scholarly journals Design Specifications for Cellular Regulation

2016 ◽  
Author(s):  
David C. Krakauer ◽  
Lydia Müller ◽  
Sonja J. Prohaska ◽  
Peter F. Stadler
Keyword(s):  
Regulatory Networks ◽  
Metabolic Flux ◽  
Cellular Regulation ◽  
Critical Feature ◽  
Cellular Processes ◽  
Design Specifications ◽  
Regulatory Systems ◽  
Common Framework ◽  
The Many ◽  
And Control

AbstractA critical feature of all cellular processes is the ability to control the rate of gene or protein expression and metabolic flux in changing environments through regulatory feedback. We review the many ways that regulation is represented through causal, logical and dynamical components. Formalizing the nature of these components promotes effective comparison among distinct regulatory networks and provides a common framework for the potential design and control of regulatory systems in synthetic biology.

scholarly journals The role of actin and myosin II in the cell cortex of adhered and suspended cells

2021 ◽  
Author(s):  
Daniel Flormann ◽  
Kevin Kaub ◽  
Doriane Vesperini ◽  
Moritz Schu ◽  
Christoph Anton ◽  
...  
Keyword(s):  
Myosin Ii ◽  
Cell Cortex ◽  
Cellular Processes ◽  
Actin Cortex ◽  
Nonmuscle Myosin Ii ◽  
Prediction And Control ◽  
The Many ◽  
A Minor ◽  
Microscopy Techniques ◽  
And Control

Adhesion induces dramatic morphological and mechanical changes to cells, which are reflected by changes to the actin cortex. Among the many different proteins involved in this sub-membranous layer, motor proteins (e.g., nonmuscle myosin II [NMII]) and actin nucleators (e.g., Arp2/3, formins) are known to have significant influences on its dynamics and structure. The different roles of NMII, Arp2/3, and formins in the dynamics, structure, and mechanics of the actin cortex depend on the adhesion state of the cell. In this study, we unravel the interplay between the dynamics, structure, and mechanics of the actin cortex in adhered cells and in cells in suspension. We show that treatments with extrinsic cellular perturbants lead to alterations of all three properties that are correlated. However, intrinsic actin cortex variations between different cell adhesion states lead to unexpected correlations. Surprisingly, we find that NMII minifilaments have a minor influence on the actin cortex. Using new microscopy techniques, we show that NMII minifilaments are not localized within the actin cortex, as previously thought, but concentrated in a layer beneath it. Our treatments affecting Arp2/3 and formin reveal correlations between the actin cortex characteristics. Our data build towards a comprehensive understanding of the actin cortex. This understanding allows the prediction and control of cortical changes, which is essential for the study of general cellular processes, such as cell migration, metastasis, and differentiation.

scholarly journals Genome-Wide Identification of Putative MicroRNAs in Cassava (Manihot esculenta Crantz) and Their Functional Landscape in Cellular Regulation

2019 ◽  
Vol 2019 ◽  
pp. 1-16 ◽  
Author(s):  
Amika Yawichai ◽  
Saowalak Kalapanulak ◽  
Chinae Thammarongtham ◽  
Treenut Saithong
Keyword(s):  
Target Gene ◽  
Mature Mirnas ◽  
Cellular Regulation ◽  
Manihot Esculenta Crantz ◽  
Small Noncoding Rnas ◽  
Cellular Processes ◽  
Regulatory Systems ◽  
Genome Wide ◽  
The Comparative Study ◽  
Posttranscriptional Level

MicroRNAs are small noncoding RNAs, involved in the regulation of many cellular processes in plants. Hundreds of miRNAs have been identified in cassava by various techniques, yet these identifications were constrained by a lack of miRNA templates and the narrow range of conditions in transcriptome study. In this research, we conducted genome-wide analysis identification, whereby miRNAs from cassava genome were thoroughly screened using bioinformatics approach independent of predefined templates and studied conditions. Our work provided a catalog of putative mature miRNAs and explored the landscape of miRNAome in cassava. These putative miRNAs were validated using statistical analysis as well as available cassava expression data. We showed that the crowded locations of cassava miRNAs are consistent with other plants and animals and hypothesized to have the same evolutionary origin. At least 10 conserved miRNAs were identified in cassava based on the comparative study of miRNA conservation. Finally, investigation of miRNAs and target gene relationships enabled us to envisage the complexities of cellular regulatory systems modulated at posttranscriptional level.

Computers for data, control and simulation

1988 ◽  
Vol 46 ◽  
pp. 920-921
Author(s):  
David C. Joy
Keyword(s):  
Personal Computers ◽  
Monitoring And Control ◽  
Data Logging ◽  
Data Logger ◽  
Operational Conditions ◽  
Data Control ◽  
The Many ◽  
And Control

Personal computers (PCs) are a powerful resource in the EM Laboratory, both as a means of automating the monitoring and control of microscopes, and as a tool for quantifying the interpretation of data. Not only is a PC more versatile than a piece of dedicated data logging equipment, but it is also substantially cheaper. In this tutorial the practical principles of using a PC for these types of activities will be discussed.The PC can form the basis of a system to measure, display, record and store the many parameters which characterize the operational conditions of the EM. In this mode it is operating as a data logger. The necessary first step is to find a suitable source from which to measure each of the items of interest. It is usually possible to do this without having to make permanent corrections or modifications to the EM.

scholarly journals The Amazing Acrobat: Yeast’s Histone H3K56 Juggles Several Important Roles While Maintaining Perfect Balance

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 342
Author(s):  
Lihi Gershon ◽  
Martin Kupiec
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Entry And Exit ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cellular Processes ◽  
M Phase ◽  
Dna Replication And Repair ◽  
H3k56 Acetylation ◽  
Timely Fashion ◽  
The Many

Acetylation on lysine 56 of histone H3 of the yeast Saccharomyces cerevisiae has been implicated in many cellular processes that affect genome stability. Despite being the object of much research, the complete scope of the roles played by K56 acetylation is not fully understood even today. The acetylation is put in place at the S-phase of the cell cycle, in order to flag newly synthesized histones that are incorporated during DNA replication. The signal is removed by two redundant deacetylases, Hst3 and Hst4, at the entry to G2/M phase. Its crucial location, at the entry and exit points of the DNA into and out of the nucleosome, makes this a central modification, and dictates that if acetylation and deacetylation are not well concerted and executed in a timely fashion, severe genomic instability arises. In this review, we explore the wealth of information available on the many roles played by H3K56 acetylation and the deacetylases Hst3 and Hst4 in DNA replication and repair.

scholarly journals The Role of Autophagy and lncRNAs in the Maintenance of Cancer Stem Cells

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1239
Author(s):  
Leila Jahangiri ◽  
Tala Ishola ◽  
Perla Pucci ◽  
Ricky M. Trigg ◽  
Joao Pereira ◽  
...  
Keyword(s):  
Stem Cells ◽  
Cancer Stem Cells ◽  
Cancer Progression ◽  
Regulatory Networks ◽  
Epithelial To Mesenchymal Transition ◽  
Tumour Microenvironment ◽  
Repair Capacity ◽  
Mesenchymal Transition ◽  
Cellular Processes

Cancer stem cells (CSCs) possess properties such as self-renewal, resistance to apoptotic cues, quiescence, and DNA-damage repair capacity. Moreover, CSCs strongly influence the tumour microenvironment (TME) and may account for cancer progression, recurrence, and relapse. CSCs represent a distinct subpopulation in tumours and the detection, characterisation, and understanding of the regulatory landscape and cellular processes that govern their maintenance may pave the way to improving prognosis, selective targeted therapy, and therapy outcomes. In this review, we have discussed the characteristics of CSCs identified in various cancer types and the role of autophagy and long noncoding RNAs (lncRNAs) in maintaining the homeostasis of CSCs. Further, we have discussed methods to detect CSCs and strategies for treatment and relapse, taking into account the requirement to inhibit CSC growth and survival within the complex backdrop of cellular processes, microenvironmental interactions, and regulatory networks associated with cancer. Finally, we critique the computationally reinforced triangle of factors inclusive of CSC properties, the process of autophagy, and lncRNA and their associated networks with respect to hypoxia, epithelial-to-mesenchymal transition (EMT), and signalling pathways.

Exploring ‘digital placemaking’

2021 ◽  
Vol 27 (3) ◽  
pp. 573-578
Author(s):  
Germaine Halegoua ◽  
Erika Polson
Keyword(s):  
Digital Media ◽  
Sense Of Place ◽  
Media Use ◽  
Special Issue ◽  
Social Actors ◽  
Broad Framework ◽  
The Many ◽  
And Control ◽  
Connected Spaces

This brief essay introduces the special issue on the topic of ‘digital placemaking’ – a concept describing the use of digital media to create a sense of place for oneself and/or others. As a broad framework that encompasses a variety of practices used to create emotional attachments to place through digital media use, digital placemaking can be examined across a variety of domains. The concept acknowledges that, at its core, a drive to create and control a sense of place is understood as primary to how social actors identify with each other and express their identities and how communities organize to build more meaningful and connected spaces. This idea runs through the articles in the issue, exploring the many ways people use digital media, under varied conditions, to negotiate differential mobilities and become placemakers – practices that may expose or amplify preexisting inequities, exclusions, or erasures in the ways that certain populations experience digital media in place and placemaking.

scholarly journals Interphotoreceptor coupling: an evolutionary perspective

2021 ◽  
Author(s):  
Lorenzo Cangiano ◽  
Sabrina Asteriti
Keyword(s):  
Visual Information ◽  
Signal To Noise Ratio ◽  
Electrical Coupling ◽  
Physiological Role ◽  
Cellular Processes ◽  
Contact Points ◽  
Highly Sensitive ◽  
The Many ◽  
The Impact

AbstractIn the vertebrate retina, signals generated by cones of different spectral preference and by highly sensitive rod photoreceptors interact at various levels to extract salient visual information. The first opportunity for such interaction is offered by electrical coupling of the photoreceptors themselves, which is mediated by gap junctions located at the contact points of specialised cellular processes: synaptic terminals, telodendria and radial fins. Here, we examine the evolutionary pressures for and against interphotoreceptor coupling, which are likely to have shaped how coupling is deployed in different species. The impact of coupling on signal to noise ratio, spatial acuity, contrast sensitivity, absolute and increment threshold, retinal signal flow and colour discrimination is discussed while emphasising available data from a variety of vertebrate models spanning from lampreys to primates. We highlight the many gaps in our knowledge, persisting discrepancies in the literature, as well as some major unanswered questions on the actual extent and physiological role of cone-cone, rod-cone and rod-rod communication. Lastly, we point toward limited but intriguing evidence suggestive of the ancestral form of coupling among ciliary photoreceptors.

scholarly journals The Many Faces of Amphipathic Helices

Biomolecules ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 45 ◽  
Author(s):  
Manuel Giménez-Andrés ◽  
Alenka Čopič ◽  
Bruno Antonny
Keyword(s):  
Lipid Bilayers ◽  
General Scheme ◽  
Membrane Curvature ◽  
Hydrophobic Residues ◽  
Cellular Processes ◽  
Amphipathic Helices ◽  
Polar Residues ◽  
Secondary Feature ◽  
Helical Turn ◽  
The Many

Amphipathic helices (AHs), a secondary feature found in many proteins, are defined by their structure and by the segregation of hydrophobic and polar residues between two faces of the helix. This segregation allows AHs to adsorb at polar–apolar interfaces such as the lipid surfaces of cellular organelles. Using various examples, we discuss here how variations within this general scheme impart membrane-interacting AHs with different interfacial properties. Among the key parameters are: (i) the size of hydrophobic residues and their density per helical turn; (ii) the nature, the charge, and the distribution of polar residues; and (iii) the length of the AH. Depending on how these parameters are tuned, AHs can deform lipid bilayers, sense membrane curvature, recognize specific lipids, coat lipid droplets, or protect membranes from stress. Via these diverse mechanisms, AHs play important roles in many cellular processes.

Initial Impressions of Others

2012 ◽  
pp. 336-366 ◽  
Author(s):  
James S. Uleman ◽  
S. Adil Saribay
Keyword(s):  
Cognitive Processes ◽  
Attribution Theory ◽  
Impression Formation ◽  
Social Cognitive ◽  
Controlled Attention ◽  
The Social ◽  
Social Cognitive Processes ◽  
The Many ◽  
And Control ◽  
Initial Impressions

“Initial impressions” bring together personality and social psychology like no other field of study—“personality” because (1) impressions are about personalities, and (2) perceivers’ personalities affect these impressions; and “social” because (3) social cognitive processes of impression formation, and (4) sociocultural contexts have major effects on impressions. To make these points, we first review how people explicitly describe others: the terms we use, how these descriptions reveal our theories about others, the important roles of traits and types (including stereotypes) in these descriptions, and other prominent frameworks (e.g., narratives and social roles). Then we highlight recent research on the social cognitive processes underlying these descriptions: automatic and controlled attention, the many effects of primes (semantic and affective) and their dependence on contexts, the acquisition of valence, spontaneous inferences about others, and the interplay of automatic and control processes. Third, we examine how accurate initial impressions are, and what accuracy means, as well as deception and motivated biases and distortions. Fourth, we review recent research on effects of target features, perceiver features, and relations between targets and perceivers. Finally, we look at frameworks for understanding explanations, as distinct from descriptions: attribution theory, theory of mind, and simulation theory.

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