scholarly journals How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing

2018 ◽  
Vol 46 (13) ◽  
pp. 6435-6454 ◽  
Author(s):  
Yannik Bollen ◽  
Jasmin Post ◽  
Bon-Kyoung Koo ◽  
Hugo J G Snippert
Keyword(s):  
Genome Editing ◽  
Genetic Model ◽  
State Of The Art ◽  
Model Systems

scholarly journals Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gregory R. Keele ◽  
Jeremy W. Prokop ◽  
Hong He ◽  
Katie Holl ◽  
John Littrell ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Model ◽  
Association Studies ◽  
Model Systems ◽  
Linear Mixed Effect Model ◽  
Genome Wide Association Studies ◽  
Tubulointerstitial Injury ◽  
Heritable Variation ◽  
Mixed Effect

AbstractChronic kidney disease (CKD), which can ultimately progress to kidney failure, is influenced by genetics and the environment. Genes identified in human genome wide association studies (GWAS) explain only a small proportion of the heritable variation and lack functional validation, indicating the need for additional model systems. Outbred heterogeneous stock (HS) rats have been used for genetic fine-mapping of complex traits, but have not previously been used for CKD traits. We performed GWAS for urinary protein excretion (UPE) and CKD related serum biochemistries in 245 male HS rats. Quantitative trait loci (QTL) were identified using a linear mixed effect model that tested for association with imputed genotypes. Candidate genes were identified using bioinformatics tools and targeted RNAseq followed by testing in a novel in vitro model of human tubule, hypoxia-induced damage. We identified two QTL for UPE and five for serum biochemistries. Protein modeling identified a missense variant within Septin 8 (Sept8) as a candidate for UPE. Sept8/SEPTIN8 expression increased in HS rats with elevated UPE and tubulointerstitial injury and in the in vitro hypoxia model. SEPTIN8 is detected within proximal tubule cells in human kidney samples and localizes with acetyl-alpha tubulin in the culture system. After hypoxia, SEPTIN8 staining becomes diffuse and appears to relocalize with actin. These data suggest a role of SEPTIN8 in cellular organization and structure in response to environmental stress. This study demonstrates that integration of a rat genetic model with an environmentally induced tubule damage system identifies Sept8/SEPTIN8 and informs novel aspects of the complex gene by environmental interactions contributing to CKD risk.

scholarly journals Antifungal Activities of Antineoplastic Agents:Saccharomyces cerevisiae as a Model System To Study Drug Action

1999 ◽  
Vol 12 (4) ◽  
pp. 583-611 ◽  
Author(s):  
Maria E. Cardenas ◽  
M. Cristina Cruz ◽  
Maurizio Del Poeta ◽  
Namjin Chung ◽  
John R. Perfect ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Kinase Inhibitor ◽  
Genetic Model ◽  
Fungal Infections ◽  
Study Drug ◽  
Drug Action ◽  
Mechanisms Of Action ◽  
Model Systems ◽  
Screening Tools ◽  
Sphingolipid Metabolism

SUMMARY Recent evolutionary studies reveal that microorganisms including yeasts and fungi are more closely related to mammals than was previously appreciated. Possibly as a consequence, many natural-product toxins that have antimicrobial activity are also toxic to mammalian cells. While this makes it difficult to discover antifungal agents without toxic side effects, it also has enabled detailed studies of drug action in simple genetic model systems. We review here studies on the antifungal actions of antineoplasmic agents. Topics covered include the mechanisms of action of inhibitors of topoisomerases I and II; the immunosuppressants rapamycin, cyclosporin A, and FK506; the phosphatidylinositol 3-kinase inhibitor wortmannin; the angiogenesis inhibitors fumagillin and ovalicin; the HSP90 inhibitor geldanamycin; and agents that inhibit sphingolipid metabolism. In general, these natural products inhibit target proteins conserved from microorganisms to humans. These studies highlight the potential of microorganisms as screening tools to elucidate the mechanisms of action of novel pharmacological agents with unique effects against specific mammalian cell types, including neoplastic cells. In addition, this analysis suggests that antineoplastic agents and derivatives might find novel indications in the treatment of fungal infections, for which few agents are presently available, toxicity remains a serious concern, and drug resistance is emerging.

scholarly journals A circadian clock in Saccharomyces cerevisiae

2010 ◽  
Vol 107 (5) ◽  
pp. 2043-2047 ◽  
Author(s):  
Zheng Eelderink-Chen ◽  
Gabriella Mazzotta ◽  
Marcel Sturre ◽  
Jasper Bosman ◽  
Till Roenneberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Model ◽  
Circadian Clocks ◽  
Model Systems ◽  
Model Organisms ◽  
Biological Clocks ◽  
Experimental Systems ◽  
Fundamental Biological Process ◽  
Free Running ◽  
And Behavior

Circadian timing is a fundamental biological process, underlying cellular physiology in animals, plants, fungi, and cyanobacteria. Circadian clocks organize gene expression, metabolism, and behavior such that they occur at specific times of day. The biological clocks that orchestrate these daily changes confer a survival advantage and dominate daily behavior, for example, waking us in the morning and helping us to sleep at night. The molecular mechanism of circadian clocks has been sketched out in genetic model systems from prokaryotes to humans, revealing a combination of transcriptional and posttranscriptional pathways, but the clock mechanism is far from solved. Although Saccharomyces cerevisiae is among the most powerful genetic experimental systems and, as such, could greatly contribute to our understanding of cellular timing, it still remains absent from the repertoire of circadian model organisms. Here, we use continuous cultures of yeast, establishing conditions that reveal characteristic clock properties similar to those described in other species. Our results show that metabolism in yeast shows systematic circadian entrainment, responding to cycle length and zeitgeber (stimulus) strength, and a (heavily damped) free running rhythm. Furthermore, the clock is obvious in a standard, haploid, auxotrophic strain, opening the door for rapid progress into cellular clock mechanisms.

scholarly journals Efficient genome editing in multiple salmonid cell lines using ribonucleoprotein complexes

2020 ◽  
Author(s):  
Remi L. Gratacap ◽  
Ye Hwa Jin ◽  
Marina Mantsopoulou ◽  
Ross D. Houston
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Infectious Diseases ◽  
Genome Editing ◽  
Cell Lines ◽  
Chinook Salmon ◽  
Model Systems ◽  
Fish Cell ◽  
Ribonucleoprotein Complexes ◽  
Salmonid Species

AbstractInfectious and parasitic diseases have major negative economic and animal welfare impacts on aquaculture of salmonid species. Improved knowledge of the functional basis of host response and genetic resistance to these diseases is key to developing preventative and treatment options. Cell lines provide a valuable model to study infectious diseases in salmonids, and genome editing using CRISPR provides an exciting avenue to evaluate the function of specific genes in those systems. While CRISPR/Cas9 has been successfully performed in a Chinook salmon cell line (CHSE-214), there are no reports to date of editing of cell lines derived from the most commercially relevant salmonid species Atlantic salmon and rainbow trout, which are difficult to transduce and therefore edit using lentivirus-mediated methods. In the current study, a method of genome editing of salmonid cell lines using ribonucleoprotein (RNP) complexes was optimised and tested in the most commonly-used salmonid fish cell lines; Atlantic salmon (SHK-1 and ASK cell lines), rainbow trout (RTG-2) and Chinook salmon (CHSE-214). Electroporation of RNP based on either Cas9 or Cas12a was efficient at targeted editing of all the tested lines (typically > 90 % cells edited), and the choice of enzyme expands the number of potential target sites for editing within the genomes of these species. These optimised protocols will facilitate functional genetic studies in salmonid cell lines, which are widely used as model systems for infectious diseases in aquaculture.

Prime editing: The state-of-the-art of genome editing

Meta Gene ◽  
2020 ◽  
Vol 24 ◽  
pp. 100661
Author(s):  
Fatemeh Khatami ◽  
Maryam Aghaii ◽  
Seyed Mohammad Kazem Aghamir
Keyword(s):  
Genome Editing ◽  
State Of The Art ◽  
The State

scholarly journals Finding the molecular basis of complex genetic variation in humans and mice

2006 ◽  
Vol 361 (1467) ◽  
pp. 393-401 ◽  
Author(s):  
Richard Mott
Keyword(s):  
Genetic Variation ◽  
Association Mapping ◽  
Molecular Basis ◽  
State Of The Art ◽  
Complex Trait ◽  
The State ◽  
Rodent Model ◽  
Model Systems ◽  
Trait Analysis

I survey the state of the art in complex trait analysis, including the use of new experimental and computational technologies and resources becoming available, and the challenges facing us. I also discuss how the prospects of rodent model systems compare with association mapping in humans.

Modelling Nitrogen Deposition on a Local Scale—A Review of the Current State of the Art

2006 ◽  
Vol 3 (5) ◽  
pp. 317 ◽  
Author(s):  
Ole Hertel ◽  
Carsten Ambelas Skjøth ◽  
Per Løfstrøm ◽  
Camilla Geels ◽  
Lise Marie Frohn ◽  
...  
Keyword(s):  
Nitrogen Deposition ◽  
Environmental Assessment ◽  
State Of The Art ◽  
N Deposition ◽  
Model Systems ◽  
Special Focus ◽  
Ammonia Emissions ◽  
High Nitrogen ◽  
Current State ◽  
The Impact

Abstract. Local ammonia emissions from agricultural activities are often associated with high nitrogen deposition in the close vicinity of the sources. High nitrogen (N) inputs may significantly affect the local ecosystems. Over a longer term, high loads may change the composition of the ecosystems, leading to a general decrease in local biodiversity. In Europe there is currently a significant focus on the impact of atmospheric N load on local ecosystems among environmental managers and policy makers. Model tools designed for application in N deposition assessment and aimed for use in the regulation of anthropogenic nitrogen emissions are, therefore, under development in many European countries. The aim of this paper is to present a review of the current understanding and modelling parameterizations of atmospheric N deposition. A special focus is on the development of operational tools for use in environmental assessment and regulation related to agricultural ammonia emissions. For the often large number of environmental impact assessments needed to be carried out by local environmental managers there is, furthermore, a need for simple and fast model systems. These systems must capture the most important aspects of dispersion and deposition of N in the nearby environment of farms with animal production. The paper includes a discussion on the demands on the models applied in environmental assessment and regulation and how these demands are fulfilled in current state-of-the-art models.

Critical evaluation of the state of the art of the analysis of light elements in thin films demonstrated using the examples of SiOXNY and AlOXNY films (IUPAC Technical Report)

2004 ◽  
Vol 76 (6) ◽  
pp. 1161-1213 ◽  
Author(s):  
Sabine Dreer ◽  
P. Wilhartitz
Keyword(s):  
Thin Films ◽  
State Of The Art ◽  
Relevant Literature ◽  
Critical Evaluation ◽  
Analytical Techniques ◽  
The State ◽  
Model Systems ◽  
Light Elements ◽  
Comprehensive Overview ◽  
Technical Report

The quantitative analysis of thin films containing light elements is very important in improving the coating processes and technological properties of the products. In order to review the state of the art of modern analytical techniques for such applications, the model systems SiOXNY and AlOXNY were selected. Over 1000 abstracts were screened, and the relevant literature was evaluated to give a comprehensive overview of instruments, analytical procedures and results, film types, deposition methods, and investigation goals. From more than 150 citations, the limitations, drawbacks, and pitfalls of the different methods were extracted and reviewed critically, while in addition, improvements were proposed where possible. These suggestions are combined with the newest results of investigation by the authors of this paper. Recommendations concerning the optimized combination of analytical methods for different analytical problems have been worked out on the basis of all results. Analysis of various multicomponent systems containing light elements demonstrated the applicability of the different methods of analysis in combination to all film systems with related compositions.

The Aryl Hydrocarbon ReceptorsansXenobiotics: Endogenous Function in Genetic Model Systems

2007 ◽  
Vol 72 (3) ◽  
pp. 487-498 ◽  
Author(s):  
Brian J. McMillan ◽  
Christopher A. Bradfield
Keyword(s):  
Genetic Model ◽  
Model Systems ◽  
Aryl Hydrocarbon

scholarly journals A practical guide to CRISPR/Cas9 genome editing in Lepidoptera

2017 ◽  
Author(s):  
Linlin Zhang ◽  
Robert D. Reed
Keyword(s):  
Experimental Design ◽  
Genome Editing ◽  
Model Systems ◽  
Strong Impact ◽  
Practical Advice ◽  
Entire Process ◽  
Practical Guide ◽  
Recent Advances ◽  
Detailed Protocol

AbstractCRISPR/Cas9 genome editing has revolutionized functional genetic work in many organisms and is having an especially strong impact in emerging model systems. Here we summarize recent advances in applying CRISPR/Cas9 methods in Lepidoptera, with a focus on providing practical advice on the entire process of genome editing from experimental design through to genotyping. We also describe successful targeted GFP knockins that we have achieved in butterflies. Finally, we provide a complete, detailed protocol for producing targeted long deletions in butterflies.

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