scholarly journals Quantitative study of the somitogenetic wavefront in zebrafish

2018 ◽  
Author(s):  
Weiting Zhang ◽  
Bertrand Ducos ◽  
Marine Delagrange ◽  
Sophie Vriz ◽  
David Bensimon
Keyword(s):  
Quantitative Description ◽  
Molecular Networks ◽  
Model Organisms ◽  
Stable States ◽  
Genetic Oscillator ◽  
Mrna Concentration ◽  
Exponential Decrease ◽  
Negative Feedbacks ◽  
Molecular Components ◽  
Somitic Mesoderm

ABSTRACTA quantitative description of the molecular networks that sustain morphogenesis is one of the challenges of developmental biology. Specifically, a molecular understanding of the segmentation of the antero-posterior axis in vertebrates has yet to be achieved. This process known as somitogenesis is believed to result from the interactions between a genetic oscillator and a posterior-moving determination wavefront. Here we quantitatively study and perturb the network in zebrafish that sustains this wavefront and compare our observations to a model whereby the wavefront is due to a switch between stable states resulting from reciprocal negative feedbacks of Retinoic Acid (RA) on the activation of ERK and of ERK on RA synthesis. This model quantitatively accounts for the near linear shortening of the post-somitic mesoderm (PSM) in response to the observed exponential decrease during somitogenesis of the mRNA concentration of a morphogen (Fgf8). It also accounts for the observed dynamics of the PSM when the molecular components of the network are perturbed. The generality of our model and its robustness allows for its test in other model organisms.

scholarly journals Bacillus velezensisWall Teichoic Acids Are Required for Biofilm Formation and Root Colonization

2018 ◽  
Vol 85 (5) ◽  
Author(s):  
Zhihui Xu ◽  
Huihui Zhang ◽  
Xinli Sun ◽  
Yan Liu ◽  
Wuxia Yan ◽  
...  
Keyword(s):  
Plant Growth ◽  
Biofilm Formation ◽  
Root Colonization ◽  
Molecular Networks ◽  
Model Organisms ◽  
Bacillus Velezensis ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Colonization Process ◽  
Growth Promoting

ABSTRACTRhizosphere colonization by plant growth-promoting rhizobacteria (PGPR) along plant roots facilitates the ability of PGPR to promote plant growth and health. Thus, an understanding of the molecular mechanisms of the root colonization process by plant-beneficialBacillusstrains is essential for the use of these strains in agriculture. Here, we observed that ansfpgene mutant of the plant growth-promoting rhizobacteriumBacillus velezensisSQR9 was unable to form normal biofilm architecture, and differential protein expression was observed by proteomic analysis. A minor wall teichoic acid (WTA) biosynthetic protein, GgaA, was decreased over 4-fold in the Δsfpmutant, and impairment of theggaAgene postponed biofilm formation and decreased cucumber root colonization capabilities. In addition, we provide evidence that the major WTA biosynthetic enzyme GtaB is involved in both biofilm formation and root colonization. The deficiency in biofilm formation of the ΔgtaBmutant may be due to an absence of UDP-glucose, which is necessary for the synthesis of biofilm matrix exopolysaccharides (EPS). These observations provide insights into the root colonization process by a plant-beneficialBacillusstrain, which will help improve its application as a biofertilizer.IMPORTANCEBacillus velezensisis a Gram-positive plant-beneficial bacterium which is widely used in agriculture. Additionally,Bacillusspp. are some of the model organisms used in the study of biofilms, and as such, the molecular networks and regulation systems of biofilm formation are well characterized. However, the molecular processes involved in root colonization by plant-beneficialBacillusstrains remain largely unknown. Here, we showed that WTAs play important roles in the plant root colonization process. The loss of thegtaBgene affects the ability ofB. velezensisSQR9 to sense plant polysaccharides, which are important environmental cues that trigger biofilm formation and colonization in the rhizosphere. This knowledge provides new insights into theBacillusroot colonization process and can help improve our understanding of plant-rhizobacterium interactions.

scholarly journals Applications of molecular networks in biomedicine

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Monica Chagoyen ◽  
Juan A G Ranea ◽  
Florencio Pazos
Keyword(s):  
Single Gene ◽  
Point Of View ◽  
Molecular Networks ◽  
Large Sets ◽  
Software Packages ◽  
Number Of Genes ◽  
Complex Phenomena ◽  
Network Approaches ◽  
Molecular Components ◽  
Standard Software

Abstract Due to the large interdependence between the molecular components of living systems, many phenomena, including those related to pathologies, cannot be explained in terms of a single gene or a small number of genes. Molecular networks, representing different types of relationships between molecular entities, embody these large sets of interdependences in a framework that allow their mining from a systemic point of view to obtain information. These networks, often generated from high-throughput omics datasets, are used to study the complex phenomena of human pathologies from a systemic point of view. Complementing the reductionist approach of molecular biology, based on the detailed study of a small number of genes, systemic approaches to human diseases consider that these are better reflected in large and intricate networks of relationships between genes. These networks, and not the single genes, provide both better markers for diagnosing diseases and targets for treating them. Network approaches are being used to gain insight into the molecular basis of complex diseases and interpret the large datasets associated with them, such as genomic variants. Network formalism is also suitable for integrating large, heterogeneous and multilevel datasets associated with diseases from the molecular level to organismal and epidemiological scales. Many of these approaches are available to nonexpert users through standard software packages.

scholarly journals Stepwise in vitro induction of human somitic mesoderm and its derivatives

2020 ◽  
Author(s):  
Yoshihiro Yamanaka ◽  
Maya Uemura ◽  
Cantas Alev
Keyword(s):  
Pluripotent Stem Cells ◽  
Pluripotent Stem Cell ◽  
Developmental Process ◽  
Cell Types ◽  
Model Organisms ◽  
Human Segmentation ◽  
Induced Pluripotent ◽  
Somitic Mesoderm ◽  
In Vitro Induction

Abstract Our understanding of human somitogenesis is limited and largely based on insights gained from model organisms. Pluripotent stem cell-based in vitro approaches aiming to recapitulate distinct aspects of this core developmental process have recently been reported, including our recent paper on the in vitro recapitulation of the human segmentation clock1. Here we describe in detail our stepwise induction protocol of presomitic mesoderm (PSM), somitic mesoderm (SM), and its two major derivatives, sclerotome (SCL) and dermomyotome (DM) from human induced pluripotent stem cells (iPSCs). We further briefly address the subsequent molecular and functional analysis of these in vitro induced human mesodermal lineages and cell-types.

scholarly journals Hub genes in a pan-cancer co-expression network show potential for predicting drug responses

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1906
Author(s):  
Francisco Azuaje ◽  
Tony Kaoma ◽  
Céline Jeanty ◽  
Petr V. Nazarov ◽  
Arnaud Muller ◽  
...  
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Topological Analysis ◽  
Molecular Networks ◽  
Model Organisms ◽  
Hub Genes ◽  
Diverse Range ◽  
Drug Responses ◽  
Using Data

Background: The topological analysis of networks extracted from different types of “omics” data is a useful strategy for characterizing biologically meaningful properties of the complex systems underlying these networks. In particular, the biological significance of highly connected genes in diverse molecular networks has been previously determined using data from several model organisms and phenotypes. Despite such insights, the predictive potential of candidate hubs in gene co-expression networks in the specific context of cancer-related drug experiments remains to be deeply investigated. The examination of such associations may offer opportunities for the accurate prediction of anticancer drug responses.  Methods: Here, we address this problem by: a) analyzing a co-expression network obtained from thousands of cancer cell lines, b) detecting significant network hubs, and c) assessing their capacity to predict drug sensitivity using data from thousands of drug experiments. We investigated the prediction capability of those genes using a multiple linear regression model, independent datasets, comparisons with other models and our own in vitro experiments. Results: These analyses led to the identification of 47 hub genes, which are implicated in a diverse range of cancer-relevant processes and pathways. Overall, encouraging agreements between predicted and observed drug sensitivities were observed in public datasets, as well as in our in vitro validations for four glioblastoma cell lines and four drugs. To facilitate further research, we share our hub-based drug sensitivity prediction model as an online tool. Conclusions: Our research shows that co-expression network hubs are biologically interesting and exhibit potential for predicting drug responses in vitro. These findings motivate further investigations about the relevance and application of our unbiased discovery approach in pre-clinical, translationally-oriented research.

Engineering crystals built from molecules containing boron

2006 ◽  
Vol 78 (7) ◽  
pp. 1305-1321 ◽  
Author(s):  
Kenneth E. Maly ◽  
Nadia Malek ◽  
Jean-Hugues Fournier ◽  
Patricia Rodríguez-Cuamatzi ◽  
Thierry Maris ◽  
...  
Keyword(s):  
Crystal Engineering ◽  
Molecular Crystals ◽  
Molecular Geometry ◽  
Molecular Networks ◽  
Structure And Properties ◽  
Structures And Properties ◽  
Structural Preferences ◽  
Direct Association ◽  
The Individual ◽  
Molecular Components

The study of compounds containing boron continues to have an important impact on virtually every area of chemistry. One of the few areas in which compounds of boron have been neglected is crystal engineering, which seeks to develop and exploit an understanding of how the structure and properties of crystals are related to the individual atomic or molecular components. Although detailed predictions of crystal structures are not yet reliable, crystal engineers have developed a sound qualitative strategy for anticipating and controlling structural preferences. This strategy is based on the design of special molecules, called tectons, which feature carefully selected cores and multiple peripheral functional groups that can direct association and thereby place neighboring molecules in predetermined positions. Recent work has demonstrated that molecular crystals with unique properties can be constructed logically from tectons with boron in their cores or sticky sites of association. In particular, the -B(OH)2 group of boronic acids engages in reliable patterns of hydrogen bonding, and its use as a sticky site in tectons has emerged as an effective tool for controlling association predictably. In addition, replacement of tetraphenylsilyl or tetraphenylmethyl cores in tectons by tetraphenylborate leaves the overall molecular geometry little changed, but it has the profound effect of introducing charge. Tectons derived from tetraphenylborate can be used rationally to construct porous charged molecular networks that resemble zeolites and undergo selective ion exchange. In such ways, boron offers chemists exciting new ways to engineer molecular crystals with predetermined structures and properties.

scholarly journals Sex Determination and Differentiation in Decapod and Cladoceran Crustaceans: An Overview of Endocrine Regulation

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 305
Author(s):  
Kenji Toyota ◽  
Hitoshi Miyakawa ◽  
Chizue Hiruta ◽  
Tomomi Sato ◽  
Hidekazu Katayama ◽  
...  
Keyword(s):  
Sex Determination ◽  
High Throughput Sequencing ◽  
Keystone Species ◽  
Model Organisms ◽  
Endocrine Regulation ◽  
Determination System ◽  
Commercially Important ◽  
Sex Determination System ◽  
Molecular Components ◽  
Reference Genomes

Mechanisms underlying sex determination and differentiation in animals are known to encompass a diverse array of molecular clues. Recent innovations in high-throughput sequencing and mass spectrometry technologies have been widely applied in non-model organisms without reference genomes. Crustaceans are no exception. They are particularly diverse among the Arthropoda and contain a wide variety of commercially important fishery species such as shrimps, lobsters and crabs (Order Decapoda), and keystone species of aquatic ecosystems such as water fleas (Order Branchiopoda). In terms of decapod sex determination and differentiation, previous approaches have attempted to elucidate their molecular components, to establish mono-sex breeding technology. Here, we overview reports describing the physiological functions of sex hormones regulating masculinization and feminization, and gene discovery by transcriptomics in decapod species. Moreover, this review summarizes the recent progresses of studies on the juvenile hormone-driven sex determination system of the branchiopod genus Daphnia, and then compares sex determination and endocrine systems between decapods and branchiopods. This review provides not only substantial insights for aquaculture research, but also the opportunity to re-organize the current and future trends of this field.

Towards of Quantitative Model of Stacked Actor-Network Dynamics

2017 ◽  
Vol 9 (2) ◽  
pp. 42-62
Author(s):  
Peter Kopanov ◽  
Ivan Tchalakov
Keyword(s):  
Social Sciences ◽  
Differential Equation ◽  
Quantitative Description ◽  
Quantitative Model ◽  
Cultural Dynamics ◽  
Stable States ◽  
The Third ◽  
Equation Analysis ◽  
Actor Networks ◽  
Technology Growth

This article further develops the stacked actor-networks (SAN) approach in modelling socio-economic and cultural dynamics. Following the Lee and Schiesser application of differential equation analysis in biological and social sciences, the authors used a basic SAN model. This model is composed of three subnetworks where each two subnetworks dominate over the third one to build a quantitative description that identifies three stable states in the dynamics of their interactions – cyclical development, linear, and exponential growth. Describing the latter, the notion of ‘technology growth' is introduced that bears on the pattern of hyper-fast growth.

Hybrid Organic/Inorganic Magnets

MRS Bulletin ◽  
2000 ◽  
Vol 25 (11) ◽  
pp. 52-57 ◽  
Author(s):  
Kunio Awaga ◽  
Eugenio Coronado ◽  
Marc Drillon
Keyword(s):  
Molecular Electronics ◽  
Electronic Conductivity ◽  
Hybrid Approach ◽  
Magnetic Layer ◽  
Building Blocks ◽  
Molecular Networks ◽  
Molecular Materials ◽  
Hybrid Compound ◽  
The Individual ◽  
Molecular Components

The construction of more and more complex systems starting from elemental molecular units used as building blocks is propelling several disciplines of burgeoning interest, such as supramolecular chemistry, molecular electronics, and molecular magnetism. In the particular context of magnetic molecular materials, an attractive possibility for adding complexity to the material is to use a hybrid approach in which an organic component is combined with an inorganic one. Both purely organic and purely inorganic approaches (see the articles in this issue by Veciana and Iwamura and by Miller, respectively) have been used extensively to obtain molecule-based magnets. The combination of these two kinds of magnetic molecular components has also been successfully explored to design polymeric magnets of different dimensionalities (the metal-radical approach). In this last case, both components play a magnetic role. A step forward in achieving multifunctionality is to design hybrid molecular materials formed by two independent molecular networks, such as anion/cation salts or host/guest solids, whereby each network furnishes distinct physical properties to the solid. This novel class of materials is interesting because it can give rise to the development of materials in which two properties in the same crystal lattice coexist, or materials that exhibit improved properties over those of the individual networks, or to new, unexpected properties due to the mutual interactions between them. One can imagine, for example, the combination of an extended inorganic magnetic layer opening the pathway to cooperative magnetism, with an organic or organometallic molecule that acts as a structural component controlling the interlayer separation. If the molecule inserted between the layers has unpaired electrons, a hybrid compound is produced that combines cooperative magnetism and paramagnetism. Other suitable combinations, such as electronic conductivity and magnetism, or nonlinear optics and magnetism, can also be achieved by wisely choosing the constituent molecules. In this article, we report some relevant examples that illustrate the potential of this hybrid approach in the context of molecule-based magnetic materials.

scholarly journals Stepwise in vitro induction of human somitic mesoderm and its derivatives

2020 ◽  
Author(s):  
Cantas Alev ◽  
Yoshihiro Yamanaka ◽  
Maya Uemura
Keyword(s):  
Pluripotent Stem Cells ◽  
Pluripotent Stem Cell ◽  
Developmental Process ◽  
Cell Types ◽  
Model Organisms ◽  
Human Segmentation ◽  
Induced Pluripotent ◽  
Somitic Mesoderm ◽  
In Vitro Induction

Abstract Our understanding of human somitogenesis is limited and largely based on insights gained from model organisms. Pluripotent stem cell-based in vitro approaches aiming to recapitulate distinct aspects of this core developmental process have recently been reported, including our recent paper on the in vitro recapitulation of the human segmentation clock 1 . Here we describe in detail our stepwise induction protocol of presomitic mesoderm (PSM), somitic mesoderm (SM), and its two major derivatives, sclerotome (SCL) and dermomyotome (DM) from human induced pluripotent stem cells (iPSCs). We further briefly address the subsequent molecular and functional analysis of these in vitro induced human mesodermal lineages and cell-types.

scholarly journals Hub genes in a pan-cancer co-expression network show potential for predicting drug responses

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1906 ◽  
Author(s):  
Francisco Azuaje ◽  
Tony Kaoma ◽  
Céline Jeanty ◽  
Petr V. Nazarov ◽  
Arnaud Muller ◽  
...  
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Topological Analysis ◽  
Molecular Networks ◽  
Model Organisms ◽  
Hub Genes ◽  
Diverse Range ◽  
Drug Responses ◽  
Using Data

Background: The topological analysis of networks extracted from different types of “omics” data is a useful strategy for characterizing biologically meaningful properties of the complex systems underlying these networks. In particular, the biological significance of highly connected genes in diverse molecular networks has been previously determined using data from several model organisms and phenotypes. Despite such insights, the predictive potential of candidate hubs in gene co-expression networks in the specific context of cancer-related drug experiments remains to be deeply investigated. The examination of such associations may offer opportunities for the accurate prediction of anticancer drug responses.  Methods: Here, we address this problem by: a) analyzing a co-expression network obtained from thousands of cancer cell lines, b) detecting significant network hubs, and c) assessing their capacity to predict drug sensitivity using data from thousands of drug experiments. We investigated the prediction capability of those genes using a multiple linear regression model, independent datasets, comparisons with other models and our own in vitro experiments. Results: These analyses led to the identification of 47 hub genes, which are implicated in a diverse range of cancer-relevant processes and pathways. Overall, encouraging agreements between predicted and observed drug sensitivities were observed in public datasets, as well as in our in vitro validations for four glioblastoma cell lines and four drugs. To facilitate further research, we share our hub-based drug sensitivity prediction model as an online tool. Conclusions: Our research shows that co-expression network hubs are biologically interesting and exhibit potential for predicting drug responses in vitro. These findings motivate further investigations about the relevance and application of our unbiased discovery approach in pre-clinical, translationally-oriented research.

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