scholarly journals Embryonic geometry underlies phenotypic variation in decanalized conditions

2019 ◽  
Author(s):  
A. Huang ◽  
T. E. Saunders
Keyword(s):  
Phenotypic Variation ◽  
Regulatory Network ◽  
Physical Space ◽  
Model Organisms ◽  
Wild Type ◽  
Environmental Perturbations ◽  
Key Factor ◽  
In The Wild ◽  
Gene Regulatory ◽  
Anterior Posterior

AbstractDuring development, many mutations cause increased variation in phenotypic outcomes, a phenomenon termed decanalization. Such variations can often be attributed to genetic and environmental perturbations. However, phenotypic discordance remains even in isogenic model organisms raised in homogeneous environments. To understand the mechanisms underlying phenotypic variation, we used as a model the highly precise anterior-posterior (AP) patterning of the early Drosophila embryo. We decanalized the system by depleting the maternal bcd product and found that in contrast to the highly scaled patterning in the wild-type, the segmentation gene boundaries shift away from the scaled positions according to the total embryonic length. Embryonic geometry is hence a key factor predetermining patterning outcomes in such decanalized conditions. Embryonic geometry was also found to predict individual patterning outcomes under bcd overexpression, another decanalizing condition. Further analysis of the gene regulatory network acting downstream of the morphogen identified vulnerable points in the networks due to limitations in the available physical space.

scholarly journals Embryonic geometry underlies phenotypic variation in decanalized conditions

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Anqi Huang ◽  
Jean-François Rupprecht ◽  
Timothy E Saunders
Keyword(s):  
Gene Expression ◽  
Aspect Ratio ◽  
Phenotypic Variation ◽  
Drosophila Embryo ◽  
Wild Type ◽  
Gap Gene ◽  
Key Factor ◽  
Segmentation Gene Expression ◽  
Environmental Variations ◽  
Anterior Posterior

During development, many mutations cause increased variation in phenotypic outcomes, a phenomenon termed decanalization. Phenotypic discordance is often observed in the absence of genetic and environmental variations, but the mechanisms underlying such inter-individual phenotypic discordance remain elusive. Here, using the anterior-posterior (AP) patterning of the Drosophila embryo, we identified embryonic geometry as a key factor predetermining patterning outcomes under decanalizing mutations. With the wild-type AP patterning network, we found that AP patterning is robust to variations in embryonic geometry; segmentation gene expression remains reproducible even when the embryo aspect ratio is artificially reduced by more than twofold. In contrast, embryonic geometry is highly predictive of individual patterning defects under decanalized conditions of either increased bicoid (bcd) dosage or bcd knockout. We showed that the phenotypic discordance can be traced back to variations in the gap gene expression, which is rendered sensitive to the geometry of the embryo under mutations.

scholarly journals The Hybrid Histidine Kinase HrmK Is an Early-Acting Factor in the Hormogonium Gene Regulatory Network

2019 ◽  
Vol 202 (5) ◽  
Author(s):  
Esthefani G. Zuniga ◽  
Natalie M. Figueroa ◽  
Alfonso Gonzalez ◽  
Adriana P. Pantoja ◽  
Douglas D. Risser
Keyword(s):  
Gene Regulatory Network ◽  
Histidine Kinase ◽  
Sigma Factor ◽  
Regulatory Network ◽  
Gliding Motility ◽  
Model Organisms ◽  
Putative Hybrid ◽  
Nitrogen Fixing ◽  
Gene Regulatory ◽  
Hybrid Histidine Kinase

ABSTRACT Filamentous, heterocyst-forming cyanobacteria belonging to taxonomic subsections IV and V are developmentally complex multicellular organisms capable of differentiating an array of cell and filament types, including motile hormogonia. Hormogonia exhibit gliding motility that facilitates dispersal, phototaxis, and the establishment of nitrogen-fixing symbioses. The gene regulatory network (GRN) governing hormogonium development involves a hierarchical sigma factor cascade, but the factors governing the activation of this cascade are currently undefined. Here, using a forward genetic approach, we identified hrmK, a gene encoding a putative hybrid histidine kinase that functions upstream of the sigma factor cascade. The deletion of hrmK produced nonmotile filaments that failed to display hormogonium morphology or accumulate hormogonium-specific proteins or polysaccharide. Targeted transcriptional analyses using reverse transcription-quantitative PCR (RT-qPCR) demonstrated that hormogonium-specific genes both within and outside the sigma factor cascade are drastically downregulated in the absence of hrmK and that hrmK may be subject to indirect, positive autoregulation via sigJ and sigC. Orthologs of HrmK are ubiquitous among, and exclusive to, heterocyst-forming cyanobacteria. Collectively, these results indicate that hrmK functions upstream of the sigma factor cascade to initiate hormogonium development, likely by modulating the phosphorylation state of an unknown protein that may serve as the master regulator of hormogonium development in heterocyst-forming cyanobacteria. IMPORTANCE Filamentous cyanobacteria are morphologically complex, with several representative species amenable to routine genetic manipulation, making them excellent model organisms for the study of development. Furthermore, two of the developmental alternatives, nitrogen-fixing heterocysts and motile hormogonia, are essential to establish nitrogen-fixing symbioses with plant partners. These symbioses are integral to global nitrogen cycles and could be artificially recreated with crop plants to serve as biofertilizers, but to achieve this goal, detailed understanding and manipulation of the hormogonium and heterocyst gene regulatory networks may be necessary. Here, using the model organism Nostoc punctiforme, we identify a previously uncharacterized hybrid histidine kinase that is confined to heterocyst-forming cyanobacteria as the earliest known participant in hormogonium development.

scholarly journals An inside look at a biofilm: Pseudomonas aeruginosa flagella biotracking

2021 ◽  
Vol 7 (24) ◽  
pp. eabg8581
Author(s):  
Eden Ozer ◽  
Karin Yaniv ◽  
Einat Chetrit ◽  
Anastasya Boyarski ◽  
Michael M. Meijler ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Life Cycle ◽  
Opportunistic Pathogen ◽  
Model Organisms ◽  
Wild Type ◽  
Bacterial Flagella ◽  
Knockout Strain ◽  
In The Wild ◽  
Order Of Magnitude ◽  
Genetic Code Expansion

The opportunistic pathogen, Pseudomonas aeruginosa, a flagellated bacterium, is one of the top model organisms for biofilm studies. To elucidate the location of bacterial flagella throughout the biofilm life cycle, we developed a new flagella biotracking tool. Bacterial flagella were site-specifically labeled via genetic code expansion. This enabled us to track bacterial flagella during biofilm maturation. Live flagella imaging revealed the presence and synthesis of flagella throughout the biofilm life cycle. To study the possible role of flagella in a biofilm, we produced a flagella knockout strain and compared its biofilm to that of the wild-type strain. Results showed a one order of magnitude stronger biofilm structure in the wild type in comparison with the flagella knockout strain. This suggests a possible structural role for flagella in a biofilm, conceivably as a scaffold. Our findings suggest a new model for biofilm maturation dynamic which underscores the importance of direct evidence from within the biofilm.

Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction

2021 ◽  
Author(s):  
Gianvito Pio ◽  
Paolo Mignone ◽  
Giuseppe Magazzù ◽  
Guido Zampieri ◽  
Michelangelo Ceci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Transfer Learning ◽  
Regulatory Network ◽  
Drug Targets ◽  
Human Gene ◽  
Supplementary Information ◽  
Model Organisms ◽  
Metabolic Modelling ◽  
Gene Regulatory

Abstract Motivation Gene regulation is responsible for controlling numerous physiological functions and dynamically responding to environmental fluctuations. Reconstructing the human network of gene regulatory interactions is thus paramount to understanding the cell functional organisation across cell types, as well as to elucidating pathogenic processes and identifying molecular drug targets. Although significant effort has been devoted towards this direction, existing computational methods mainly rely on gene expression levels, possibly ignoring the information conveyed by mechanistic biochemical knowledge. Moreover, except for a few recent attempts, most of the existing approaches only consider the information of the organism under analysis, without exploiting the information of related model organisms. Results We propose a novel method for the reconstruction of the human gene regulatory network, based on a transfer learning strategy that synergically exploits information from human and mouse, conveyed by gene-related metabolic features generated in-silico from gene expression data. Specifically, we learn a predictive model from metabolic activity inferred via tissue-specific metabolic modelling of artificial gene knockouts. Our experiments show that the combination of our transfer learning approach with the constructed metabolic features provides a significant advantage in terms of reconstruction accuracy, as well as additional clues on the contribution of each constructed metabolic feature. Availability The system, the datasets and all the results obtained in this study are available at: https://doi.org/10.6084/m9.figshare.c.5237687 Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Nr4a1 Is Required for Fasting-Induced Down-Regulation of Pparγ2 in White Adipose Tissue

2013 ◽  
Vol 27 (1) ◽  
pp. 135-149 ◽  
Author(s):  
Kalina Duszka ◽  
Juliane G. Bogner-Strauss ◽  
Hubert Hackl ◽  
Dietmar Rieder ◽  
Claudia Neuhold ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
White Adipose Tissue ◽  
Expression Profiles ◽  
Receptor Gene ◽  
Wild Type ◽  
Adrenergic Stimulation ◽  
Down Regulation ◽  
In The Wild ◽  
Gene Regulatory ◽  
Direct Target

Expression of the nuclear receptor gene, Nur77 (Nr4a1), is induced in white adipose tissue (WAT) in response to β-adrenergic stimulation and fasting. Recently, Nur77 has been shown to play a gene regulatory role in the fasting response of several other major metabolic tissues. Here we investigated the effects of Nur77 on the WAT transcriptome after fasting. For this purpose, we performed gene expression profiling of WAT from wild-type and Nur77−/− mice submitted to prolonged fasting. Results revealed Nur77-dependent changes in expression profiles of 135 transcripts, many involved in insulin signaling, lipid and fatty acid metabolism, and glucose metabolism. Network analysis identified the deregulated genes Pparγ2 and Nur77 as central hubs and closely connected in the network, indicating overlapping biological function. We further assayed the expression level of Pparγ2 in a bigger cohort of fasted mice and found a significant Nur77-dependent down-regulation of Pparγ2 in the wild-type mice (P = 0.021, n = 10). Consistently, the expression of several known Pparγ2 targets, found among the Nur77-regulated genes (i.e. G0s2, Grp81, Fabp4, and Adipoq), were up-regulated in WAT of fasted Nur77−/− mice. Finally, we show with chromatin immunoprecipitation and luciferase assays that the Pparγ2 promoter is a direct target of Nurr-related 77-kDa protein (Nur77)-dependent repressive regulation and that the N-terminal domain of Nur77 is required for this regulation. In conclusion, we present data implicating Nur77 as a mediator of fasting-induced Pparγ2 regulation in WAT.

Mouse Polycomb M33 is required for splenic vascular and adrenal gland formation through regulating Ad4BP/SF1 expression

Blood ◽  
2005 ◽  
Vol 106 (5) ◽  
pp. 1612-1620 ◽  
Author(s):  
Yuko Katoh-Fukui ◽  
Akiko Owaki ◽  
Yoshiro Toyama ◽  
Masatomo Kusaka ◽  
Yuko Shinohara ◽  
...  
Keyword(s):  
Polycomb Group ◽  
Wild Type ◽  
Steroidogenic Factor 1 ◽  
Knock Out ◽  
Polycomb Group Genes ◽  
Upstream Regulator ◽  
Skeletal Transformation ◽  
In The Wild ◽  
Direct Binding ◽  
Anterior Posterior

Abstract Mice with disrupted mammalian PcG (Polycomb group) genes commonly show skeletal transformation of anterior-posterior identities. Disruption of the murine M33 gene, a PcG member, displayed posterior transformation of the vertebral columns and sternal ribs. In addition, failure of T-cell expansion and hypoplasia and sex-reversal of the gonads, have been observed. In the present study, we identified defects in the splenic and adrenal formation of M33–knock-out (KO) mice on a C57BL/6 genetic background. The spleen in these animals was smaller than in the wild-type mice and was spotted red because of nonuniform distribution of blood cells. Histologic examination revealed disorganization of the vascular endothelium and its surrounding structures, and immunohistochemistry demonstrated disturbances in vascular formation and colonization of immature hematopoietic cells. These splenic phenotypes observed in the M33-KO mice were quite similar to those seen in Ad4BP/SF1 (Nr5a1) knock-outs. Moreover, the adrenal glands of M33-KO and Ad4BP/SF1 heterozygous KO mice were smaller than those of the wild-type mice. Western blot, immunohistochemistry, and reverse transcriptase–polymerase chain reaction (RT-PCR) analyses of the M33 knock-outs all indicated significantly low expression of adrenal 4 binding protein/steroidogenic factor-1 (Ad4BP/SF-1), indicating that M33 is an essential upstream regulator of Ad4BP/SF1. In agreement with these observations, chromatin immunoprecipitation assays with adrenocortical Y-1 cells revealed direct binding of the M33-containing PcG to the Ad4BP/SF1 gene locus.

scholarly journals A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos.

2016 ◽  
Author(s):  
Alys Jarvela ◽  
Kristen Yankura ◽  
Veronica Hinman
Keyword(s):  
Regulatory Network ◽  
Apical Organ ◽  
Spatial Patterning ◽  
Sea Star ◽  
Spatial Control ◽  
Neural Fate ◽  
Multipotent Progenitors ◽  
Asymmetric Divisions ◽  
Gene Regulatory ◽  
Anterior Posterior

How neural stem cells generate the correct number and type of differentiated neurons in appropriate places is an important question in developmental biology. Although nervous systems are diverse across phyla, many taxa have a larva that forms an anterior concentration of neurons, or apical organ. The number of neurons in these organs is highly variable. We show that neurogenesis in the sea star larvae begins with soxc-expressing multipotent progenitors. These give rise to restricted progenitors that express lhx2/9. Soxc- and lhx2/9-expressing cells are capable of undergoing both asymmetric divisions, which allow for progression towards a particular neural fate, and symmetric proliferative divisions. Nested concentric domains of gene expression along the anterior-posterior (AP) axis, which have been observed in a great diversity of metazoans, control neurogenesis in the sea star by promoting particular division modes and progression towards becoming a neuron. This work, therefore, explains how spatial patterning in the ectoderm controls progression of neurogenesis. Modification to the sizes of these AP territories provides a simple mechanism to explain the diversity of neuron number found among apical organs.

scholarly journals When development is constantly but weakly perturbed - Canalization by microRNAs

2021 ◽  
Author(s):  
GuangAn Lu ◽  
Yixin Zhao ◽  
Qingjian Chen ◽  
Pei Lin ◽  
Tian Tang ◽  
...  
Keyword(s):  
High Temperature ◽  
Culture Condition ◽  
Regulatory Network ◽  
Complete Removal ◽  
Adult Longevity ◽  
Larval Stages ◽  
Environmental Perturbations ◽  
Gene Regulatory ◽  
Optimal Culture Condition ◽  
Late Stages

AbstractRecent studies have increasingly pointed to microRNAs (miRNAs) as the agent of GRN (gene regulatory network) stabilization as well as developmental canalization against constant but small environmental perturbations. Since the complete removal of miRNAs is lethal, we construct a Dicer-1 knockdown line (dcr-1 KD) in Drosophila that modestly reduces all miRNAs. We hypothesize that flies with modest miRNA reductions will gradually deviate from the developmental norm, resulting in late-stage failures such as shortened longevity. In the optimal culture condition, the survival to adulthood is indeed normal in the dcr-1 KD line but, importantly, adult longevity is reduced by ∼ 90%. When flies are stressed by high temperature, dcr-1 KD induces lethality earlier in late pupation and, as the perturbations are shifted earlier, the affected stages are shifted correspondingly. We further show that the developmental failure is associated with GRN aberration in the larval stages even before phenotypic aberrations become observable. Hence, in late stages of development with deviations piling up, GRN would be increasingly in need of stabilization. In conclusion, miRNAs appear to be the genome’s solution to weak but constant environmental perturbations.

scholarly journals Single-cell gene regulatory network inference at scale: The Inferelator 3.0

2021 ◽  
Author(s):  
Claudia Skok Gibbs ◽  
Christopher A Jackson ◽  
Giuseppe-Antonio Saldi ◽  
Aashna Shah ◽  
Andreas Tj&aumlrnberg ◽  
...  
Keyword(s):  
Single Cell ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Cell Types ◽  
Cellular Growth ◽  
Model Organisms ◽  
Gene Regulatory Network Inference ◽  
Data Set ◽  
Gene Regulatory ◽  
Cell Gene

Gene regulatory networks define regulatory relationships between transcription factors and target genes within a biological system, and reconstructing them is essential for understanding cellular growth and function. In this work, we present the Inferelator 3.0, which has been significantly updated to integrate data from distinct cell types to learn context-specific regulatory networks and aggregate them into a shared regulatory network, while retaining the functionality of the previous versions. The Inferelator 3.0 reliably learns informative networks from the model organisms Bacillus subtilis and Saccharomyces cerevisiae. We demonstrate its capabilities by learning networks for multiple distinct neuronal and glial cell types in the developing Mus musculus brain at E18 from a large (1.3 million) single-cell gene expression data set with paired single-cell chromatin accessibility data.

Freeze-substituted fungal cells of Nectria haematococca: A comparison of the macroconidial walls of the adhesion-competent wild type with an adhesion-reduced mutant

1990 ◽  
Vol 48 (3) ◽  
pp. 688-689
Author(s):  
Thecan Caesar-Ton That ◽  
Lynn Epstein
Keyword(s):  
Freeze Substitution ◽  
Uranyl Acetate ◽  
Wild Type ◽  
Nectria Haematococca ◽  
Fruit Extract ◽  
Dialysis Tubing ◽  
Tube Emergence ◽  
Contrast Microscopy ◽  
In The Wild ◽  
Freeze Damage

Nectria haematococca mating population I (anamorph, Fusarium solani) macroconidia attach to its host (squash) and non-host surfaces prior to germ tube emergence. The macroconidia become adhesive after a brief period of protein synthesis. Recently, Hickman et al. (1989) isolated N. haematococca adhesion-reduced mutants. Using freeze substitution, we compared the development of the macroconidial wall in the wild type in comparison to one of the mutants, LEI.Macroconidia were harvested at 1C, washed by centrifugation, resuspended in a dilute zucchini fruit extract and incubated from 0 - 5 h. During the incubation period, wild type macroconidia attached to uncoated dialysis tubing. Mutant macroconidia did not attach and were collected on poly-L-lysine coated dialysis tubing just prior to freezing. Conidia on the tubing were frozen in liquid propane at 191 - 193C, substituted in acetone with 2% OsO4 and 0.05% uranyl acetate, washed with acetone, and flat-embedded in Epon-Araldite. Using phase contrast microscopy at 1000X, cells without freeze damage were selected, remounted, sectioned and post-stained sequentially with 1% Ba(MnO4)2 2% uranyl acetate and Reynold’s lead citrate. At least 30 cells/treatment were examined.

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