scholarly journals Septins From Protists to People

2022 ◽  
Vol 9 ◽  
Author(s):  
Brent Shuman ◽  
Michelle Momany
Keyword(s):  
Tetrahymena Thermophila ◽  
Homo Sapiens ◽  
Model Organisms ◽  
Evolutionary Relationships ◽  
Cellular Processes ◽  
The Core ◽  
High Conservation ◽  
Group 5 ◽  
Septin Gtpases ◽  
Insight Into

Septin GTPases form nonpolar heteropolymers that play important roles in cytokinesis and other cellular processes. The ability to form heteropolymers appears to be critical to many septin functions and to have been a major driver of the high conservation of many septin domains. Septins fall into five orthologous groups. Members of Groups 1–4 interact with each other to form heterooligomers and are known as the “core septins.” Representative core septins are present in all fungi and animals so far examined and show positional orthology with monomer location in the heteropolymer conserved within groups. In contrast, members of Group 5 are not part of canonical heteropolymers and appear to interact only transiently, if at all, with core septins. Group 5 septins have a spotty distribution, having been identified in specific fungi, ciliates, chlorophyte algae, and brown algae. In this review we compare the septins from nine well-studied model organisms that span the tree of life (Homo sapiens, Drosophila melanogaster, Schistosoma mansoni, Caenorhabditis elegans, Saccharomyces cerevisiae, Aspergillus nidulans, Magnaporthe oryzae, Tetrahymena thermophila, and Chlamydomonas reinhardtii). We focus on classification, evolutionary relationships, conserved motifs, interfaces between monomers, and positional orthology within heteropolymers. Understanding the relationships of septins across kingdoms can give new insight into their functions.

Y RNAs: recent developments

2013 ◽  
Vol 4 (2) ◽  
pp. 103-110 ◽  
Author(s):  
Adam E. Hall ◽  
Carly Turnbull ◽  
Tamas Dalmay
Keyword(s):  
Molecular Mechanisms ◽  
Biological Function ◽  
Recent Literature ◽  
Chromosomal Dna ◽  
Cellular Processes ◽  
Recent Developments ◽  
Rna Fragments ◽  
High Conservation ◽  
Non Coding Rnas ◽  
Insight Into

AbstractNon-coding RNAs have emerged as key regulators in diverse cellular processes. Y RNAs are ∼100-nucleotide-long non-coding RNAs that show high conservation in metazoans. Human Y RNAs are known to bind to the Ro60 and La proteins to form the Ro ribonucleoprotein complex. Their main biological function appears to be in mediating the initiation of chromosomal DNA replication, regulating the autoimmune protein Ro60, and generating smaller RNA fragments following cellular stress, although the precise molecular mechanisms underlying these functions remain elusive. Here, we aim to review the most recent literature on Y RNAs and gain insight into the function of these intriguing molecules.

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.

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.

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 Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

2012 ◽  
Vol 6 ◽  
pp. BBI.S9902 ◽  
Author(s):  
Divya P. Syamaladevi ◽  
Margaret S Sunitha ◽  
S. Kalaimathy ◽  
Chandrashekar C. Reddy ◽  
Mohammed Iftekhar ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Homo Sapiens ◽  
Relevant Literature ◽  
Myosin Ii ◽  
Coiled Coil ◽  
Structural Features ◽  
Model Organisms ◽  
Congenital Diseases ◽  
C Elegans

Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different domains resulting in a variety of functions. Myosins are molecules driving various kinds of cellular processes and motility until the level of organisms. These are ATPases that utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. Myosins are important as they are involved in almost all cellular activities ranging from cell division to transcriptional regulation. They are crucial due to their involvement in many congenital diseases symptomatized by muscular malfunctions, cardiac diseases, deafness, neural and immunological dysfunction, and so on, many of which lead to death at an early age. We present Myosinome, a database of selected myosin classes (myosin II, V, and VI) from five model organisms. This knowledge base provides the sequences, phylogenetic clustering, domain architectures of myosins and molecular models, structural analyses, and relevant literature of their coiled-coil domains. In the current version of Myosinome, information about 71 myosin sequences belonging to three myosin classes (myosin II, V, and VI) in five model organisms ( Homo Sapiens, Mus musculus, D. melanogaster, C. elegans and S. cereviseae) identified using bioinformatics surveys are presented, and several of them are yet to be functionally characterized. As these proteins are involved in congenital diseases, such a database would be useful in short-listing candidates for gene therapy and drug development. The database can be accessed from http://caps.ncbs.res.in/myosinome .

scholarly journals Deciphering the Enigma of the Histone H2A.Z-1/H2A.Z-2 Isoforms: Novel Insights and Remaining Questions

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1167
Author(s):  
Manjinder S. Cheema ◽  
Katrina V. Good ◽  
Bohyun Kim ◽  
Heddy Soufari ◽  
Connor O’Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Dna Damage ◽  
Chromosome Segregation ◽  
Multiple Roles ◽  
Histone H2a ◽  
The Core ◽  
Structural Differences ◽  
Functional Involvement ◽  
Insight Into

The replication independent (RI) histone H2A.Z is one of the more extensively studied variant members of the core histone H2A family, which consists of many replication dependent (RD) members. The protein has been shown to be indispensable for survival, and involved in multiple roles from DNA damage to chromosome segregation, replication, and transcription. However, its functional involvement in gene expression is controversial. Moreover, the variant in several groups of metazoan organisms consists of two main isoforms (H2A.Z-1 and H2A.Z-2) that differ in a few (3–6) amino acids. They comprise the main topic of this review, starting from the events that led to their identification, what is currently known about them, followed by further experimental, structural, and functional insight into their roles. Despite their structural differences, a direct correlation to their functional variability remains enigmatic. As all of this is being elucidated, it appears that a strong functional involvement of isoform variability may be connected to development.

scholarly journals Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Lori A. McEachern
Keyword(s):  
Molecular Mechanisms ◽  
Model Organism ◽  
Evolutionary Conservation ◽  
Model Organisms ◽  
Valuable Insight ◽  
Epigenetic Control ◽  
Transgenic Organisms ◽  
Epigenetic Analysis ◽  
Insight Into ◽  
Epigenetic Processes

Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.

scholarly journals Audio Mining: The Role of Vocal Tone in Persuasion

2021 ◽  
Author(s):  
Xin (Shane) Wang ◽  
Shijie Lu ◽  
X I Li ◽  
Mansur Khamitov ◽  
Neil Bendle
Keyword(s):  
Empirical Study ◽  
Large Scale ◽  
Controlled Experiments ◽  
The Core ◽  
Content Model ◽  
Stereotype Content ◽  
Key Indicators ◽  
The Impact ◽  
Insight Into

Abstract Persuasion success is often related to hard-to-measure characteristics, such as the way the persuader speaks. To examine how vocal tones impact persuasion in an online appeal, this research measures persuaders’ vocal tones in Kickstarter video pitches using novel audio mining technology. Connecting vocal tone dimensions with real-world funding outcomes offers insight into the impact of vocal tones on receivers’ actions. The core hypothesis of this paper is that a successful persuasion attempt is associated with vocal tones denoting (1) focus, (2) low stress, and (3) stable emotions. These three vocal tone dimensions—which are in line with the stereotype content model—matter because they allow receivers to make inferences about a persuader’s competence. The hypotheses are tested with a large-scale empirical study using Kickstarter data, which is then replicated in a different category. In addition, two controlled experiments provide evidence that perceptions of competence mediate the impact of the three vocal tones on persuasion attempt success. The results identify key indicators of persuasion attempt success and suggest a greater role for audio mining in academic consumer research.

scholarly journals Zingerone Ameliorates Hepatotoxicity

2020 ◽  
Vol 11 (1) ◽  
pp. 280-284 ◽  
Author(s):  
Julietpoornamathy J ◽  
Parameswari C.S.
Keyword(s):  
The Body ◽  
Control Group ◽  
Medical Sciences ◽  
Toxic Compounds ◽  
Group 4 ◽  
Group 3 ◽  
Group 5 ◽  
Group 2 ◽  
Insight Into ◽  
Group 1

In medical sciences, toxicity is an area wherein extensive studies have been carried to improve the diseases as well as to prevent. So, there is a high requirement for novel and improved alternative therapeutic strategies to manage diseases. The liver is the largest gland in the body, which executes several important mechanisms; it stores minerals and vitamins and releases them in periods of need. The main aim of this study was to give a closer insight into potent non- toxic compounds that is capable of modifying the responses. Animals were divided into five equal groups viz control (Group 1), administered with food and water ad libitum, (Group 2) administered with olive oil, (Group 3) administered with zingerone, (Group 4) administered with concanavalin A, (Group 5) administered with cyclosporine A followed by zingerone. Our results revealed significant changes in liver marker enzymes and liver histology of zingerone treated rats when compared to control rats.  A corollary, zingerone has no toxic effect on hepatocytes and was found to be safe at a dose of 10mg/kg b wt and also ameliorates hepatotoxicity.

scholarly journals Identification of high-efficiency 3′GG gRNA motifs in indexed FASTA files with ngg2

2015 ◽  
Vol 1 ◽  
pp. e33 ◽  
Author(s):  
Elisha D. Roberson
Keyword(s):  
High Efficiency ◽  
Homo Sapiens ◽  
Model Organisms ◽  
Proof Of Concept ◽  
Protein Coding ◽  
C Elegans ◽  
Protein Coding Genes ◽  
Starting Point ◽  
Command Line Tool ◽  
Reference Genomes

CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3′GG motif, which substantially increases the efficiency of editing at all sites tested inC. elegans. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a Python command-line tool, ngg2, to identify 3′GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes:Saccharomyces cerevisiae,Caenorhabditis elegans,Drosophila melanogaster,Danio rerio,Mus musculus, andHomo sapiens. I also scanned the genomes of pig (Sus scrofa) and African elephant (Loxodonta africana) to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3′GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3′GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3′GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3′GG editing sites in any species with an available genome sequence.

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