scholarly journals Limitations of Quantitative Gene Regulation Models: A Case Study

2003 ◽  
Vol 13 (11) ◽  
pp. 2391-2395 ◽  
Author(s):  
P. M. Kim
Keyword(s):  
Gene Regulation

scholarly journals A Model for Resource Competition in CRISPR-Mediated Gene Repression

2018 ◽  
Author(s):  
Pin-Yi Chen ◽  
Yili Qian ◽  
Domitilla Del Vecchio
Keyword(s):  
Gene Regulation ◽  
General Model ◽  
Resource Competition ◽  
Gene Repression ◽  
Multiple Targets ◽  
Network Function ◽  
Perfect Adaptation ◽  
Modular Nature

AbstractCRISPR-mediated gene regulation is known for its ability to control multiple targets simultaneously due to its modular nature: the same dCas9 effector can target different genes simply by changing the associated gRNA. However, multiplexing requires the sharing of limited amounts of dCas9 proteins among multiple gRNAs, leading to resource competition. In turn, competition between gRNAs for the same resource may hamper network function. In this work, we develop a general model that takes into account the sharing of a limited amount of dCas9 protein for arbitrary CRISPR-mediated gene repression networks. We demonstrate that, as a result of resource competition, hidden interactions appear, that modify the intended network regulations. As a case study, we analyze the effects of these hidden interactions in repression cascades. In particular, we illustrate that perfect adaptation to resource fluctuations can be achieved in cascades with an even number of repressors. In contrast, cascades with an odd number of repressors are substantially impacted by resource competition.

scholarly journals Algorithmic considerations when analysing capture Hi-C data

2020 ◽  
Vol 5 ◽  
pp. 289
Author(s):  
Linden Disney-Hogg ◽  
Ben Kinnersley ◽  
Richard Houlston
Keyword(s):  
Gene Regulation ◽  
Cell Lines ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Targeting Efficiency ◽  
Chromatin Interactions ◽  
Genomic Architecture ◽  
Insight Into ◽  
Recent Extension

Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by enriching for defined regions of biological relevance. The varying targeting efficiency between capture regions, however, introduces bias not present in conventional Hi-C, making analysis more complicated. Here we consider salient features of an algorithm that should be considered in evaluating the performance of a program used to analyse CHi-C data in order to infer meaningful interactions. We use the program CHICAGO to analyse promotor capture Hi-C data generated on 28 different cell lines as a case study.

The Genesis and Internal Dynamics of El Salvador's People's Revolutionary Army, 1970–1976

2014 ◽  
Vol 38 (01) ◽  
pp. 102-129
Author(s):  
ALBERTO MARTÍN ÁLVAREZ ◽  
EUDALD CORTINA ORERO
Keyword(s):  
Latin America ◽  
El Salvador ◽  
Early Years ◽  
Left Wing ◽  
Internal Dynamics ◽  
Internal Coherence ◽  
The 1960S

AbstractUsing interviews with former militants and previously unpublished documents, this article traces the genesis and internal dynamics of the Ejército Revolucionario del Pueblo (People's Revolutionary Army, ERP) in El Salvador during the early years of its existence (1970–6). This period was marked by the inability of the ERP to maintain internal coherence or any consensus on revolutionary strategy, which led to a series of splits and internal fights over control of the organisation. The evidence marshalled in this case study sheds new light on the origins of the armed Salvadorean Left and thus contributes to a wider understanding of the processes of formation and internal dynamics of armed left-wing groups that emerged from the 1960s onwards in Latin America.

Culture and the plasticity of perception

2020 ◽  
Vol 43 ◽  
Author(s):  
Michael Lifshitz ◽  
T. M. Luhrmann
Keyword(s):  
Cultural Context ◽  
Sensory Experience ◽  
Cultural Learning ◽  
The World

Abstract Culture shapes our basic sensory experience of the world. This is particularly striking in the study of religion and psychosis, where we and others have shown that cultural context determines both the structure and content of hallucination-like events. The cultural shaping of hallucinations may provide a rich case-study for linking cultural learning with emerging prediction-based models of perception.

Dual systems for all: Higher-order, role-based relational reasoning as a uniquely derived feature of human cognition

2019 ◽  
Vol 42 ◽  
Author(s):  
Daniel J. Povinelli ◽  
Gabrielle C. Glorioso ◽  
Shannon L. Kuznar ◽  
Mateja Pavlic
Keyword(s):  
Temporal Reasoning ◽  
Higher Order ◽  
Important Case ◽  
Human Cognition ◽  
Relational Reasoning ◽  
Dual Systems ◽  
First Order ◽  
Reasoning System ◽  
Role Based

Abstract Hoerl and McCormack demonstrate that although animals possess a sophisticated temporal updating system, there is no evidence that they also possess a temporal reasoning system. This important case study is directly related to the broader claim that although animals are manifestly capable of first-order (perceptually-based) relational reasoning, they lack the capacity for higher-order, role-based relational reasoning. We argue this distinction applies to all domains of cognition.

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