Sequence Specificity in the Higher-Order Interaction of the Rev Protein of HIV-1 with its Target Sequence, the RRE

1995 ◽  
Vol 10 (3) ◽  
pp. 317???323 ◽  
Author(s):  
Douglas M. Powell ◽  
Ming Jie Zhang ◽  
Danielle A. M. Konings ◽  
Paul T. Wingfield ◽  
Stephen J. Stahl ◽  
...  
Keyword(s):  
Higher Order ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Order Interaction ◽  
Hiv 1 ◽  
Rev Protein

Functional analysis of CAR, the target sequence for the Rev protein of HIV-1

Science ◽  
1989 ◽  
Vol 246 (4937) ◽  
pp. 1625-1629 ◽  
Author(s):  
E. Dayton ◽  
D. Powell ◽  
A. Dayton
Keyword(s):  
Functional Analysis ◽  
Target Sequence ◽  
Hiv 1 ◽  
Rev Protein

Stable Competitive Dynamics Emerge from Multispike Interactions in a Stochastic Model of Spike-Timing-Dependent Plasticity

2006 ◽  
Vol 18 (10) ◽  
pp. 2414-2464 ◽  
Author(s):  
Peter A. Appleby ◽  
Terry Elliott
Keyword(s):  
Synaptic Plasticity ◽  
Stochastic Model ◽  
Higher Order ◽  
Spike Timing ◽  
Competitive Dynamics ◽  
Spike Timing Dependent Plasticity ◽  
Interaction Function ◽  
Dependent Plasticity ◽  
Order Interaction ◽  
Synaptic Dynamics

In earlier work we presented a stochastic model of spike-timing-dependent plasticity (STDP) in which STDP emerges only at the level of temporal or spatial synaptic ensembles. We derived the two-spike interaction function from this model and showed that it exhibits an STDP-like form. Here, we extend this work by examining the general n-spike interaction functions that may be derived from the model. A comparison between the two-spike interaction function and the higher-order interaction functions reveals profound differences. In particular, we show that the two-spike interaction function cannot support stable, competitive synaptic plasticity, such as that seen during neuronal development, without including modifications designed specifically to stabilize its behavior. In contrast, we show that all the higher-order interaction functions exhibit a fixed-point structure consistent with the presence of competitive synaptic dynamics. This difference originates in the unification of our proposed “switch” mechanism for synaptic plasticity, coupling synaptic depression and synaptic potentiation processes together. While three or more spikes are required to probe this coupling, two spikes can never do so. We conclude that this coupling is critical to the presence of competitive dynamics and that multispike interactions are therefore vital to understanding synaptic competition.

scholarly journals Higher-order temporal network effects through triplet evolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qing Yao ◽  
Bingsheng Chen ◽  
Tim S. Evans ◽  
Kim Christensen
Keyword(s):  
Real World ◽  
Link Prediction ◽  
Higher Order ◽  
Prediction Algorithm ◽  
Interaction Patterns ◽  
Temporal Networks ◽  
World Systems ◽  
Order Interaction ◽  
Space And Time ◽  
Pairwise Interactions

AbstractWe study the evolution of networks through ‘triplets’—three-node graphlets. We develop a method to compute a transition matrix to describe the evolution of triplets in temporal networks. To identify the importance of higher-order interactions in the evolution of networks, we compare both artificial and real-world data to a model based on pairwise interactions only. The significant differences between the computed matrix and the calculated matrix from the fitted parameters demonstrate that non-pairwise interactions exist for various real-world systems in space and time, such as our data sets. Furthermore, this also reveals that different patterns of higher-order interaction are involved in different real-world situations. To test our approach, we then use these transition matrices as the basis of a link prediction algorithm. We investigate our algorithm’s performance on four temporal networks, comparing our approach against ten other link prediction methods. Our results show that higher-order interactions in both space and time play a crucial role in the evolution of networks as we find our method, along with two other methods based on non-local interactions, give the best overall performance. The results also confirm the concept that the higher-order interaction patterns, i.e., triplet dynamics, can help us understand and predict the evolution of different real-world systems.

scholarly journals Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

2009 ◽  
Vol 10 (Suppl 8) ◽  
pp. S10 ◽  
Author(s):  
Omar Haq ◽  
Ronald M Levy ◽  
Alexandre V Morozov ◽  
Michael Andrec
Keyword(s):  
Drug Resistance ◽  
Higher Order ◽  
Resistance Mutations ◽  
Drug Resistance Mutations ◽  
Subtype B ◽  
Hiv 1

Symmetry-conserving higher-order interaction terms in the interacting boson model

1985 ◽  
Vol 32 (3) ◽  
pp. 1049-1056 ◽  
Author(s):  
G. Vanden Berghe ◽  
H. E. De Meyer ◽  
P. Van Isacker
Keyword(s):  
Higher Order ◽  
Interacting Boson Model ◽  
Order Interaction ◽  
Interaction Terms ◽  
Boson Model

The roles of nucleolar structure and function in the subcellular location of the HIV-1 Rev protein

1995 ◽  
Vol 108 (8) ◽  
pp. 2811-2823 ◽  
Author(s):  
M. Dundr ◽  
G.H. Leno ◽  
M.L. Hammarskjold ◽  
D. Rekosh ◽  
C. Helga-Maria ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Critical Role ◽  
Regulation Of Expression ◽  
Rna Transcription ◽  
Nucleolar Structure ◽  
Class 1 ◽  
Protein B23 ◽  
Hiv 1 ◽  
Rev Protein

The human immunodeficiency virus 1 (HIV-1) Rev transactivator protein plays a critical role in the regulation of expression of structural proteins by controlling the pathway of mRNA transport. The Rev protein is located predominantly in the nucleoli of HIV-1 infected or Rev-expressing cells. Previous studies demonstrated that the Rev protein forms a specific complex in vitro with protein B23 which is suggested to be a nucleolar receptor and/or carrier for the Rev protein. To study the role of the nucleolus and nucleolar proteins in Rev function, transfected COS-7 or transformed CMT3 cells expressing the Rev protein were examined for subcellular locations of Rev and other proteins using indirect immunofluorescence and immunoelectron microscopy. One day after transfection the Rev protein was found in most cells only in the nucleolar dense fibrillar and granular components where it colocalized with protein B23. These were designated class 1 cells. In a second class of cells Rev and B23 accumulated in the nucleoplasm as well as in nucleoli. Treatment of class 1 cells with actinomycin D (AMD) under conditions that blocked only RNA polymerase I transcription caused Rev to completely redistribute from nucleoli to the cytoplasm. Simultaneously, protein B23 was partially released from nucleoli, mostly into the nucleoplasm, with detectable amounts in the cytoplasm. In cells recovering from AMD treatment in the presence of cycloheximide Rev and B23 showed coincident relocation to nucleoli. Class 2 cells were resistant to AMD-induced Rev redistribution. Selective inhibition of RNA polymerase II transcription by alpha-amanitin or by DRB did not cause Rev to be released into the cytoplasm suggesting that active preribosomal RNA transcription is required for the nucleolar location of Rev. However, treatment with either of the latter two drugs at higher doses and for longer times caused partial disruption of nucleoli accompanied by translocation of the Rev protein to the cytoplasm. These results suggest that the nucleolar location of Rev depends on continuous preribosomal RNA transcription and a substantially intact nucleolar structure.

scholarly journals Ground states of Bose–Einstein condensates with higher order interaction

2019 ◽  
Vol 386-387 ◽  
pp. 38-48 ◽  
Author(s):  
Weizhu Bao ◽  
Yongyong Cai ◽  
Xinran Ruan
Keyword(s):  
Ground States ◽  
Higher Order ◽  
Order Interaction ◽  
Bose Einstein
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