Optogenetics in Complex Model Systems (Non-Human Primate)

2022 ◽  
pp. 305-321
Author(s):  
Robijanto Soetedjo ◽  
Yoshiko Kojima
Keyword(s):  
Complex Model ◽  
Model Systems ◽  
Human Primate

scholarly journals Health Dynamics Through Psychometric Networks in Gynecology, Obstetrics, Reproductive Health And COVID-19 Research

2021 ◽  
Vol 5 (2) ◽  
Keyword(s):  
Network Analysis ◽  
Maternal Health ◽  
Reproductive Health ◽  
Clinical Importance ◽  
Complex Model ◽  
Model Systems ◽  
Health Conditions ◽  
Clinical Population ◽  
Concomitant Variables ◽  
Health Dynamics

Network analysis offers a valuable methodological and practical contribution to research in gynecology, obstetrics and reproductive health. This analysis enables clinicians to interpret and translate the information derived from their research into better integrated care in the clinical population of interest, allowing them to focus a concrete intervention based on network results, from the perspective of complex model systems. The evaluation of the network reinforces a better explanation of the functioning of various reproductive and maternal health conditions to explain how their etiological mechanisms and concomitant variables interact with each other, of major clinical importance in the current COVID-19 pandemic context.

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 Spatially resolved transcriptomics reveals plant host responses to pathogens

2019 ◽  
Author(s):  
Michael Giolai ◽  
Walter Verweij ◽  
Ashleigh Lister ◽  
Darren Heavens ◽  
Iain Macaulay ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cell Types ◽  
Complex Model ◽  
Model Systems ◽  
Host Responses ◽  
Plant Host ◽  
Preparation Methods ◽  
Small Areas

AbstractBackgroundThorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present Grid-seq, an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.ResultsWe compare the Grid-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the Grid-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22.ConclusionWe show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.

scholarly journals An Improved Curvilinear Gradient Method for Parameter Estimation in Complex Model Systems: Application to Gating of A Cardiac Ion Channel

2010 ◽  
Vol 98 (3) ◽  
pp. 140a-141a
Author(s):  
David Szekely ◽  
Socrates Dokos ◽  
Jamie I. Vandenberg ◽  
Adam P. Hill
Keyword(s):  
Parameter Estimation ◽  
Ion Channel ◽  
Gradient Method ◽  
Complex Model ◽  
Model Systems

scholarly journals Spatially resolved transcriptomics reveals plant host responses to pathogens

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Michael Giolai ◽  
Walter Verweij ◽  
Ashleigh Lister ◽  
Darren Heavens ◽  
Iain Macaulay ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cell Types ◽  
Complex Model ◽  
Model Systems ◽  
Host Responses ◽  
Plant Host ◽  
Preparation Methods ◽  
Small Areas

Abstract Background Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present GaST-seq (Grid-assisted, Spatial Transcriptome sequencing), an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods. Results We compare the GaST-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the GaST-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22, and show that with eukaryotic (Albugo laibachii) infection both host and pathogen spatial transcriptomes are obtained. Conclusion We show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.

scholarly journals Understanding brain development – Indian researchers’ past, present and growing contribution

2020 ◽  
Vol 64 (1-2-3) ◽  
pp. 123-132
Author(s):  
Bhavana Muralidharan
Keyword(s):  
Brain Development ◽  
Complex Model ◽  
The Body ◽  
Model Systems ◽  
Centers Of Excellence ◽  
Vast Number ◽  
Regional Specialization ◽  
Evo Devo ◽  
Work Done ◽  
Higher Order Functions

The brain is the seat of all higher-order functions in the body. Brain development and the vast array of neurons and glia it produces is a baffling mystery to be studied. Neuroscientists using a vast number of model systems have been able to crack many of the nitty-gritty details using various model systems. One way has been to size down the problem by utilizing the power of genetics using simple model systems such as Drosophila to create a fundamental framework in order to unravel the basic principles of brain development. Scientists have used simpler organisms to uncover the fundamental principles of brain development and also to study the evo-devo angle to brain development. Complex circuitry has been unraveled in complex model systems, such as the mouse, to reveal the intricacies and regional specialization of brain function. This is an ever-growing field, and with newer genetic and molecular tools, together with several new centers of excellence, India’s contribution to this fascinating field of study is continually rising. Here, I review the pioneering work done by Indian developmental neurobiologists in the past and their mounting contribution in the present.

scholarly journals Multi-omics Integrative Analysis of Acute and Relapsing Malaria in a Non-Human Primate Model ofP. vivaxinfection

2019 ◽  
Author(s):  
Yan Tang ◽  
Chester J Joyner ◽  
Regina J Cordy ◽  
Mary R Galinski ◽  
Tracey J Lamb ◽  
...  
Keyword(s):  
Large Scale ◽  
Model Systems ◽  
Primate Model ◽  
Plasmodium Cynomolgi ◽  
Machine Learning Approach ◽  
Study Designs ◽  
Host Parasite ◽  
Relapsing Malaria ◽  
Human Primate ◽  
Infection Study

SummarySystems-scale analysis of multiple layers of molecular and cellular data has significant potential for providing novel insights into malaria pathology and immunity. We present here a unique longitudinal multi-omics dataset encompassingMacaca mulattablood and bone marrow responses to infection byPlasmodium cynomolgi, a non-human primate (NHP) parasite species used to modelP. vivaxmalaria acute and relapsing infections in humans. We analyzed relationships across multiple biological layers using a mutual information-based machine learning approach to integrate heterogeneous longitudinal datasets and constructed an atlas of multi-omics relatedness networks (MORNs). Using this technique, we were able to detect signatures that defined both acute and relapsing infections. Importantly, relapse infections could be distinguished from both acutely-infected and uninfected NHP, suggesting that the host-parasite interactions during relapses are unique compared to acutePlasmodiuminfections. To our knowledge, this is the first report of large-scale, longitudinal multi-omics analysis of malaria in any system. This dataset, along with the method used to analyze it, provides a unique resource for the malaria research community and demonstrates the power of longitudinal infection study designs, NHP model systems and integrative multi-omics analyses.

scholarly journals Amnion signals are essential for mesoderm formation in primates

2020 ◽  
Author(s):  
Ran Yang ◽  
Alexander Goedel ◽  
Yu Kang ◽  
Chenyang Si ◽  
Chu Chu ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Embryonic Stem ◽  
Cellular Level ◽  
Model Systems ◽  
Loss Of Function ◽  
Primate Model ◽  
Mesoderm Formation ◽  
Human Primate

AbstractEssential genes for murine embryonic development can demonstrate a disparate phenotype in human cohorts. By generating a transcriptional atlas containing >30,000 cells from postimplantation non-human primate embryos, we discovered that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 resulted in non-human primate embryos which did not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos displayed a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirmed a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development.

scholarly journals Amnion signals are essential for mesoderm formation in primates

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ran Yang ◽  
Alexander Goedel ◽  
Yu Kang ◽  
Chenyang Si ◽  
Chu Chu ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Embryonic Stem ◽  
Cellular Level ◽  
Model Systems ◽  
Loss Of Function ◽  
Primate Model ◽  
Mesoderm Formation ◽  
Human Primate

AbstractEmbryonic development is largely conserved among mammals. However, certain genes show divergent functions. By generating a transcriptional atlas containing >30,000 cells from post-implantation non-human primate embryos, we uncover that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 results in non-human primate embryos which do not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos display a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirm a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development.

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