scholarly journals Tracing the footsteps of autophagy in computational biology

2020 ◽  
Author(s):  
Dipanka Tanu Sarmah ◽  
Nandadulal Bairagi ◽  
Samrat Chatterjee
Keyword(s):  
Network Analysis ◽  
Computational Methods ◽  
Regulatory Mechanisms ◽  
Future Perspective ◽  
System Of Differential Equations ◽  
Computational Tools ◽  
The Core ◽  
Regulatory Machinery ◽  
Extracellular Environment ◽  
Insight Into

Abstract Autophagy plays a crucial role in maintaining cellular homeostasis through the degradation of unwanted materials like damaged mitochondria and misfolded proteins. However, the contribution of autophagy toward a healthy cell environment is not only limited to the cleaning process. It also assists in protein synthesis when the system lacks the amino acids’ inflow from the extracellular environment due to diet consumptions. Reduction in the autophagy process is associated with diseases like cancer, diabetes, non-alcoholic steatohepatitis, etc., while uncontrolled autophagy may facilitate cell death. We need a better understanding of the autophagy processes and their regulatory mechanisms at various levels (molecules, cells, tissues). This demands a thorough understanding of the system with the help of mathematical and computational tools. The present review illuminates how systems biology approaches are being used for the study of the autophagy process. A comprehensive insight is provided on the application of computational methods involving mathematical modeling and network analysis in the autophagy process. Various mathematical models based on the system of differential equations for studying autophagy are covered here. We have also highlighted the significance of network analysis and machine learning in capturing the core regulatory machinery governing the autophagy process. We explored the available autophagic databases and related resources along with their attributes that are useful in investigating autophagy through computational methods. We conclude the article addressing the potential future perspective in this area, which might provide a more in-depth insight into the dynamics of autophagy.

An exon-centric perspective1Canadian Society of Molecular Biosciences (CSMB) Senior Investigator Award

2012 ◽  
Vol 90 (5) ◽  
pp. 603-612 ◽  
Author(s):  
Benjamin J. Blencowe
Keyword(s):  
Alternative Splicing ◽  
Computational Methods ◽  
Large Datasets ◽  
Regulatory Mechanisms ◽  
The Past ◽  
Human Genes ◽  
Insight Into ◽  
Remarkable Progress ◽  
Discrete Networks ◽  
Made In

During the past ten years, remarkable progress has been made in our understanding of the complexity and regulation of alternative splicing. The generation of large datasets of quantitative alternative splicing profiling information has revealed that transcripts from at least 95% of multi-exon human genes undergo alternative splicing, and that thousands of exons in mammalian transcriptomes are subject to striking regulatory patterns. Together with advanced computational methods, these datasets have enabled the inference of a predictive code for tissue-dependent alternative splicing. This code has further provided new insight into splicing regulatory mechanisms. Collectively, these approaches are revealing the existence of discrete networks of exons that are coordinately regulated in diverse biologically normal and disease contexts. A major challenge ahead is to systematically determine the functions of exons comprising these exon networks as well as the factors and mechanisms responsible for their regulation. This perspective provides an account of progress in these areas and also discusses future avenues of exon-centric exploration.

Will Love Tear Us Apart: Adapting the Lyrical to the Ludic

CounterText ◽  
2016 ◽  
Vol 2 (2) ◽  
pp. 217-235
Author(s):  
Gordon Calleja
Keyword(s):  
Design Process ◽  
Game Design ◽  
Digital Games ◽  
Design Decisions ◽  
The Core ◽  
Lyrical Poetry ◽  
Insight Into ◽  
Made In

This paper gives an insight into the design process of a game adaptation of Joy Division's Love Will Tear Us Apart (1980). It outlines the challenges faced in attempting to reconcile the diverging qualities of lyrical poetry and digital games. In so doing, the paper examines the design decisions made in every segment of the game with a particular focus on the tension between the core concerns of the lyrical work being adapted and established tenets of game design.

Computational Approaches to Predict the Non-canonical DNAs

2019 ◽  
Vol 14 (6) ◽  
pp. 470-479 ◽  
Author(s):  
Nazia Parveen ◽  
Amen Shamim ◽  
Seunghee Cho ◽  
Kyeong Kyu Kim
Keyword(s):  
Computational Methods ◽  
Genetic Instability ◽  
Computational Prediction ◽  
Structure And Function ◽  
Sequence Motifs ◽  
Computational Approaches ◽  
Functional Roles ◽  
And Function ◽  
Genetic Events ◽  
Insight Into

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

Force in Nature

2020 ◽  
pp. 146-160
Author(s):  
David Carus
Keyword(s):  
Natural Science ◽  
The Body ◽  
The Core ◽  
Thing In Itself ◽  
The Will ◽  
Insight Into

This chapter explores Schopenhauer’s concept of force, which lies at the root of his philosophy. It is force in nature and thus in natural science that is inexplicable and grabs Schopenhauer’s attention. To answer the question of what this inexplicable term is at the root of all causation, Schopenhauer looks to the will within us. Through will, he maintains that we gain immediate insight into forces in nature and hence into the thing in itself at the core of everything and all things. Will is thus Schopenhauer’s attempt to answer the question of the essence of appearance. Yet will, as it turns out, cannot be known immediately as it is subject to time, and the acts of will, which we experience within us, do not correlate immediately with the actions of the body (as Schopenhauer had originally postulated). Hence, the acts of will do not lead to an explanation of force, which is at the root of causation in nature. Schopenhauer sets out to explain what is at the root of all appearances, derived from the question of an original cause, or as Schopenhauer states “the cause of causation,” but cannot determine this essence other than by stating that it is will; a will, however, that cannot be immediately known.

Insight into the formation of H-bonds propagating the monomeric zinc complexes of a tridentate reduced Schiff base to form an infinite chain

CrystEngComm ◽  
2021 ◽  
Author(s):  
Mainak Karmakar ◽  
Antonio Frontera ◽  
Shouvik Chattopadhyay
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Dft Calculations ◽  
Zinc Complexes ◽  
Infinite Chain ◽  
State Structure ◽  
Computational Tools ◽  
Solid State Structure ◽  
Reduced Schiff Base ◽  
Insight Into

The formation of an infinite 1D assembly is governed by the H-bonding interactions in the solid state structure of the two zinc complexes. It has been analyzed energetically using DFT calculations and several computational tools.

scholarly journals Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mehrshad Golesorkhi ◽  
Javier Gomez-Pilar ◽  
Shankar Tumati ◽  
Maia Fraser ◽  
Georg Northoff
Keyword(s):  
Time Window ◽  
Human Cortex ◽  
The Core ◽  
Novel Variant ◽  
Open Issue ◽  
Task Differences ◽  
Spatial Hierarchy ◽  
Fundamental Insight ◽  
Insight Into ◽  
And Task

AbstractThe human cortex exhibits intrinsic neural timescales that shape a temporal hierarchy. Whether this temporal hierarchy follows the spatial hierarchy of its topography, namely the core-periphery organization, remains an open issue. Using magnetoencephalography data, we investigate intrinsic neural timescales during rest and task states; we measure the autocorrelation window in short (ACW-50) and, introducing a novel variant, long (ACW-0) windows. We demonstrate longer ACW-50 and ACW-0 in networks located at the core compared to those at the periphery with rest and task states showing a high ACW correlation. Calculating rest-task differences, i.e., subtracting the shared core-periphery organization, reveals task-specific ACW changes in distinct networks. Finally, employing kernel density estimation, machine learning, and simulation, we demonstrate that ACW-0 exhibits better prediction in classifying a region’s time window as core or periphery. Overall, our findings provide fundamental insight into how the human cortex’s temporal hierarchy converges with its spatial core-periphery hierarchy.

scholarly journals Visualising Ostia’s Processional Landscape Through a Multi-Layered Computational Approach: Case Study of the Cult of the Magna Mater

2019 ◽  
Vol 5 (1) ◽  
pp. 444-467
Author(s):  
Katherine A. Crawford
Keyword(s):  
Network Analysis ◽  
Computational Approach ◽  
Urban Network ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Existing Problems ◽  
Layered Approach ◽  
Religious Landscape ◽  
Insight Into

AbstractOstia, the ancient port of Rome, had a rich religious landscape. How processional rituals further contributed to this landscape, however, has seen little consideration. This is largely due to a lack of evidence that attests to the routes taken by processional rituals. The present study aims to address existing problems in studying processions by questioning what factors motivated processional movement routes. A novel computational approach that integrates GIS, urban network analysis, and agent-based modelling is introduced. This multi-layered approach is used to question how spectators served as attractors in the creation of a processional landscape using Ostia’s Campo della Magna Mater as a case study. The analysis of these results is subsequently used to gain new insight into how a greater processional landscape was created surrounding the sanctuary of the Magna Mater.

scholarly journals MicroRNA biogenesis: Epigenetic modifications as another layer of complexity to the microRNA expression regulation

2017 ◽  
Vol 63 (4) ◽  
Author(s):  
Susheel Sagar Bhat ◽  
Artur Jarmolowski ◽  
Zofia Szweykowska-Kulinska
Keyword(s):  
Epigenetic Modifications ◽  
Expression Regulation ◽  
Microrna Expression ◽  
Regulatory Mechanisms ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Critical Importance ◽  
Microrna Biogenesis ◽  
Regulatory Machinery

Since their discovery, microRNAs have led to a huge shift in our understanding of the regulation of key biological processes. The discovery of epigenetic modifications that affect microRNA expression has added another layer of complexity to the already tightly controlled regulatory machinery. The presence of N6-methyl-adenosine (m6A) mark and its critical importance in miRNA biogenesis in animals adds to our understanding of the regulatory mechanisms.

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