Abstract:
:Patterning of periodic stripes during development requires mechanisms to control both stripe spacing and orientation. A number of models can explain how stripe spacing is controlled, including molecular mechanisms, such as Turing's reaction-diffusion model, as well as cell-based and mechanical mechanisms. However, how stripe orientation is controlled in each of these cases is poorly understood. Here, we model stripe orientation using a simple, yet generic model of periodic patterning, with the aim of finding qualitative features of stripe orientation that are mechanism-independent. Our model predicts three qualitatively distinct classes of orientation mechanism: gradients in production rates, gradients in model parameters, and anisotropies (e.g. in diffusion or growth). We provide evidence that the results from our minimal model may also apply to more specific and complex models, revealing features of stripe orientation that may be common to a variety of biological systems.
journal_name
Cell Systjournal_title
Cell systemsauthors
Hiscock TW,Megason SGdoi
10.1016/j.cels.2015.12.001subject
Has Abstractpub_date
2015-12-23 00:00:00pages
408-416issue
6eissn
2405-4712issn
2405-4720pii
S2405-4712(15)00215-Xjournal_volume
1pub_type
杂志文章相关文献
Cell Systems文献大全abstract::One snapshot of the peer review process for "Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast" (Kuroda et al., 2019). ...
journal_title:Cell systems
pub_type: 评论,杂志文章
doi:10.1016/j.cels.2020.01.005
更新日期:2020-02-26 00:00:00
abstract::The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data,...
journal_title:Cell systems
pub_type: 杂志文章,评审
doi:10.1016/j.cels.2017.11.001
更新日期:2018-01-24 00:00:00
abstract::Alterations of circadian clock genes are associated with patient survival, tumor stage, and clinical subtype across various cancer types, highlighting the importance of timing in cancer treatment. ...
journal_title:Cell systems
pub_type: 评论
doi:10.1016/j.cels.2018.03.006
更新日期:2018-03-28 00:00:00
abstract::The tumor-suppressing transcription factor p53 is highly conserved at the protein level and plays a key role in the DNA damage response. One important aspect of p53 regulation is its dynamics in response to DNA damage, which include oscillations. Here, we observe that, while the qualitative oscillatory nature of p53 d...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.09.012
更新日期:2017-10-25 00:00:00
abstract::Machine learning can be used to predict compounds acting synergistically, and this could greatly expand the universe of available potential treatments for diseases that are currently hidden in the dark chemical matter. ...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2015.12.005
更新日期:2015-12-23 00:00:00
abstract::Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes that affects their activity and/or function a...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2020.01.001
更新日期:2020-02-26 00:00:00
abstract::The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a comput...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2019.10.007
更新日期:2019-12-18 00:00:00
abstract::Escherichia coli gene expression knockdown using synthetic small RNA (sRNA) can be fine-tuned by altering sRNA sequences to modulate target mRNA-binding ability, but this requires thorough checking for off-target effects. Here, we present an sRNA gene expression knockdown system fine-tuned by using different promoters...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.08.016
更新日期:2017-10-25 00:00:00
abstract::This month: imaging the organelle interactome (Lippincott-Schwartz), big data immunology (Pulendran, Ginhoux), protein interactomes expand (Barna, Harper, Marcotte), and computation/engineering insights (Milinkovitch, Silver, and Sastry). ...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.06.010
更新日期:2017-06-28 00:00:00
abstract::Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2016.04.004
更新日期:2016-05-25 00:00:00
abstract::The construction of complex gene-regulatory networks requires both inhibitory and upregulatory modules. However, the vast majority of RNA-based regulatory "parts" are inhibitory. Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions ...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2019.04.007
更新日期:2019-07-24 00:00:00
abstract::Although molecular mechanisms that prompt cell-cycle arrest in response to DNA damage have been elucidated, the systems-level properties of DNA damage checkpoints are not understood. Here, using time-lapse microscopy and simulations that model the cell cycle as a series of Poisson processes, we characterize DNA damage...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.09.015
更新日期:2017-11-22 00:00:00
abstract::Racism and COVID-19 represent a pandemic on a pandemic for Blacks. The pandemics find themselves synergized to the detriment of Blacks and their health. The complexity of the combination of these pandemics are evident when examining the interplay between racist policing practices and health. ...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2020.07.002
更新日期:2020-07-22 00:00:00
abstract::Recent mass spectrometry maps of the human interactome independently support the existence of a large multiprotein complex, dubbed "Commander." Broadly conserved across animals and ubiquitously expressed in nearly every human cell type examined thus far, Commander likely plays a fundamental cellular function, akin to ...
journal_title:Cell systems
pub_type: 杂志文章,评审
doi:10.1016/j.cels.2017.04.006
更新日期:2017-05-24 00:00:00
abstract::How do rich biological behaviors arise from bi-molecular collisions? ...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2015.09.006
更新日期:2015-09-23 00:00:00
abstract::A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share meth...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.04.007
更新日期:2017-05-24 00:00:00
abstract::The accumulation of protein damage in aging organisms is thought to contribute to many aging-related diseases. Yet the properties determining which proteins are most susceptible remain poorly understood. Are certain conformations more vulnerable? Which chaperones are the main guardians? We address these questions with...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2018.05.001
更新日期:2018-06-27 00:00:00
abstract::Robust biological oscillators retain the critical ability to function in the presence of environmental perturbations. Although central architectures that support robust oscillations have been extensively studied, networks containing the same core vary drastically in their potential to oscillate, and it remains elusive...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.06.013
更新日期:2017-07-26 00:00:00
abstract::Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2019.10.004
更新日期:2019-11-27 00:00:00
abstract::Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally observed correlations between mother-daughter generation times that...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.08.015
更新日期:2017-10-25 00:00:00
abstract::A new bioinformatics tool predicts natively disordered protein control elements that function in cis, opening the door to more systematic studies of this biomedically important class of protein modules. ...
journal_title:Cell systems
pub_type: 评论,杂志文章
doi:10.1016/j.cels.2016.02.011
更新日期:2016-02-24 00:00:00
abstract::Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multi...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2017.05.001
更新日期:2017-06-28 00:00:00
abstract::One snapshot of the peer review process for "Death Rate of E. coli during Starvation Is Set by Maintenance Cost and Biomass Recycling" (Schink et al., 2019). ...
journal_title:Cell systems
pub_type: 评论,杂志文章
doi:10.1016/j.cels.2019.07.004
更新日期:2019-07-24 00:00:00
abstract::All mammals progress through similar physiological stages throughout life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects underlying genomic events is unclear. Here, we map the common methylation changes experienced by mammalian genomes as they age, foc...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2020.06.006
更新日期:2020-08-26 00:00:00
abstract::Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA and identify the key parameters that govern the overall rate of protein synthesis,...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2019.12.003
更新日期:2020-02-26 00:00:00
abstract::Hemizygous deletion of a gene in tumor cells frequently causes reduced expression of its encoded mRNA and protein, as well as reduced protein-but not mRNA-expression of other members in the same protein complex. ...
journal_title:Cell systems
pub_type: 评论,杂志文章
doi:10.1016/j.cels.2017.10.005
更新日期:2017-10-25 00:00:00
abstract::Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2019.06.004
更新日期:2019-08-28 00:00:00
abstract::Many data sets exhibit well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here we introduce a framework for similarity search based on characterizing a data set's entropy and fractal dimension. We prove that searching scales in tim...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2015.08.004
更新日期:2015-08-26 00:00:00
abstract::Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2016.10.020
更新日期:2016-11-23 00:00:00
abstract::Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with s...
journal_title:Cell systems
pub_type: 杂志文章
doi:10.1016/j.cels.2018.10.008
更新日期:2018-11-28 00:00:00