scholarly journals Variation under domestication in animal models: the case of the Mexican axolotl

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
María Torres-Sánchez

Abstract Background Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864. Results Using gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations. Conclusions Awareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.

2021 ◽  
pp. 1-1
Author(s):  
Francisco Javier Buils

Animals, from the pomace fly to the mouse, are widely utilized in research project. They are crucial for allowing scientists to find out more about human biology and health, and for developing new medicines. The use of animals in research project has long been the topic of heated debate. On the one hand it's considered morally wrong to use animals during this way solely for human benefit. On the other hand, our understanding of health and disease would impede after removing animals completely from the lab, and consequently affect the event of latest and vital treatments [1]. No responsible scientist wants to use animals or cause them unnecessary suffering if it are often avoided, and thus scientists accept controls on the utilization of animals in research [2]. Are animal models useful? Animal models are wont to address a spread of scientific questions, from basic science to the event and assessment of novel vaccines, or therapies. The use of animals is not only supported the vast commonalities within the biology of most mammals, but also on the very fact that human diseases often affect other animal species. It is particularly the case for many infectious diseases but also for quite common conditions like Type I diabetes, hypertension, allergies, cancer, epilepsy, myopathies then on. Not only are these diseases shared but the mechanisms are often also so similar that 90% of the veterinary drugs wont to treat animals are identical or very similar to those used to treat humans. Due to observations and testing on animal models, a number of major breakthroughs in basic science and medical research are possible. Most vaccines, which save many human and animal lives per annum, are successfully developed using animal models. However the results obtained on animals aren't necessarily confirmed in further human studies [3]. No animal model is ever perfect and there are still many differences between model organisms and humans [1]. To help minimise the harm animals may experience while being studied within the laboratory, researchers are required to follow a group of principles, the ‘three Rs’. These three Rs Reduction, Refinement, Replacement was proposed by Russel and Birch in 1959 [4]. Replace: Replacing an animal experiment to the best possible extent, as long as adequate alternatives are available. Reduce: The reduction of animal experiments and therefore the number of laboratory animals to the best possible extent. In so doing, it's important to use as many animals as are needed to get a statistically significant outcome. An adequate number of animals are required for the results to be sufficiently significant. Refine: The methods and treatment of the animals during the experiments, and with reference to the way they're kept, should make sure that the distress caused to them is minimized to the best possible extent which their well-being is taken under consideration as far as possible [5]. The inspection and licensing of animal premises, the training and competence of all personal designing projects, performing animal procedures and taking care of animals are the regulatory provisions with which research on animals is conducted and therefore the mandatory authorization of each project by a competent authority upon ethical evaluation by an Animal ethics panel. The criteria for evaluation are supported the 3Rs rules and a cost-benefit analysis to guage if the potential harm to the animals, which must be reduced to the lowest possible level, is outweighed by significant progress in terms of data on human or animal health. Modern medical research facing the greatest challenges that concern complex, multifactorial, diseases such as cancer, infectious diseases, cardiovascular diseases, neurodegenerative disorders, pathological consequences of aging among others, for which all experimental approaches are indispensable. Research on animal models will remain for an extended time a crucial step for fundamental discoveries, for testing hypotheses at the organism level and for the validation of human data. Likewise, animal protection requires permanent consideration. These two objectives, far away from being antagonistic, must be anchored in high-quality science [3].


eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Lise Frézal ◽  
Marie-Anne Félix

The roundworm Caenorhabditis elegans has risen to the status of a top model organism for biological research in the last fifty years. Among laboratory animals, this tiny nematode is one of the simplest and easiest organisms to handle. And its life outside the laboratory is beginning to be unveiled. Like other model organisms, C. elegans has a boom-and-bust lifestyle. It feasts on ephemeral bacterial blooms in decomposing fruits and stems. After resource depletion, its young larvae enter a migratory diapause stage, called the dauer. Organisms known to be associated with C. elegans include migration vectors (such as snails, slugs and isopods) and pathogens (such as microsporidia, fungi, bacteria and viruses). By deepening our understanding of the natural history of C. elegans, we establish a broader context and improved tools for studying its biology.


2019 ◽  
Vol 42 ◽  
Author(s):  
Nicole M. Baran

AbstractReductionist thinking in neuroscience is manifest in the widespread use of animal models of neuropsychiatric disorders. Broader investigations of diverse behaviors in non-model organisms and longer-term study of the mechanisms of plasticity will yield fundamental insights into the neurobiological, developmental, genetic, and environmental factors contributing to the “massively multifactorial system networks” which go awry in mental disorders.


HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 534e-534 ◽  
Author(s):  
J. Staub ◽  
Felix Sequen ◽  
Tom Horejsi ◽  
Jin Feng Chen

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.


Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.


Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 291
Author(s):  
Biao Ni ◽  
Jian You ◽  
Jiangnan Li ◽  
Yingda Du ◽  
Wei Zhao ◽  
...  

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.


2008 ◽  
Vol 101 (5) ◽  
pp. 633-658 ◽  
Author(s):  
Amy R. Lomax ◽  
Philip C. Calder

β2-1 Fructans are carbohydrate molecules with prebiotic properties. Through resistance to digestion in the upper gastrointestinal tract, they reach the colon intact, where they selectively stimulate the growth and/or activity of beneficial members of the gut microbiota. Through this modification of the intestinal microbiota, and by additional mechanisms, β2-1 fructans may have beneficial effects upon immune function, ability to combat infection, and inflammatory processes and conditions. In this paper, we have collated, summarised and evaluated studies investigating these areas. Twenty-one studies in laboratory animals suggest that some aspects of innate and adaptive immunity of the gut and the systemic immune systems are modified by β2-1 fructans. In man, two studies in children and nine studies in adults indicate that the adaptive immune system may be modified by β2-1 fructans. Thirteen studies in animal models of intestinal infections conclude a beneficial effect of β2-1 fructans. Ten trials involving infants and children have mostly reported benefits on infectious outcomes; in fifteen adult trials, little effect was generally seen, although in specific situations, certain β2-1 fructans may be beneficial. Ten studies in animal models show benefit of β2-1 fructans with regard to intestinal inflammation. Human studies report some benefits regarding inflammatory bowel disease (four positive studies) and atopic dermatitis (one positive study), but findings in irritable bowel syndrome are inconsistent. Therefore, overall the results indicate that β2-1 fructans are able to modulate some aspects of immune function, to improve the host's ability to respond successfully to certain intestinal infections, and to modify some inflammatory conditions.


2011 ◽  
Vol 12 (2) ◽  
pp. 119-145 ◽  
Author(s):  
Lucy Suchman

The focus of my inquiry in this article is the figure of the Human that is enacted in the design of the humanoid robot. The humanoid or anthropomorphic robot is a model (in)organism, engineered in the roboticist’s laboratory in ways that both align with and diverge from the model organisms of biology. Like other model organisms, the laboratory robot’s life is inextricably infused with its inherited materialities and with the ongoing — or truncated — labours of its affiliated humans. But while animal models are rendered progressively more standardised and replicable as tools for the biological sciences, the humanoid robot is individuated and naturalised. Three stagings of human— robot encounters (with the robots Mertz, Kismet and Robota respectively) demonstrate different possibilities for conceptualising these subject objects, for the claims about humanness that they corporealise, and for the kinds of witnessing that they presuppose.


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