scholarly journals A Reference Genome from the symbiotic hydrozoan, Hydra viridissima

2020 ◽  
Author(s):  
Mayuko Hamada ◽  
Noriyuki Satoh ◽  
Konstantin Khalturin
Keyword(s):  
Genome Assembly ◽  
Life Histories ◽  
Molecular Mechanisms ◽  
18Th Century ◽  
Sister Group ◽  
Model Systems ◽  
Model Organisms ◽  
Axis Formation ◽  
Symbiotic Relationships ◽  
Characteristic Features

ABSTRACTCnidarians are one of the oldest eumetazoan taxa, and are thought to be a sister group to all bilaterians. In spite of comparatively simple morphology, cnidarians exhibit diverse body forms and life histories. In addition, many cnidarian species establish symbiotic relationships with microalgae. Various Hydra species have been employed as model organisms since the 18th century. Introduction of transgenic and knock-down technologies made them ideal experimental systems for studying cellular and molecular mechanisms involved in regeneration, body-axis formation, senescence, symbiosis, and holobiosis. In order to provide an important reference for genetic studies, the Hydra magnipapillata genome was sequenced. However, the initial published version of the H. magnipapillata genome did not achieve assembly continuity comparable to those of other model systems, due mainly to a large number of transposable elements. For almost a decade, the highly fragmented genome assembly of H. magnipapillata (scaffold N50=128Kb) has remained the only genomic resource for this genus with several dozen species. Here we report a draft 280-Mbp genome assembly for Hydra viridissima strain A99, a symbiotic, early diverging member of the Hydra clade, with a scaffold N50 of 1.1 Mbp. The H. viridissima genome contains an estimated 21,476 protein-coding genes. Comparative analysis of Pfam domains and orthologous proteins highlights characteristic features of H. viridissima, such as diversification of innate immunity genes that are important for host-symbiont interactions. Thus, the Hydra viridissima assembly provides an important hydrozoan genome reference that will facilitate symbiosis research and better comparisons of metazoan genome architectures.

scholarly journals A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima

2020 ◽  
Vol 10 (11) ◽  
pp. 3883-3895
Author(s):  
Mayuko Hamada ◽  
Noriyuki Satoh ◽  
Konstantin Khalturin
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Interspecific Interactions ◽  
Model Organisms ◽  
Axis Formation ◽  
Protein Coding ◽  
Green Hydra ◽  
Experimental Systems ◽  
Characteristic Features ◽  
Hydra Magnipapillata

Various Hydra species have been employed as model organisms since the 18th century. Introduction of transgenic and knock-down technologies made them ideal experimental systems for studying cellular and molecular mechanisms involved in regeneration, body-axis formation, senescence, symbiosis, and holobiosis. In order to provide an important reference for genetic studies, the Hydra magnipapillata genome (species name has been changed to H. vulgaris) was sequenced a decade ago (Chapman et al., 2010) and the updated genome assembly, Hydra 2.0, was made available by the National Human Genome Research Institute in 2017. While H. vulgaris belongs to the non-symbiotic brown hydra lineage, the green hydra, Hydra viridissima, harbors algal symbionts and belongs to an early diverging clade that separated from the common ancestor of brown and green hydra lineages at least 100 million years ago (Schwentner and Bosch 2015; Khalturin et al., 2019). While interspecific interactions between H. viridissima and endosymbiotic unicellular green algae of the genus Chlorella have been a subject of interest for decades, genomic information about green hydras was nonexistent. Here we report a draft 280-Mbp genome assembly for Hydra viridissima strain A99, with a scaffold N50 of 1.1 Mbp. The H. viridissima genome contains an estimated 21,476 protein-coding genes. Comparative analysis of Pfam domains and orthologous proteins highlights characteristic features of H. viridissima, such as diversification of innate immunity genes that are important for host-symbiont interactions. Thus, the H. viridissima assembly provides an important hydrozoan genome reference that will facilitate symbiosis research and better comparisons of metazoan genome architectures.

scholarly journals An Electrochemical Investigation of Interfacial Electron Uptake by the Sulfur Oxidizing Bacterium Thioclava electrotropha ElOx9

2019 ◽  
Author(s):  
Amruta Karbelkar ◽  
Annette R Rowe ◽  
Moh El-Naggar
Keyword(s):  
Microbial Fuel Cells ◽  
Molecular Mechanisms ◽  
Model Organism ◽  
Sulfur Oxidation ◽  
Model Systems ◽  
Model Organisms ◽  
Extracellular Electron Transfer ◽  
Solid State Electron ◽  
Marine Microbe ◽  
Sulfur Oxidizing

Extracellular electron transfer (EET) allows microbes to acquire energy from solid state electron acceptors and donors, such as environmental minerals. This process can also be harnessed at electrode interfaces in bioelectrochemical technologies including microbial fuel cells, microbial electrosynthesis, bioremediation, and wastewater treatment. Improving the performance of these technologies will benefit from a better fundamental understanding of EET in diverse microbial systems. While the mechanisms of outward (i.e. microbe-to-anode) EET is relatively well characterized, specifically in a few metal-reducing bacteria, the reverse process of inward EET from redox-active minerals or cathodes to bacteria remains poorly understood. This knowledge gap stems, at least partly, from the lack of well-established model organisms and general difficulties associated with laboratory studies in existing model systems. Recently, a sulfur oxidizing marine microbe, <i>Thioclava electrotropha</i> ElOx9, was demonstrated to perform electron uptake from cathodes. However, a detailed analysis of the electron uptake pathways has yet to be established, and electrochemical characterization has been limited to aerobic conditions. Here, we report a detailed amperometric and voltammetric characterization of ElOx9 cells coupling cathodic electron uptake to reduction of nitrate as the sole electron acceptor. We demonstrate that this inward EET by ElOx9 is facilitated by a direct-contact mechanism through a redox center with a formal potential of -94 mV vs SHE, rather than soluble intermediate electron carriers. In addition to the implications for understanding microbial sulfur oxidation in marine environments, this study highlights the potential for ElOx9 to serve as a convenient and readily culturable model organism for understanding the molecular mechanisms of inward EET.

scholarly journals Strength in numbers: collaborative science for new experimental model systems

2018 ◽  
Author(s):  
Ross F. Waller ◽  
Phillip A. Cleves ◽  
Maria Rubio-Brotons ◽  
April Woods ◽  
Sara J. Bender ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Experimental Models ◽  
Lessons Learned ◽  
Model Systems ◽  
Model Organisms ◽  
Community Based ◽  
Collaborative Community ◽  
Important Challenge ◽  
Experimental Model Systems ◽  
Marine Protists

AbstractOur current understanding of biology is heavily based on the contributions from a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster development of ecologically and taxonomically diverse marine protist genetic models. This multifaceted, complex but important challenge required a highly collaborative community-based approach. Herein we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research.

scholarly journals Development in a Dish—In Vitro Models of Mammalian Embryonic Development

2021 ◽  
Vol 9 ◽  
Author(s):  
Yasmine el Azhar ◽  
Katharina F. Sonnen
Keyword(s):  
Embryonic Development ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
In Vitro Models ◽  
Model Systems ◽  
Model Organisms ◽  
Mammalian Development ◽  
Complex Processes ◽  
Mechanisms Of Development

Despite decades of research, the complex processes of embryonic development are not fully understood. The study of mammalian development poses particular challenges such as low numbers of embryos, difficulties in culturing embryos in vitro, and the time to generate mutant lines. With new approaches we can now address questions that had to remain unanswered in the past. One big contribution to studying the molecular mechanisms of development are two- and three-dimensional in vitro model systems derived from pluripotent stem cells. These models, such as blastoids, gastruloids, and organoids, enable high-throughput screens and straightforward gene editing for functional testing without the need to generate mutant model organisms. Furthermore, their use reduces the number of animals needed for research and allows the study of human development. Here, we outline and discuss recent advances in such in vitro model systems to investigate pre-implantation and post-implantation development.

scholarly journals An Electrochemical Investigation of Interfacial Electron Uptake by the Sulfur Oxidizing Bacterium Thioclava electrotropha ElOx9

2019 ◽  
Author(s):  
Amruta Karbelkar ◽  
Annette R Rowe ◽  
Moh El-Naggar
Keyword(s):  
Microbial Fuel Cells ◽  
Molecular Mechanisms ◽  
Model Organism ◽  
Sulfur Oxidation ◽  
Model Systems ◽  
Model Organisms ◽  
Extracellular Electron Transfer ◽  
Solid State Electron ◽  
Marine Microbe ◽  
Sulfur Oxidizing

Extracellular electron transfer (EET) allows microbes to acquire energy from solid state electron acceptors and donors, such as environmental minerals. This process can also be harnessed at electrode interfaces in bioelectrochemical technologies including microbial fuel cells, microbial electrosynthesis, bioremediation, and wastewater treatment. Improving the performance of these technologies will benefit from a better fundamental understanding of EET in diverse microbial systems. While the mechanisms of outward (i.e. microbe-to-anode) EET is relatively well characterized, specifically in a few metal-reducing bacteria, the reverse process of inward EET from redox-active minerals or cathodes to bacteria remains poorly understood. This knowledge gap stems, at least partly, from the lack of well-established model organisms and general difficulties associated with laboratory studies in existing model systems. Recently, a sulfur oxidizing marine microbe, <i>Thioclava electrotropha</i> ElOx9, was demonstrated to perform electron uptake from cathodes. However, a detailed analysis of the electron uptake pathways has yet to be established, and electrochemical characterization has been limited to aerobic conditions. Here, we report a detailed amperometric and voltammetric characterization of ElOx9 cells coupling cathodic electron uptake to reduction of nitrate as the sole electron acceptor. We demonstrate that this inward EET by ElOx9 is facilitated by a direct-contact mechanism through a redox center with a formal potential of -94 mV vs SHE, rather than soluble intermediate electron carriers. In addition to the implications for understanding microbial sulfur oxidation in marine environments, this study highlights the potential for ElOx9 to serve as a convenient and readily culturable model organism for understanding the molecular mechanisms of inward EET.

scholarly journals Longevity: Lesson from Model Organisms

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 518 ◽  
Author(s):  
Giusi Taormina ◽  
Federica Ferrante ◽  
Salvatore Vieni ◽  
Nello Grassi ◽  
Antonio Russo ◽  
...  
Keyword(s):  
Healthy Aging ◽  
Molecular Mechanisms ◽  
Economic Effects ◽  
Model Systems ◽  
Model Organisms ◽  
Human Longevity ◽  
Short Lifespan ◽  
Aging Theories ◽  
Aging Mechanisms ◽  
Shed Light

Research on longevity and healthy aging promises to increase our lifespan and decrease the burden of degenerative diseases with important social and economic effects. Many aging theories have been proposed, and important aging pathways have been discovered. Model organisms have had a crucial role in this process because of their short lifespan, cheap maintenance, and manipulation possibilities. Yeasts, worms, fruit flies, or mammalian models such as mice, monkeys, and recently, dogs, have helped shed light on aging processes. Genes and molecular mechanisms that were found to be critical in simple eukaryotic cells and species have been confirmed in humans mainly by the functional analysis of mammalian orthologues. Here, we review conserved aging mechanisms discovered in different model systems that are implicated in human longevity as well and that could be the target of anti-aging interventions in human.

The genetics of cell migration in Drosophila melanogaster and Caenorhabditis elegans development

Development ◽  
1999 ◽  
Vol 126 (14) ◽  
pp. 3035-3046 ◽  
Author(s):  
D.J. Montell
Keyword(s):  
Cell Migration ◽  
Caenorhabditis Elegans ◽  
Simple Model ◽  
Molecular Mechanisms ◽  
Small Gtpases ◽  
Model Systems ◽  
Model Organisms ◽  
Cell Movements

Cell migrations are found throughout the animal kingdom and are among the most dramatic and complex of cellular behaviors. Historically, the mechanics of cell migration have been studied primarily in vitro, where cells can be readily viewed and manipulated. However, genetic approaches in relatively simple model organisms are yielding additional insights into the molecular mechanisms underlying cell movements and their regulation during development. This review will focus on these simple model systems where we understand some of the signaling and receptor molecules that stimulate and guide cell movements. The chemotactic guidance factor encoded by the Caenorhabditis elegans unc-6 locus, whose mammalian homolog is Netrin, is perhaps the best known of the cell migration guidance factors. In addition, receptor tyrosine kinases (RTKs), and FGF receptors in particular, have emerged as key mediators of cell migration in vivo, confirming the importance of molecules that were initially identified and studied in cell culture. Somewhat surprisingly, screens for mutations that affect primordial germ cell migration in Drosophila have revealed that enzymes involved in lipid metabolism play a role in guiding cell migration in vivo, possibly by producing and/or degrading lipid chemoattractants or chemorepellents. Cell adhesion molecules, such as integrins, have been extensively characterized with respect to their contribution to cell migration in vitro and genetic evidence now supports a role for these receptors in certain instances in vivo as well. The role for non-muscle myosin in cell motility was controversial, but has now been demonstrated genetically, at least in some cell types. Currently the best characterized link between membrane receptor signaling and regulation of the actin cytoskeleton is that provided by the Rho family of small GTPases. Members of this family are clearly essential for the migrations of some cells; however, key questions remain concerning how chemoattractant and chemorepellent signals are integrated within the cell and transduced to the cytoskeleton to produce directed cell migration. New types of genetic screens promise to fill in some of these gaps in the near future.

scholarly journals Recent Progress Regarding the Evolution and Molecular Aspect of Insect Gall Formation

2021 ◽  
Author(s):  
Antoine Guiget ◽  
Seiji Takeda ◽  
Tomoko Hirano ◽  
Ohishima Issei ◽  
Masa H. Sato
Keyword(s):  
Life Histories ◽  
Recent Progress ◽  
Molecular Mechanisms ◽  
Model Organisms ◽  
Gall Formation ◽  
Insect Gall ◽  
In The Wild ◽  
Molecular Aspects ◽  
Gall Induction ◽  
Evolutionary Aspects

Galls are characteristic plant structures formed by hypertrophy (excessive increase in cell size) and/or hyperplasia (cell proliferation) induced by parasitic or pathogenic organisms. Insects are a major inducer of galls, and insect galls can occur on plant leaves, stems, floral buds, flowers, fruits, or roots. Many of these exhibit unique shapes, providing shelter and nutrients to the insects. To form unique gall structures, all-inducing insects are believed to secrete certain effector molecules and hijack host developmental programs. However, the molecular mechanisms of insect gall induction and development is still largely unknown because of the difficulty of studying non-model plants in the wild. Recent progress in next-generation sequencing has allowed us to determine the structure of biological processes in non-model organisms, including gall-inducing insects and their host plants. In this review, we first summarize the evolutionary aspects of gall-inducing life histories and their adaptive significance for insects and plants. Then, we briefly summarize recent progress regarding the molecular aspects of insect gall formation.

Regulation of microRNAs in Inflammation-Associated Colorectal Cancer: A Mechanistic Approach

2020 ◽  
Vol 20 ◽  
Author(s):  
Sridhar Muthusami ◽  
Ilangovan Ramachandran ◽  
Sneha Krishnamoorthy ◽  
Yuvaraj Sambandam ◽  
Satish Ramalingam ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Mechanisms ◽  
Colorectal Carcinogenesis ◽  
Model Systems ◽  
Necrosis Factor Alpha ◽  
Multi Stage ◽  
Mechanistic Approach ◽  
Tnf Α ◽  
Factor Alpha

: The development of colorectal cancer (CRC) is a multi-stage process. The inflammation of the colon as in inflammatory bowel disease (IBD) such as ulcerative colitis (UC) or Crohn’s disease (CD) is often regarded as the initial trigger for the development of CRC. Many cytokines such as tumor necrosis factor alpha (TNF-α) and several interleukins (ILs) are known to exert proinflammatory actions, and inflammation initiates or promotes tumorigenesis of various cancers, including CRC through differential regulation of microRNAs (miRNAs/miRs). miRNAs can be oncogenic miRNAs (oncomiRs) or anti-oncomiRs/tumor suppressor miRNAs, and they play key roles during colorectal carcinogenesis. However, the functions and molecular mechanisms of regulation of miRNAs involved in inflammation-associated CRC are still anecdotal and largely unknown. Consolidating the published results and offering perspective solutions to circumvent CRC, the current review is focused on the role of miRNAs and their regulation in the development of CRC. We have also discussed the model systems adapted by researchers to delineate the role of miRNAs in inflammation-associated CRC.

scholarly journals The TGFβ Family in Human Placental Development at the Fetal-Maternal Interface

Biomolecules ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 453
Author(s):  
Susana M. Chuva de Sousa Lopes ◽  
Marta S. Alexdottir ◽  
Gudrun Valdimarsdottir
Keyword(s):  
Stem Cell ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Transforming Growth Factor ◽  
Cell Model ◽  
Embryonic Stem ◽  
Model Systems ◽  
Special Focus ◽  
Placental Development

Emerging data suggest that a trophoblast stem cell (TSC) population exists in the early human placenta. However, in vitro stem cell culture models are still in development and it remains under debate how well they reflect primary trophoblast (TB) cells. The absence of robust protocols to generate TSCs from humans has resulted in limited knowledge of the molecular mechanisms that regulate human placental development and TB lineage specification when compared to other human embryonic stem cells (hESCs). As placentation in mouse and human differ considerably, it is only with the development of human-based disease models using TSCs that we will be able to understand the various diseases caused by abnormal placentation in humans, such as preeclampsia. In this review, we summarize the knowledge on normal human placental development, the placental disease preeclampsia, and current stem cell model systems used to mimic TB differentiation. A special focus is given to the transforming growth factor-beta (TGFβ) family as it has been shown that the TGFβ family has an important role in human placental development and disease.

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