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 Collecting eco-evolutionary data in the dark: Impediments to subterranean research and how to overcome them

2020 ◽  
Author(s):  
Stefano Mammola ◽  
Enrico Lunghi ◽  
Helena Bilandžija ◽  
Pedro Cardoso ◽  
Volker Grimm ◽  
...  
Keyword(s):  
Model Systems ◽  
Ex Situ ◽  
Model Organisms ◽  
Physiological Tolerance ◽  
Advantages And Disadvantages ◽  
General Scientific ◽  
Experimental Model Systems ◽  
Scientific Questions ◽  
Subterranean Species

(1) Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research(2) Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represent the elective habitat for the so-called “cave species.” Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating lab experiments.(3) We explore the advantages and disadvantages of four general experimental setups (in-situ, quasi in-situ, ex-situ, and in-silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.(4) Our over-arching goal is to promote caves as model systems where one can perform standardised scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.

scholarly journals Endothelin-1 contributes to the development of virus-induced demyelinating disease

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Young-Hee Jin ◽  
Bongsu Kang ◽  
Hyun S. Kang ◽  
Chang-Sung Koh ◽  
Byung S. Kim
Keyword(s):  
T Cell ◽  
Demyelinating Disease ◽  
Autoimmune Encephalitis ◽  
T Cell Responses ◽  
Experimental Models ◽  
Demyelinating Diseases ◽  
Model Systems ◽  
Endothelin 1 ◽  
Cell Responses ◽  
Experimental Model Systems

Abstract Background Experimental autoimmune encephalitis (EAE) and virally induced demyelinating disease are two major experimental model systems used to study human multiple sclerosis. Although endothelin-1 level elevation was previously observed in the CNS of mice with EAE and viral demyelinating disease, the potential role of endothelin-1 in the development of these demyelinating diseases is unknown. Methods and results In this study, the involvement of endothelin-1 in the development and progression of demyelinating diseases was investigated using these two experimental models. Administration of endothelin-1 significantly promoted the progression of both experimental diseases accompanied with elevated inflammatory T cell responses. In contrast, administration of specific endothelin-1 inhibitors (BQ610 and BQ788) significantly inhibited progression of these diseases accompanied with reduced T cell responses to the respective antigens. Conclusions These results strongly suggest that the level of endothelin-1 plays an important role in the pathogenesis of immune-mediated CNS demyelinating diseases by promoting immune responses.

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 Tetris in the Nervous System: What Principles of Neuronal Tiling Can Tell Us About How Glia Play the Game

2021 ◽  
Vol 15 ◽  
Author(s):  
Dana F. DeSantis ◽  
Cody J. Smith
Keyword(s):  
Nervous System ◽  
Molecular Mechanisms ◽  
New Technologies ◽  
Imaging Techniques ◽  
Receptive Fields ◽  
Spatial Arrangement ◽  
Lessons Learned ◽  
Model Organisms ◽  
Neural Cells ◽  
Cell Diversity

The precise organization and arrangement of neural cells is essential for nervous system functionality. Cellular tiling is an evolutionarily conserved phenomenon that organizes neural cells, ensuring non-redundant coverage of receptive fields in the nervous system. First recorded in the drawings of Ramon y Cajal more than a century ago, we now have extensive knowledge of the biochemical and molecular mechanisms that mediate tiling of neurons. The advent of live imaging techniques in both invertebrate and vertebrate model organisms has enhanced our understanding of these processes. Despite advancements in our understanding of neuronal tiling, we know relatively little about how glia, an essential non-neuronal component of the nervous system, tile and contribute to the overall spatial arrangement of the nervous system. Here, we discuss lessons learned from neurons and apply them to potential mechanisms that glial cells may use to tile, including cell diversity, contact-dependent repulsion, and chemical signaling. We also discuss open questions in the field of tiling and what new technologies need to be developed in order to better understand glial tiling.

Evaluating the Implementation of a Collaborative Juvenile Reentry System in Oakland, California

2018 ◽  
Vol 62 (12) ◽  
pp. 3662-3680 ◽  
Author(s):  
Sonia Jain ◽  
Alison K. Cohen ◽  
Priya Jagannathan ◽  
Yvette Leung ◽  
Henrissa Bassey ◽  
...  
Keyword(s):  
Lessons Learned ◽  
Integrated System ◽  
System Level ◽  
Youth Engagement ◽  
Community Based ◽  
Alameda County ◽  
Complex Needs ◽  
Collaborative Community ◽  
Specialty Courts ◽  
Using Data

Traditional juvenile reentry systems often inadequately meet offenders’ complex needs. Policymakers and researchers increasingly recognize the importance of a collaborative community- and development-based reentry system to improve recidivism, youth developmental outcomes, and public safety. Yet, system-level process evaluations of integrated reentry systems are scarce. California’s Alameda County juvenile reentry system implemented evidence-based strategies and practices to better serve reentry youth. We report findings from a process evaluation, using data from 15 key stakeholder interviews, focus groups with community-based providers, a reentry system-wide stakeholder survey, site visit observations, and document reviews. We identified strengths, challenges, and lessons learned. System-level strengths included increased multidisciplinary assessments, interagency collaboration, and specialty courts. Challenges included differing agency agendas, limited family and youth engagement, and data sharing. We recommend future researchers and practitioners to further examine and implement integrated system-level processes and organizational change, informed by the ecological-developmental perspective, to help promote positive outcomes for reentry youth.

scholarly journals Sorting Nexin 10 as a Key Regulator of Membrane Trafficking in Bone-Resorbing Osteoclasts: Lessons Learned From Osteopetrosis

2021 ◽  
Vol 9 ◽  
Author(s):  
Ari Elson ◽  
Merle Stein ◽  
Grace Rabie ◽  
Maayan Barnea-Zohar ◽  
Sabina Winograd-Katz ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Lessons Learned ◽  
Model Systems ◽  
Bone Homeostasis ◽  
Sorting Nexin ◽  
Sequence Of Events ◽  
Ruffled Border ◽  
Regulated Gene Expression

Bone homeostasis is a complex, multi-step process, which is based primarily on a tightly orchestrated interplay between bone formation and bone resorption that is executed by osteoblasts and osteoclasts (OCLs), respectively. The essential physiological balance between these cells is maintained and controlled at multiple levels, ranging from regulated gene expression to endocrine signals, yet the underlying cellular and molecular mechanisms are still poorly understood. One approach for deciphering the mechanisms that regulate bone homeostasis is the characterization of relevant pathological states in which this balance is disturbed. In this article we describe one such “error of nature,” namely the development of acute recessive osteopetrosis (ARO) in humans that is caused by mutations in sorting nexin 10 (SNX10) that affect OCL functioning. We hypothesize here that, by virtue of its specific roles in vesicular trafficking, SNX10 serves as a key selective regulator of the composition of diverse membrane compartments in OCLs, thereby affecting critical processes in the sequence of events that link the plasma membrane with formation of the ruffled border and with extracellular acidification. As a result, SNX10 determines multiple features of these cells either directly or, as in regulation of cell-cell fusion, indirectly. This hypothesis is further supported by the similarities between the cellular defects observed in OCLs form various models of ARO, induced by mutations in SNX10 and in other genes, which suggest that mutations in the known ARO-associated genes act by disrupting the same plasma membrane-to-ruffled border axis, albeit to different degrees. In this article, we describe the population genetics and spread of the original arginine-to-glutamine mutation at position 51 (R51Q) in SNX10 in the Palestinian community. We further review recent studies, conducted in animal and cellular model systems, that highlight the essential roles of SNX10 in critical membrane functions in OCLs, and discuss possible future research directions that are needed for challenging or substantiating our hypothesis.

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.

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