scholarly journals Protein interaction probability landscapes for yeast replicative aging

2020 ◽  
Author(s):  
Hao-Bo Guo ◽  
Mehran Ghafari ◽  
Weiwei Dang ◽  
Hong Qin
Keyword(s):  
Gene Networks ◽  
Essential Gene ◽  
Replicative Aging ◽  
Transcript Levels ◽  
Essential Proteins ◽  
Network Profile ◽  
Profile Changes ◽  
Level Profile ◽  
Profile Change ◽  
Hub Proteins

AbstractWe proposed a novel probability landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions. We showed that essential proteins play different roles from hub proteins on the age-dependent landscapes. We verified that hub proteins tend to avoid other hub proteins, but essential proteins are attractive to other essential proteins. Overall, we showed that the probability landscape is promising for inferring network profile change during aging and that the essential hub proteins may play an important role in the uncoupling between protein and transcript levels during replicative aging.

scholarly journals Protein interaction potential landscapes for yeast replicative aging

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hao-Bo Guo ◽  
Mehran Ghafari ◽  
Weiwei Dang ◽  
Hong Qin
Keyword(s):  
Interaction Potential ◽  
Gene Networks ◽  
Essential Gene ◽  
Replicative Aging ◽  
Transcript Levels ◽  
Essential Proteins ◽  
Network Profile ◽  
Profile Changes ◽  
Potential Landscape ◽  
Hub Proteins

AbstractWe proposed a novel interaction potential landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the interaction landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions. We showed that essential proteins play different roles from hub proteins on the age-dependent interaction potential landscapes. We verified that hub proteins tend to avoid other hub proteins, but essential proteins prefer to interact with other essential proteins. Overall, we showed that the interaction potential landscape is promising for inferring network profile change during aging and that the essential hub proteins may play an important role in the uncoupling between protein and transcript levels during replicative aging.

scholarly journals EXPERIMENTS ON BEACH PROFILE CHANGE WITH A LARGE WAVE FLUME

1982 ◽  
Vol 1 (18) ◽  
pp. 85 ◽  
Author(s):  
Ryoichi Kajima ◽  
Takao Shimizu ◽  
Kohki Maruyama ◽  
Shozo Saito
Keyword(s):  
Simple Model ◽  
Transport Rate ◽  
Sand Transport ◽  
Two Dimensional ◽  
Beach Profile ◽  
Large Wave ◽  
Wave Flume ◽  
Grain Sizes ◽  
Profile Changes ◽  
Profile Change

Two-dimensional beach profile changes were investigated with a newly constructed prototype-scale wave flume. The flume is 205 m long, 3.4 m wide and 6 m deep. Sand of two grain sizes was used in the experiments. Analysis of the results was made through use of the parameter C, introduced by Sunamura and Horikawa (1974) to classify beaches as either erosional and accretionary. Beach profile changes obtained in the flume were similar to those in the prototype (field). Net sand transport rate distributions were classified into five types, two of which do not seem to have been observed in laboratory (smallscale) experiments. A simple model describing the five types was developed for evaluating two-dimensional beach profile changes.

scholarly journals The structure balance of gene-gene networks beyond pairwise interactions

2021 ◽  
Author(s):  
Gholamreza Jafari ◽  
Nastaran Allahyari ◽  
Amir Kargaran ◽  
Ali Hosseiny
Keyword(s):  
Gene Networks ◽  
Gene Network ◽  
Essential Gene ◽  
Gene Interaction ◽  
Interaction Networks ◽  
Underlying Structure ◽  
Yeast Saccharomyces Cerevisiae ◽  
Gene Interaction Networks ◽  
Nonessential Gene ◽  
Strong Notion

Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction networks of the yeast Saccharomyces cerevisiae beyond pairwise interaction using the structural balance theory (SBT). Specifically, we ask whether essential and nonessential gene interaction networks are structurally balanced. We study triadic interactions in the weighted signed undirected gene networks and observe that balanced and unbalanced triads are over and underrepresented in both networks, thus beautifully in line with the strong notion of balance. Moreover, we note that the energy distribution of triads is significantly different in both essential and nonessential networks compared with the shuffled networks. Yet, this difference is greater in the essential network regarding the frequency as well as the energy of triads. Additionally, results demonstrate that triads in the essential gene network are more interconnected through sharing common links, while in the nonessential network they tend to be isolated. Last but not least, we investigate the contribution of all-length signed walks and its impact on the degree of balance. Our findings reveal that interestingly when considering longer cycles the nonessential gene network is more balanced compared to the essential network.

scholarly journals Bumper Stickers on the Twitter Highway: Analyzing the Speed and Substance of Profile Changes

2018 ◽  
Author(s):  
Ryan Wesslen ◽  
Sagar Nandu ◽  
Omar Eltayeby ◽  
Tiffany Gallicano ◽  
Sara Levens ◽  
...  
Keyword(s):  
Social Media ◽  
Longitudinal Study ◽  
Topic Modeling ◽  
Signaling Theory ◽  
Baseline Data ◽  
Social Contagion ◽  
Self Construal ◽  
Profile Changes ◽  
Profile Change

We describe a novel longitudinal study of the frequency and significance of social media users' profile changes. Drawing upon two formative theories from communication and psychology: self-construal and signaling theory, we examine the likelihood that users will change their profiles and what constitutes a significant profile change. Our findings indicate that users are more likely to change their Profile Summaries and Display Names than their Locations and Screen Names (i.e. handles). Further, we used topic modeling to partition users based on their profiles to identify themes and explored how profile changes differ among these thematic groups (e.g., Trump supporters). Last, we identified the most significant word changes by users in their profiles. Our findings provide valuable baseline data for further study of Twitter profiles, including the spread of social contagion through these profiles.

scholarly journals DESCRIPTION OF BEACH CHANGES USING AN EMPIRICAL PREDICTIVE MODEL OF BEACH PROFILE CHANGES

1982 ◽  
Vol 1 (18) ◽  
pp. 86 ◽  
Author(s):  
Takaaki Uda ◽  
Hiroshi Hashimoto
Keyword(s):  
Predictive Model ◽  
Sand Transport ◽  
Coastal Structures ◽  
Beach Profile ◽  
Profile Data ◽  
Longshore Transport ◽  
Profile Changes ◽  
Offshore Transport ◽  
Eigenfunction Method ◽  
Profile Change

In order to analyze beach profile changes due to longshore and onshore-offshore sand transport, here is proposed a new model named the "empirical predictive model of beach profile change", which is an application of the empirical eigenfunction method. The analysis of the profile data obtained at the Misawa fishery port in Ogawarako Coast over five years from 1973 to 1977 indicates that profile changes due to longshore transport and to onshore-offshore transport can be separated. The model is shown to be effective in the analysis of profile changes near coastal structures.

scholarly journals Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Bastien Saint-Leandre ◽  
Courtney Christopher ◽  
Mia T Levine
Keyword(s):  
Genome Sequencing ◽  
Essential Gene ◽  
Chromosome Length ◽  
Close Relative ◽  
Whole Genome ◽  
Essential Proteins ◽  
Cellular Processes ◽  
Evolutionary Innovation ◽  
Telomere Binding Protein ◽  
Telomere Protein

Essential, conserved cellular processes depend not only on essential, strictly conserved proteins but also on essential proteins that evolve rapidly. To probe this poorly understood paradox, we exploited the rapidly evolving Drosophila telomere-binding protein, cav/HOAP, which protects chromosomes from lethal end-to-end fusions. We replaced the D. melanogaster HOAP with a highly diverged version from its close relative, D. yakuba. The D. yakuba HOAP ('HOAP[yak]') localizes to D. melanogaster telomeres and protects D. melanogaster chromosomes from fusions. However, HOAP[yak] fails to rescue a previously uncharacterized HOAP function: silencing of the specialized telomeric retrotransposons that, instead of telomerase, maintain chromosome length in Drosophila. Whole genome sequencing and cytogenetics of experimentally evolved populations revealed that HOAP[yak] triggers telomeric retrotransposon proliferation, resulting in aberrantly long telomeres. This evolution-generated, separation-of-function allele resolves the paradoxical observation that a fast-evolving essential gene directs an essential, strictly conserved function: telomeric retrotransposon containment, not end-protection, requires evolutionary innovation at HOAP.

scholarly journals TIME SCALES OF NEARSHORE PROFILE CHANGES

1984 ◽  
Vol 1 (19) ◽  
pp. 102 ◽  
Author(s):  
William A. Birkemeier
Keyword(s):  
Time Scales ◽  
Field Research ◽  
Research Facility ◽  
Seasonal Shift ◽  
Rapid Changes ◽  
Eigenvector Analysis ◽  
Profile Changes ◽  
Profile Change

Time scales of nearshore profile change are examined using a unique set of highly accurate surveys collected over a 3% year period at CERC's Field Research Facility. The data are analyzed in terms of the formation and movement of the nearshore bars and with empirical eigenfunctions. The largest and most rapid changes in the profiles occurred during storms. The inner bar (depth of -0.6 to 1.5 m, 1.6 to 4.5 ft) moved offshore during even minor storms and recovered relatively quickly. The outer bar (depth of 3 to 4 m, 9 to 13 ft) formed during the largest storms and recovery was considerably slower, requiring six months or longer. The eigenvector analysis confirmed the importance of storms but identified a seasonal shift of material from the beach and inner bar to the offshore.

scholarly journals Cutting-free application of CRISPR-mediated endogenous gene activation in human induced pluripotent stem cell derived cardiomyocytes and engineered human myocardium

2021 ◽  
Vol 42 (Supplement_1) ◽  
Author(s):  
E Schoger ◽  
L Argyriou ◽  
W H Zimmermann ◽  
L Cyganek ◽  
L C Zelarayan
Keyword(s):  
Transcriptional Activation ◽  
Gene Networks ◽  
Transcriptional Start Site ◽  
Gene Activation ◽  
Human Myocardium ◽  
Dose Titration ◽  
Transcriptional Networks ◽  
Limiting Factor ◽  
Transcript Levels ◽  
Endogenous Gene

Abstract Background Imbalanced transcriptional networks characterize cardiomyocyte stress and result in cardiac remodelling. We hypothesize that re-establishing homeostatic gene networks in cardiomyocytes will prevent further tissue damage. To tackle this challenge, we applied CRISPR-based endogenous gene activation (CRISPRa) in vivo and in vitro. Methods We employ precision transcriptome editing tools based on CRISPR/Cas9 with enzymatically inactive Cas9 (dCas9) fused to transcriptional activators (VPR) to induce target gene expression by directing dCas9VPR to promoter regions by guide RNAs (gRNA). Results Homozygous CRISPRa hiPSC cell lines were generated by targeted integration of a CAG promoter driven dCas9VPR-T2A-tdTomato expression cassette into the AAVS1 locus by CRISPR/Cas9 editing and homology directed repair. Expression of dCas9VPR was evaluated by immunoblotting and co-expressed reporter fluorescence in spontaneously beating hiPSC-CM. We previously identified a crosstalk between WNT signalling and Krueppel-like factor 15 (KLF15) necessary for controlling cardiac homeostasis. We designed and tested 8 non-overlapping gRNAs in the –400 bp region upstream of the KLF15 transcriptional start site (TSS) and tested individual gRNA effectiveness for gene activation in HEK293T cells. Five gRNAs were identified inducing KLF15 transcript levels between 2- and 5-fold compared to non-targeted (NT) gRNA transfected cells (n=3 experiments). The single most effective gRNA was transduced by lentiviral particles into CRISPRa hiPSC-CM increasing KLF15 transcript levels to 1.5-fold compared to NT-gRNA control. Synergistic effects of 3 instead of single gRNA increased KLF15 transcript levels by 3-fold compared to controls (n≥3 experiments). We hypothesized that dCas9VPR expression could be harnessed as an additional option for gene dose titration and we generated hiPSC lines with enhanced dCas9VPR expression (v2.0). We observed up to 5-fold KLF15 gene activation when triple gRNA and v2.0 were combined (n≥4 experiments). Engineered human myocardium (EHM) was generated consisting of CRISPRa cardiomyocytes, fibroblasts and collagen and we observed similar contractility in 4-week cultured EHM suggesting innocuous dCas9VPR and gRNA expression. CRISPRa component expression was maintained over the entire culture period as evaluated by dCas9VPR immunoblotting and KLF15 transcriptional activation (1.4 fold, v1.0 CRISPRa hiPSC-CM, n≥8 tissues) indicating sustained gene activition. Conclusions Targeted gene activation with CRISPR/Cas9 is a precise and effective tool for transcriptional activation in hiPSC-CM. We observed titratability of gene activation by 1.) dCas9VPR expression levels and 2.) single versus multiple gRNA use. We furthermore elucidated general rules for effective gRNA targeting within the 5' TSS of genes of interest which confirmed a dependency of baseline gene activity as a limiting factor for endogenous gene activation. FUNDunding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): German Research Foundation (DFG) - Collaborative Research Center 1002German Center for Cardiovascular Research (DZHK)

scholarly journals TWO-DIMENSIONAL EMPIRICAL EIGENFUNCTION MODEL FOR THE ANALYSIS AND PREDICTION OF BEACH PROFILE CHANGES

1986 ◽  
Vol 1 (20) ◽  
pp. 87 ◽  
Author(s):  
T.W. Hsu ◽  
S.R. Liaw ◽  
S.K. Wang ◽  
S.H. Ou
Keyword(s):  
Breaking Waves ◽  
Relative Importance ◽  
Two Dimensional ◽  
Coastal Structures ◽  
Beach Profile ◽  
Radiation Stress ◽  
Profile Data ◽  
Profile Changes ◽  
D Model ◽  
Profile Change

A two-dimensional empirical eigenfunction model is proposed for the analysis and the prediction of beach profile change due to longshore and cross-shore sediment transports. Beach profile data from Redhill coast, Taiwan, measured every two months at 150 meters interval along the detached breakwaters are analyzed and the relative importance from two directions is investigated. Furthermore, by employing the method of Markov process and linear regression, a prediction model is formulated which takes into account the effect of breaking waves, bottom sediment and radiation stress of waves. This 2-D model is shown to be effective in the analysis and the prediction of beach changes near the coastal structures.

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