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 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 Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Lori A. McEachern
Keyword(s):  
Molecular Mechanisms ◽  
Model Organism ◽  
Evolutionary Conservation ◽  
Model Organisms ◽  
Valuable Insight ◽  
Epigenetic Control ◽  
Transgenic Organisms ◽  
Epigenetic Analysis ◽  
Insight Into ◽  
Epigenetic Processes

Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.

scholarly journals Rest Is Required to Learn an Appetitively-Reinforced Operant Task in Drosophila

2021 ◽  
Vol 15 ◽  
Author(s):  
Timothy D. Wiggin ◽  
Yungyi Hsiao ◽  
Jeffrey B. Liu ◽  
Robert Huber ◽  
Leslie C. Griffith
Keyword(s):  
Operant Conditioning ◽  
Molecular Mechanisms ◽  
Genetic Model ◽  
Model Organism ◽  
Fruit Fly ◽  
Model Organisms ◽  
Valuable Insight ◽  
Reward Contingency ◽  
Neural Basis ◽  
Operant Task

Maladaptive operant conditioning contributes to development of neuropsychiatric disorders. Candidate genes have been identified that contribute to this maladaptive plasticity, but the neural basis of operant conditioning in genetic model organisms remains poorly understood. The fruit fly Drosophila melanogaster is a versatile genetic model organism that readily forms operant associations with punishment stimuli. However, operant conditioning with a food reward has not been demonstrated in flies, limiting the types of neural circuits that can be studied. Here we present the first sucrose-reinforced operant conditioning paradigm for flies. In the paradigm, flies walk along a Y-shaped track with reward locations at the terminus of each hallway. When flies turn in the reinforced direction at the center of the track, they receive a sucrose reward at the end of the hallway. Only flies that rest early in training learn the reward contingency normally. Flies rewarded independently of their behavior do not form a learned association but have the same amount of rest as trained flies, showing that rest is not driven by learning. Optogenetically-induced sleep does not promote learning, indicating that sleep itself is not sufficient for learning the operant task. We validated the sensitivity of this assay to detect the effect of genetic manipulations by testing the classic learning mutant dunce. Dunce flies are learning-impaired in the Y-Track task, indicating a likely role for cAMP in the operant coincidence detector. This novel training paradigm will provide valuable insight into the molecular mechanisms of disease and the link between sleep and learning.

scholarly journals OMAMO: orthology-based model organism selection

2021 ◽  
Author(s):  
Alina Nicheperovich ◽  
Adrian M Altenhoff ◽  
Christophe Dessimoz ◽  
Sina Majidian
Keyword(s):  
Literature Review ◽  
Biological Process ◽  
Model Organism ◽  
Complex Model ◽  
Model Systems ◽  
Human Model ◽  
Model Organisms ◽  
Human Biology ◽  
Traditional Model ◽  
Ethical Concerns

The conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology. However, the use of traditional model systems such as mice, rats, and zebrafish is costly, time-consuming and increasingly raises ethical concerns, which highlights the need to search for less complex model organisms. Existing tools only focus on the few well-studied model systems, most of which are higher animals. To address these issues, we have developed Orthologous Matrix and Model Organisms, a software and a website that provide the user with the best simple organism for research into a biological process of interest based on orthologous relationships between the human and the species. The outputs provided by the database were supported by a systematic literature review.

scholarly journals A proteomics database for CNS proteins of the great pond snail Lymnaea stagnalis

2021 ◽  
Author(s):  
Sarah Wooller ◽  
Aikaterini Anagnostopoulou ◽  
Benno Kuropka ◽  
Michael Crossley ◽  
Paul R. Benjamin ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Lymnaea Stagnalis ◽  
Model Organism ◽  
Research Area ◽  
Biological Data ◽  
Model Organisms ◽  
Pond Snail ◽  
Data Sets ◽  
Area Of Interest ◽  
Age Related

Applications of key technologies in bioscientific and biomedical research, such as qRT-PCR or LC-MS based proteomics, are generating large biological data sets (omics data) which are useful for the identification and quantification of biomarkers involved in molecular mechanisms of any research area of interest. Genome, transcriptome and proteome databases are already available for a number of model organisms including vertebrates and invertebrates. However, there is insufficient information available for protein sequences of certain invertebrates, such as the great pond snail Lymnaea stagnalis, a model organism that has been used highly successfully in elucidating evolutionarily conserved mechanisms of learning and memory, ageing and age-related as well as amyloid beta induced memory decline. Here, we present the design and benchmarking of a new proteomics database (LymSt-PDB) for the identification of proteins from the Central Nervous System (CNS) of Lymnaea stagnalis by LC-MS based proteomics.

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 New Roles for Model Genetic Organisms in Understanding and Treating Human Disease: Report From The 2006 Genetics Society of America Meeting

Genetics ◽  
2006 ◽  
Vol 172 (4) ◽  
pp. 2025-2032
Author(s):  
Allan Spradling ◽  
Barry Ganetsky ◽  
Phil Hieter ◽  
Mark Johnston ◽  
Maynard Olson ◽  
...  
Keyword(s):  
Human Disease ◽  
Medical Science ◽  
Genetic Research ◽  
Model Organism ◽  
Model Systems ◽  
Neurological Dysfunction ◽  
Model Organisms ◽  
Biological Knowledge ◽  
Medical Disorders ◽  
The Future

Abstract Fundamental biological knowledge and the technology to acquire it have been immeasurably advanced by past efforts to understand and manipulate the genomes of model organisms. Has the utility of bacteria, yeast, worms, flies, mice, plants, and other models now peaked and are humans poised to become the model organism of the future? The Genetics Society of America recently convened its 2006 meeting entitled “Genetic Analysis: Model Organisms to Human Biology” to examine the future role of genetic research. (Because of time limitations, the meeting was unable to cover the substantial contributions and future potential of research on model prokaryotic organisms.) In fact, the potential of model-organism-based studies has grown substantially in recent years. The genomics revolution has revealed an underlying unity between the cells and tissues of eukaryotic organisms from yeast to humans. No uniquely human biological mechanisms have yet come to light. This common evolutionary heritage makes it possible to use genetically tractable organisms to model important aspects of human medical disorders such as cancer, birth defects, neurological dysfunction, reproductive failure, malnutrition, and aging in systems amenable to rapid and powerful experimentation. Applying model systems in this way will allow us to identify common genes, proteins, and processes that underlie human medical conditions. It will allow us to systematically decipher the gene–gene and gene–environment interactions that influence complex multigenic disorders. Above all, disease models have the potential to address a growing gap between our ability to collect human genetic data and to productively interpret and apply it. If model organism research is supported with these goals in mind, we can look forward to diagnosing and treating human disease using information from multiple systems and to a medical science built on the unified history of life on earth.

scholarly journals Microbial Electrochemical Technologies for Wastewater Treatment: Principles and Evolution from Microbial Fuel Cells to Bioelectrochemical-Based Constructed Wetlands

2018 ◽  
Author(s):  
Carlos A. Ramírez-Vargas ◽  
Amanda Prado ◽  
Carlos A. Arias ◽  
Pedro N. Carvalho ◽  
Abraham Esteve-Núñez ◽  
...  
Keyword(s):  
Power Generation ◽  
Wastewater Treatment ◽  
Solid State ◽  
Constructed Wetlands ◽  
Microbial Fuel Cells ◽  
High Performance ◽  
Extracellular Electron Transfer ◽  
Solid State Electron ◽  
Recent Developments ◽  
Transfer Mechanisms

Microbial electrochemical technologies (MET) rely on the presence of the metabolic activity of electroactive bacteria for the use of solid-state electrodes for oxidizing different kind of compound, that could lead to the synthesis of chemicals, bioremediation of polluted matrices, the treatment of contaminants of interest, as well as the recovery of energy. Keeping in mind those possibilities, since the beginning of the present century, there has been a growing interest in the use of electrochemical technologies for wastewater treatment, and if possible with simultaneous power generation. In the last years, there has been a growing interest to explore the possibility of merging MET with constructed wetlands, to offer a new option of intensified wetland system that could keep a high performance with a lower footprint. Based on that interest, this paper explains the general principles of MET, and the different known extracellular electron transfer mechanisms ruling the interaction between electroactive bacteria and potential solid-state electron acceptors. Also, the adoption of those principles for the development of MET set-ups for simultaneous wastewater treatment and power generation, and the challenges that the technology face. Ultimately, the most recent developments in set-ups that merges MET with constructed wetlands are presented and discussed.

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 Xenopus: An Undervalued Model Organism to Study and Model Human Genetic Disease

2018 ◽  
Vol 205 (5-6) ◽  
pp. 303-313 ◽  
Author(s):  
Martin Blum ◽  
Tim Ott
Keyword(s):  
High Speed ◽  
Molecular Mechanisms ◽  
Genetic Diseases ◽  
Model Organism ◽  
Model Organisms ◽  
Human Genetic Disease ◽  
The Past ◽  
Large Numbers ◽  
Pros And Cons ◽  
Cost Efficient

The function of normal and defective candidate genes for human genetic diseases, which are rapidly being identified in large numbers by human geneticists and the biomedical community at large, will be best studied in relevant and predictive model organisms that allow high-speed verification, analysis of underlying developmental, cellular and molecular mechanisms, and establishment of disease models to test therapeutic options. We describe and discuss the pros and cons of the frog Xenopus, which has been extensively used to uncover developmental mechanisms in the past, but which is being underutilized as a biomedical model. We argue that Xenopus complements the more commonly used mouse and zebrafish as a time- and cost-efficient animal model to study human disease alleles and mechanisms.

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