New Generation Of Animal Models Research Articles

Deep learning is widely applicable to phenotyping embryonic development and disease.

ABSTRACTGenome editing simplifies the generation of new animal models for congenital disorders. However, the detailed and unbiased phenotypic assessment of altered embryonic development remains a challenge. Here, we explore how deep learning (U-Net) can automate segmentation tasks in various imaging modalities, and we quantify phenotypes of altered renal, neural and craniofacial development in Xenopus embryos in comparison with normal variability. We demonstrate the utility of this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). We highlight how in toto light-sheet microscopy facilitates accurate reconstruction of brain and craniofacial structures within X. tropicalis embryos upon dyrk1a and six1 loss of function or treatment with retinoic acid inhibitors. These tools increase the sensitivity and throughput of evaluating developmental malformations caused by chemical or genetic disruption. Furthermore, we provide a library of pre-trained networks and detailed instructions for applying deep learning to the reader's own datasets. We demonstrate the versatility, precision and scalability of deep neural network phenotyping on embryonic disease models. By combining light-sheet microscopy and deep learning, we provide a framework for higher-throughput characterization of embryonic model organisms. This article has an associated ‘The people behind the papers’ interview.

Precision gene editing technology andapplications in nephrology.

The expanding field of precision gene editing is empowering researchers to directly modify DNA. Gene editing is made possible using synonymous technologies: a DNA-binding platform to molecularly locate user-selected genomic sequences and an associated biochemical activity that serves as a functional editor. The advent of accessible DNA-targeting molecular systems, such as zinc-finger nucleases, transcription activator-like effectors (TALEs) and CRISPR-Cas9 gene editing systems, has unlocked the ability to target nearly any DNA sequence with nucleotide-level precision. Progress has also been made in harnessing endogenous DNA repair machineries, such as non-homologous end joining, homology-directed repair and microhomology-mediated end joining, to functionally manipulate genetic sequences. As understanding of how DNA damage results in deletions, insertions and modifications increases, the genome becomes more predictably mutable. DNA-binding platforms such as TALEs and CRISPR can also be used to make locus-specific epigenetic changes and to transcriptionally enhance or suppress genes. Although many challenges remain, the application of precision geneediting technology in the field of nephrology has enabled the generation of new animal models ofdisease as well as advances in the development of novel therapeutic approaches such as gene therapy and xenotransplantation.

The Proteasome Inhibition Model ofParkinson's Disease.

The pathological hallmarks of Parkinson’s disease are the progressive loss of nigral dopaminergic neurons and the formation of intracellular inclusion bodies, termed Lewy bodies, in surviving neurons. Accumulation of proteins in large insoluble cytoplasmic aggregates has been proposed to result, partly, from a failure in the function of intracellular protein degradation pathways. Evidence in support for such a hypothesis emerged in the beginning of the years 2000 with studies demonstrating structural and functional deficits in the ubiquitin-proteasome pathway in post-mortem nigral tissue of patients with Parkinson’s disease. These fundamental findings have inspired the development of a new generation of animal models based on the use of proteasome inhibitors to disturb protein homeostasis and trigger nigral dopaminergic neurodegeneration. In this review, we provide an updated overview of the current approaches in employing proteasome inhibitors to model Parkinson’s disease, with particular emphasis on rodent studies. In addition, the mechanisms underlying proteasome inhibition-induced cell death and the validity criteria (construct, face and predictive validity) of the model will be critically discussed. Due to its distinct, but highly relevant mechanism of inducing neuronal death, the proteasome inhibition model represents a useful addition to the repertoire of toxin-based models of Parkinson’s disease that might provide novel clues to unravel the complex pathogenesis of this disorder.

Peripheral aetiopathogenic drivers and mediators of Parkinson's disease and co-morbidities: role of gastrointestinal microbiota.

We seek an aetiopathogenic model for the spectrum of Parkinson’s disease (PD), functional bowel disease, depression and cognitive impairment. The adopted concept is that systemic immuno-inflammatory processes mediate neuro-inflammation. The model would be based on phenotype, exposome (including gastrointestinal microbiome), milieu (immuno-inflammatory and metabolome), human genetics and their interactions. It would enable a patient’s position, to be understood in terms of drivers, perpetuators and mediators, and a future position, with and without intervention, predicted. Even the cardinal facets of PD may have different drivers: halting one may allow escape down subordinate pathways. Peptic ulceration is prodromal to PD. In our randomised placebo-controlled trial, hypokinesia improved over the year following biopsy-proven Helicobacter pylori eradication and rigidity worsened. This was independent of any (stable, long t½) antiparkinsonian medication. There are pointers to an autoimmune process: for example, surveillance-confirmed hypokinesia effect was indication specific. During surveillance, successive antimicrobial courses, other than for Helicobacter, were associated with cumulative increase in rigidity. Exhibiting laxatives appeared to stem the overall temporal increase, despite antiparkinsonian medication, in rigidity. Thus, intestinal dysbiosis may be a major source of bystander neuronal damage. There are biological gradients of objective measures of PD facets on circulating inflammatory markers and leucocyte subset counts. Moreover, lactulose hydrogen breath test positivity for small-intestinal bacterial overgrowth (present in two thirds of PD patients) is associated with the same subsets: higher natural killer and total CD4+ counts and lower neutrophils. With greater aetiopathogenic understanding, relatively low cost and on-the-shelf medication could have a major impact. A new generation of animal models, based on the gut microbiome, is envisaged.

GLI1 finds a new role in cancer stem cell biology

GLI1 finds a new role in cancer stem cell biology

ALS pathogenesis: Recent insights from genetics and mouse models

For the vast majority of cases of amyotrophic lateral sclerosis (ALS) the etiology remains unknown. After the discovery of missense mutations in the gene coding for the Cu/Zn superoxide dismutase 1 (SOD1) in subsets of familial ALS, several transgenic mouse lines have been generated with various forms of SOD1 mutants overexpressed at different levels. Studies with these mice yielded complex results with multiple targets of damage in disease including mitochondria, proteasomes, and secretory pathways. Many unexpected discoveries were made. For instance, the toxicity of mutant SOD1 seems unrelated to copper-mediated catalysis but rather to formation of misfolded SOD1 species and aggregates. Transgenic studies revealed a potential role of wtSOD1 in exacerbating mutant SOD1-mediated disease. Another key finding came from chimeric mouse studies and from Cre-lox mediated gene deletion experiments which have highlighted the importance of non-neuronal cells in the disease progression. Involvement of cytoskeletal components in ALS pathogenesis is supported by several mouse models of motor neuron disease with neurofilament abnormalities and with genetic defects in microtubule-based transport. Recently, the generation of new animal models of ALS has been made possible with the discovery of ALS-linked mutations in other genes encoding for alsin, dynactin, senataxin, VAPB, TDP-43 and FUS. Following the discovery of mutations in the TARDBP gene linked to ALS, there have been some reports of transgenic mice with high level overexpression of WT or mutant forms of TDP-43 under strong gene promoters. However, these TDP-43 transgenic mice do not exhibit all pathological features the human ALS disease. Here, we will describe these new TDP-43 transgenic mice and discuss their validity as animal models of human ALS.

Characterisation of the R276A gain-of-function mutation in the ectodomain of murine P2X7

The cytolytic P2X7 purinoceptor is widely expressed on leukocytes and has sparked interest because of its key role in the activation of the inflammasome, the release of the pro-inflammatory cytokine IL-1beta and cell death. We report here the functional characterisation of a R276A gain-of-function mutant analysed for its capacities to induce membrane depolarisation, calcium influx and opening of a large membrane pore permeable to YO-PRO-1. Our results highlight the particular sensitivity of R276A mutant to low micromolar adenosine triphosphate (ATP) concentrations, which possibly reflect an increased affinity for its ligands, and a slower closing kinetics of the receptor channel. Our findings support the notion that evolutionary pressures maintain the low sensitivity of P2X7 to ATP. We also believe that the R276A mutant described here may be useful for the generation of new animal models with exacerbated P2X7 functions that will serve to better characterise its role in inflammation and in immune responses.

Role of translational research advancing the understanding of the pathogenesis of light chain-mediated glomerulopathies

Glomerulopathic light chains engage in pathological interactions with mesangial cells resulting in alterations in glomerular homeostasis. The crucial pathological events are centered in the mesangium and, therefore, research dealing with pathogenesis of these disorders is focused on this glomerular compartment. Particular physicochemical characteristics of these light chains are responsible for their ability to alter mesangial milieu leading to glomerular damage. An in vitro model has been used to dissect the processes involved. This model has been instrumental in providing a solid platform from which to observe in a dynamic fashion how mesangial cells handle pathogenic light chains and the sequential steps that are involved in the progressive glomerular damage. Key steps amenable to possible modulation have been defined and should provide a solid platform to design and test therapeutic interventions. In the past significant difficulties have been encountered in the development of animal models of light chain-induced glomerular damage. However, in the last few years a new generation of animal models has emerged to address whether what has been documented in vitro retains significance in vivo. Preliminary observations appear to substantiate this.

RNA Interference Technologies for Understanding and Treating Neurodegenerative Diseases

RNA interference (RNAi) is an evolutionarily conserved process that silences gene expression through double-stranded RNA species in a sequence-specific manner. With the completion of genome sequencing in multiple organisms, RNAi provides an efficient reverse genetics tool to reveal gene functions on a genome-wide scale. Conditional/inducible RNAi offers a new way to analyze gene function at different developmental stages and to create a new generation of animal models of human diseases. The sequence-specificity of RNAi and the fact that it is a naturally occurring process in human make it an excellent therapeutic tool for a wide range of diseases. This article provides a brief review of the current understandings of the mechanism of RNAi and its application to the nervous system, with particular focus on its application to understand mechanisms of neurodegenerative diseases. The prospects of the application of RNAi in clinical setting to treat these devastating diseases will also be presented.

Transgenic Technology in Farm Animals – Progress and Perspectives

Current applications of gene transfer in farm animals include the improvement of product quality and quantity, disease resistance, the production of valuable proteins in the mammary gland or other organs, the genetic modification of pigs for xenotransplantation and the generation of new animal models in cases where rodent models are not sufficient for studying the problem under evaluation. Although DNA microinjection into pronuclei of zygotes from various farm animal species has happened since 1985, the efficiency of this method is low. Further drawbacks are related to the random integration process which may cause mosaicism, insertional mutations and varying expression due to position effects. Sperm-mediated gene transfer is not routinely established yet, although the mechanisms of binding and internalisation of DNA by sperm cells is becoming increasingly clearer. New protocols for the use of retroviral vectors to infect metaphase II oocytes which are subsequently fertilised resulted in efficient production of transgenic cattle. In spite of extensive efforts to establish pluripotent stem cells from farm animal species, no germ-line competent cells have been reported in mammalian species other than mouse so far. However, recent success in cloning sheep, cattle, goats and pigs from cultured cells provides an alternative route for efficient and targeted genetic modifications of farm animals.

Animal models of schizophrenia

Schizophrenia is a complex disorder affecting all domains of human life. Distinction is made between positive (delusions, hallucinations), negative (blunted affect, avolition, social withdrawal), cognitive (attention, executive function, thought disorder) and affective symptoms (anxiety, depression). The vulnerability-stress model is generally used to describe the evolution of the disorder over time and to guide psychosocial and pharmacological treatment. The biological vulnerability to stress is determined by the interaction of genetic and environmental influences. A neuro-developmental model is used to explain the observed structural and functional abnormalities in the brain of schizophrenic patients. In the past most animal models for schizophrenia have been used to develop new medication and to explain the mode of action of antipsychotic drugs. However, in recent years more attention has focused on developing models which may be more related to the schizophrenic (psycho)pathology. The new generation of animal models focus predominantly on mimicking the neurodevelopmental hypothesis of schizophrenia, by manipulating rats in a very early stage of life, and studying the long term consequences. These manipulations include early lesions or maternal deprivation.

Intestinal cholesterol absorption.

The strong association between intestinal cholesterol absorption and total plasma cholesterol level has renewed interest in the absorptive process and stimulated the generation of new animal models. Increasingly, new studies suggest that cholesterol absorption is genetically controlled and supports a protein-mediated mechanism for cholesterol uptake into the intestinal mucosal cell. Insights into potential mechanisms are predicted to lead to novel pharmacological approaches to inhibit cholesterol absorption.