several methods have been developed to spatially and temporally resolve individual cell populations. However, these methods are not always integrated and some of them are constrained by prior knowledge. Here, we present an integrated pipeline for inference of gene regulatory networks. The pipeline does not rely on prior knowledge, it improves inference accuracy by integrating signatures from different data dimensions and facilitates tracing variation of gene expression by visualizing gene-interacting patterns of co-expressed gene regulatory networks at distinct developmental stages.

scholarly journals Molecular characterization of gene regulatory networks in primary human tracheal and bronchial epithelial cells

2018 ◽  
Vol 17 (4) ◽  
pp. 444-453 ◽  
Author(s):  
Austin E. Gillen ◽  
Rui Yang ◽  
Calvin U. Cotton ◽  
Aura Perez ◽  
Scott H. Randell ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Molecular Characterization ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Bronchial Epithelial Cells ◽  
Bronchial Epithelial ◽  
Gene Regulatory

Sparse factor model for co-expression networks with an application using prior biological knowledge

2016 ◽  
Vol 15 (3) ◽  
Author(s):  
Yuna Blum ◽  
Magalie Houée-Bigot ◽  
David Causeur
Keyword(s):  
Regulatory Networks ◽  
Factor Model ◽  
Functional Characterization ◽  
Deep Understanding ◽  
Biological Knowledge ◽  
Expression Data ◽  
Gene Expressions ◽  
Prior Biological Knowledge ◽  
Gene Regulatory

AbstractInference on gene regulatory networks from high-throughput expression data turns out to be one of the main current challenges in systems biology. Such networks can be very insightful for the deep understanding of interactions between genes. Because genes-gene interactions is often viewed as joint contributions to known biological mechanisms, inference on the dependence among gene expressions is expected to be consistent to some extent with the functional characterization of genes which can be derived from ontologies (GO, KEGG, …). The present paper introduces a sparse factor model as a general framework either to account for a prior knowledge on joint contributions of modules of genes to latent biological processes or to infer on the corresponding co-expression network. We propose an

Development of pigment-cup eyes in the polychaetePlatynereis dumeriliiand evolutionary conservation of larval eyes in Bilateria

Development ◽  
2002 ◽  
Vol 129 (5) ◽  
pp. 1143-1154 ◽  
Author(s):  
Detlev Arendt ◽  
Kristin Tessmar ◽  
Maria-Ines Medeiros de Campos-Baptista ◽  
Adriaan Dorresteijn ◽  
Joachim Wittbrodt
Keyword(s):  
Visual System ◽  
Early Development ◽  
Developmental Stages ◽  
Photoreceptor Cells ◽  
Evolutionary Conservation ◽  
Early Developmental Stages ◽  
Platynereis Dumerilii ◽  
Differentiation Marker ◽  
Early Developmental

The role of Pax6 in eye development in insects and vertebrates supports the view that their eyes evolved from simple pigment-cup ocelli present in their last common ancestors (Urbilateria). The cerebral eyes in errant polychaetes represent prototype invertebrate pigment-cup ocelli and thus resemble the presumed ancestral eyes. We have analysed expression of conserved eye specification genes in the early development of larval and adult pigment-cup eyes in Platynereis dumerilii (Polychaeta, Annelida, Lophotrochozoa). Both larval and adult eyes form in close vicinity of the optic anlagen on both sides of the developing brain ganglia. While pax6 is expressed in the larval, but not in the developing, adult eyes, expression of six1/2 from trochophora stages onwards specifically outlines the optic anlagen and thus covers both the developing larval and adult eyes. Using Platynereis rhabdomeric opsin as differentiation marker, we show that the first pair of adult eye photoreceptor cells is detected within bilateral clusters that transitorily express ath, the Platynereis atonal orthologue, thus resembling proneural sensory clusters. Our data indicate that – similar to insects, but different from the vertebrates – polychaete six1/2 expression outlines the entire visual system from early developmental stages onwards and ath-positive clusters generate the first photoreceptor cells to appear. We propose that pax6-, six1/2- and ath-positive larval eyes, as found in today’s trochophora, were present already in Urbilateria.

scholarly journals Systems Biology Approach to Model the Life Cycle ofTrypanosoma cruzi

2015 ◽  
Author(s):  
Alejandra Carrea ◽  
Luis Diambra
Keyword(s):  
Life Cycle ◽  
Systems Biology ◽  
Network Architecture ◽  
Regulatory Networks ◽  
Developmental Stages ◽  
Environmental Cues ◽  
Cell Fates ◽  
Gene Regulatory ◽  
Cell Phenotypes ◽  
Optimisation Procedure

Due to recent advances in reprogramming cell phenotypes, many efforts have been dedicated to developing reverse engineering procedures for the identification of gene regulatory networks that emulate dynamical properties associated with the cell fates of a given biological system. In this work, we propose a systems biology approach for the reconstruction of the gene regulatory network underlying the dynamics of theTrypanosoma cruzi's life cycle. By means of an optimisation procedure, we embedded the steady state maintenance, and the known phenotypic transitions between these steady states in response to environmental cues, into the dynamics of a gene network model. In the resulting network architecture we identified a small subnetwork, formed by seven interconnected nodes, that controls the parasite's life cycle. The present approach could be useful for better understanding other single cell organisms with multiple developmental stages.

scholarly journals Gene Expression Maps in Plants: Current State and Prospects

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 309 ◽  
Author(s):  
Anna V. Klepikova ◽  
Aleksey A. Penin
Keyword(s):  
Regulatory Networks ◽  
Large Scale ◽  
Developmental Stages ◽  
Large Scale Data ◽  
Current State ◽  
Genome Wide ◽  
Plant Transcriptome ◽  
Gene Regulatory ◽  
Genome Wide Expression ◽  
Scale Data

For many years, progress in the identification of gene functions has been based on classical genetic approaches. However, considerable recent omics developments have brought to the fore indirect but high-resolution methods of gene function identification such as transcriptomics, proteomics, and metabolomics. A transcriptome map is a powerful source of functional information and the result of the genome-wide expression analysis of a broad sampling of tissues and/or organs from different developmental stages and/or environmental conditions. In plant science, the application of transcriptome maps extends from the inference of gene regulatory networks to evolutionary studies. However, only some of these data have been integrated into databases, thus enabling analyses to be conducted without raw data; without this integration, extensive data preprocessing is required, which limits data usability. In this review, we summarize the state of plant transcriptome maps, analyze the problems associated with the combined analysis of large-scale data from various studies, and outline possible solutions to these problems.

Comparative Analysis of Gene Regulatory Network Components in the Auditory Hindbrain of Mice and Chicken

2016 ◽  
Vol 88 (3-4) ◽  
pp. 161-176 ◽  
Author(s):  
Benjamin Pawlik ◽  
Tina Schlüter ◽  
Heiner Hartwich ◽  
Saskia Breuel ◽  
Lennart Heepmann ◽  
...  
Keyword(s):  
Ampa Receptors ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Terminal Differentiation ◽  
Neuronal Cell ◽  
Divergent Evolution ◽  
Superior Olivary Complex ◽  
Gene Regulatory

The neurons in the mammalian and avian auditory hindbrain nuclei share a number of significant morphological and physiological properties for fast, secure and precise neurotransmission, such as giant synapses, voltage-gated K+ channels and fast AMPA receptors. Based on the independent evolution of the middle ear in these two vertebrate lineages, on different embryonic origins of the nuclei and on marked differences on the circuit level, these similarities are assumed to reflect convergent evolution. Independent acquisition of similar phenotypes can be produced by divergent evolution of genetic mechanisms or by similar molecular mechanisms. The distinction between these two possibilities requires knowledge of the gene regulatory networks (GRNs) that orchestrate the development of auditory hindbrain structures. We therefore compared the expression pattern of GRN components, both transcription factors (TFs) and noncoding RNA, during terminal differentiation of the auditory hindbrain structures in mouse and chicken when neurons acquire their final morphological and electrophysiological properties. In general, we observed broad expression of these genes in the mouse auditory cochlear nucleus complex and the superior olivary complex at both postnatal day 4 (P4) and at P25, and for the chicken at the equivalent developmental stages, i.e. embryonic day 13 (E13) and at P14-P17. Our data are in agreement with a model based on similar molecular mechanisms underlying terminal differentiation and maintenance of neuronal cell identity in the auditory hindbrain of different vertebrate lineages. This conservation might reflect developmental constraints arising from the tagmatic organization of rhombomeres and the evolutionarily highly conserved GRNs operating in these structures.

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