Abstract:
:Organoids are engineered three-dimensional tissue cultures derived from stem cells and capable of self-renewal and self-organization into a variety of progenitors and differentiated cell types. An organoid resembles the cellular structure of an organ and retains some of its functionality, while still being amenable to in vitro experimental study. Compared with two-dimensional cultures, the three-dimensional structure of organoids provides a more realistic environment and structural organization of in vivo organs. Similarly, organoids are better suited to reproduce signaling pathway dynamics in vitro, due to a more realistic physiological environment. As such, organoids are a valuable tool to explore the dynamics of organogenesis and offer routes to personalized preclinical trials of cancer progression, invasion, and drug response. Complementary to experiments, mathematical and computational models are valuable instruments in the description of spatiotemporal dynamics of organoids. Simulations of mathematical models allow the study of multiscale dynamics of organoids, at both the intracellular and intercellular levels. Mathematical models also enable us to understand the underlying mechanisms responsible for phenotypic variation and the response to external stimulation in a cost- and time-effective manner. Many recent studies have developed laboratory protocols to grow organoids resembling different organs such as the intestine, brain, liver, pancreas, and mammary glands. However, the development of mathematical models specific to organoids remains comparatively underdeveloped. Here, we review the mathematical and computational approaches proposed so far to describe and predict organoid dynamics, reporting the simulation frameworks used and the models' strengths and limitations.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Montes-Olivas S,Marucci L,Homer Mdoi
10.3389/fgene.2019.00873subject
Has Abstractpub_date
2019-09-19 00:00:00pages
873issn
1664-8021journal_volume
10pub_type
杂志文章,评审abstract::The abundance of RNA species and their response to perturbations are set by the kinetics rates of RNA synthesis, processing, and degradation. However, the visualization, interpretation, and manipulation of these data require familiarity with mathematical modeling and command line tools. INSPEcT-GUI is an R-Shiny inter...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00759
更新日期:2020-07-17 00:00:00
abstract::Resistant Starch (RS), plays a crucial role in human health and nutrition by controlling glucose metabolism. RS or dietary fibre content in rice is low because it goes through a variety of process before it is ready for cooking and consumption. Hence, this study was carried out to develop a rice mutant with increased ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00946
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abstract::Replicative senescence of cells in vitro is often considered as counterpart for aging of the organism in vivo. In fact, both processes are associated with functional decay and similar molecular modifications. On epigenetic level, replicative senescence and aging evoke characteristic modifications in the DNA methylatio...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00303
更新日期:2019-04-03 00:00:00
abstract::The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00004
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abstract::Homozygous and compound heterozygous mutations in GNB5 gene have been associated with a wide spectrum of clinical presentations, ranging from neurodevelopmental issues with or without cardiac arrhythmia (LADCI) to severe developmental delay with epileptic encephalopathy, retinal dystrophy, and heart rhythm abnormaliti...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00399
更新日期:2020-05-13 00:00:00
abstract::Carcass weight, meat quality and muscle components are important traits economically and they underpin most of the commercial return to goat producers. In this study, the Longissimus dorsi muscle tissues were collected from five Liaoning cashmere (LC) goats and five Ziwuling black (ZB) goats with phenotypic difference...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.619399
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abstract::Studies in rats and mice have established that maternal nutrition induces epigenetic modifications, sometimes permanently, that alter gene expression in the fetus, which in turn leads to phenotypic changes. However, limited data is available on the influence of maternal diet on epigenetic modifications and gene expres...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00049
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abstract::Olfactory receptors (ORs) are a type of GTP-binding protein-coupled receptor (GPCR). These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR struc...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00061
更新日期:2012-05-03 00:00:00
abstract::RNA-binding proteins (RBPs) are a kind of gene regulatory factor that presents a significant biological effect in the initiation and development of various tumors, including bladder cancer (BLCA). However, the RBP-based prognosis signature for BLCA has not been investigated. In this study, we attempted to develop an R...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00992
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00353
更新日期:2016-01-20 00:00:00
abstract::Colorectal cancer (CRC) is the third most commonly diagnosed type of cancer worldwide. The mechanisms leading to the progression of CRC are involved in both genetic and epigenetic regulations. In this study, we applied systems biology methods to identify potential biomarkers and conduct drug discovery in a computation...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00117
更新日期:2020-03-06 00:00:00
abstract:Background:This study searched for immune-related long noncoding RNAs (lncRNAs) to predict the prognosis of patients with cervical cancer. Method:We obtained immunologically relevant lncRNA expression profiles and clinical follow-up data from cervical cancer patients from The Cancer Genome Atlas database and the Molec...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.533628
更新日期:2020-10-14 00:00:00
abstract::Lactation is a dynamic process, which evolved to meet dietary demands of growing offspring. At the same time, the mother's metabolism changes to meet the high requirements of nutrient supply to the offspring. Through strong artificial selection, the strain of milk production on dairy cows is often associated with impa...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2015.00118
更新日期:2015-03-26 00:00:00
abstract::A complete and compelling evolutionary explanation for the origin of human menopause is wanting. Menopause onset is defined clinically as the final menses, confirmed after 1 year without menstruation. The theory proposed herein explains at multiple levels - ultimately genetic but involving (1) behavioral, (2) life his...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2016.00222
更新日期:2017-01-06 00:00:00
abstract::Different genes have their protein products localized in various subcellular compartments. The diversity in protein localization may serve as a gene characteristic, revealing gene essentiality from a subcellular perspective. To measure this diversity, we introduced a Subcellular Diversity Index (SDI) based on the Gene...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01342
更新日期:2020-01-21 00:00:00
abstract::Eukaryotic protein kinases are well conserved through evolution. The genome of Schistosoma mansoni, which causes intestinal schistosomiasis, encodes over 250 putative protein kinases with all of the main eukaryotic groups represented. However, unraveling functional roles for these kinases is a considerable endeavor, p...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00229
更新日期:2014-07-31 00:00:00
abstract::Ethylmalonic encephalopathy (EE) is a very rare autosomal recessive metabolic disorder that primarily affects children. Less than one hundred EE patients have been diagnosed worldwide. The clinical manifestations include chronic diarrhea, petechiae, orthostatic acrocyanosis, psychomotor delay and regression, seizures,...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00341
更新日期:2020-04-17 00:00:00
abstract::Poultry feed constitutes the largest cost in poultry production, estimated to be up to 70% of the total cost. Moreover, there is pressure on the poultry industry to increase production to meet the protein demand of humans and simultaneously reduce emissions to protect the environment. Therefore, improving feed efficie...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00243
更新日期:2020-04-03 00:00:00
abstract::Plants are subjected to strong fluctuations in light intensity in their natural growth environment, caused both by unpredictable changes due to weather conditions and movement of clouds and upper canopy leaves and predictable changes during day-night cycle. The mechanisms of long-term acclimation to fluctuating light ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00154
更新日期:2020-03-05 00:00:00
abstract::HFE-related Hemochromatosis is the most common genetic iron overload disease in European populations, particularly of Nordic or Celtic ancestry. It is reported that the HFE p.C282Y mutation is present in 1/10 people of northern European descent, resulting in one in two hundred people will be homozygous. However, the H...
journal_title:Frontiers in genetics
pub_type:
doi:10.3389/fgene.2020.00077
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abstract::It is critical for patients who cannot undergo eradicable surgery to predict the risk of lung cancer recurrence and metastasis; therefore, the physicians can design the appropriate adjuvant therapy plan. However, traditional circulating tumor cell (CTC) detection or next-generation sequencing (NGS)-based methods are u...
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pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00393
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pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00036
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abstract::Genetic polymorphisms in β1-, β2- and β3-adrenergic receptors (β-ARs) have been associated with chronic non-communicable disorders, such as cardiovascular diseases, asthma, chronic obstructive pulmonary disease (COPD) and obesity, as well as β-agonists and antagonists response and toxicity. The purpose of this study w...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00560
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abstract::Autosomal recessive non-syndromic hearing loss (ARNSHL) is a highly heterogeneous disease involving more than 70 pathogenic genes. However, most ARNSHL families have small-sized pedigrees with limited genetic information, rendering challenges for the molecular diagnosis of these patients. Therefore, we attempted to es...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00639
更新日期:2019-07-17 00:00:00
abstract::Purpose: The present study examines the role of Sox11 in the initial response of retinal ganglion cells (RGCs) to axon damage and in optic nerve regeneration in mouse. Methods: Markers of retinal injury were identified using the normal retina database and optic nerve crush (ONC) database on GeneNetwork2 (www.genenetwo...
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pub_type: 杂志文章
doi:10.3389/fgene.2018.00633
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pub_type: 杂志文章
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更新日期:2015-06-10 00:00:00