scholarly journals Inductive inference of novel protein-molecule interactions using Heterogeneous Graph Transformer (HGT) AutoEncoder

2021 ◽  
Author(s):  
Alberto Arrigoni
Keyword(s):  
Link Prediction ◽  
Inductive Inference ◽  
Structural Information ◽  
Expression Patterns ◽  
Protein Molecule ◽  
Physicochemical Characteristics ◽  
Functional Information ◽  
Molecule Interactions ◽  
Molecule Interaction ◽  
Novel Protein

Protein-molecule interactions are promoted by the physicochemical characteristics of the actors involved, but structural information alone does not capture expression patterns, localization and pharmacokinetics. In this work we propose an integrative strategy for protein-molecule interaction discovery that combines different layers of information through the use of convolutional operators on graph, and frame the problem as missing link prediction task on an heterogeneous graph constituted by three node types: 1) molecules 2) proteins 3) diseases. Physicochemical information of the actors are encoded using shallow embedding techniques (SeqVec, Mol2Vec, Doc2Vec respectively) and are supplied as feature vectors to a Graph AutoEncoer (GAE) that uses a Heterogeneous Graph Transformer (HGT) in the encoder module. We show in this work that HGT Autoencoder can be used to accurately recapitulate the protein-molecule interactions set and propose novel relationships in inductive settings that are grounded in biological and functional information extracted from the graph.

scholarly journals Ecological plasticity to ions concentration determines genetic response and dominance of Anopheles coluzzii larvae in urban coastal habitats of Central Africa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Neil M. Longo-Pendy ◽  
Billy Tene-Fossog ◽  
Robert E. Tawedi ◽  
Ousman Akone-Ella ◽  
Celine Toty ◽  
...  
Keyword(s):  
Urban Expansion ◽  
Expression Patterns ◽  
Central Africa ◽  
Physicochemical Characteristics ◽  
Anopheles Coluzzii ◽  
Plastic Response ◽  
Coastal Habitats ◽  
Breeding Sites ◽  
Ecological Plasticity ◽  
Rural Sites

AbstractIn Central Africa, the malaria vector Anopheles coluzzii is predominant in urban and coastal habitats. However, little is known about the environmental factors that may be involved in this process. Here, we performed an analysis of 28 physicochemical characteristics of 59 breeding sites across 5 urban and rural sites in coastal areas of Central Africa. We then modelled the relative frequency of An. coluzzii larvae to these physicochemical parameters in order to investigate environmental patterns. Then, we assessed the expression variation of 10 candidate genes in An. coluzzii, previously incriminated with insecticide resistance and osmoregulation in urban settings. Our results confirmed the ecological plasticity of An. coluzzii larvae to breed in a large range of aquatic conditions and its predominance in breeding sites rich in ions. Gene expression patterns were comparable between urban and rural habitats, suggesting a broad response to ions concentrations of whatever origin. Altogether, An. coluzzii exhibits a plastic response to occupy both coastal and urban habitats. This entails important consequences for malaria control in the context of the rapid urban expansion in Africa in the coming years.

Link prediction via layer relevance of multiplex networks

2017 ◽  
Vol 28 (08) ◽  
pp. 1750101 ◽  
Author(s):  
Yabing Yao ◽  
Ruisheng Zhang ◽  
Fan Yang ◽  
Yongna Yuan ◽  
Qingshuang Sun ◽  
...  
Keyword(s):  
Structural Properties ◽  
Link Prediction ◽  
Structural Information ◽  
Similarity Index ◽  
Single Layer ◽  
Structural Features ◽  
Prediction Performance ◽  
Multiplex Networks ◽  
Multiplex Network ◽  
Node Similarity

In complex networks, the existing link prediction methods primarily focus on the internal structural information derived from single-layer networks. However, the role of interlayer information is hardly recognized in multiplex networks, which provide more diverse structural features than single-layer networks. Actually, the structural properties and functions of one layer can affect that of other layers in multiplex networks. In this paper, the effect of interlayer structural properties on the link prediction performance is investigated in multiplex networks. By utilizing the intralayer and interlayer information, we propose a novel “Node Similarity Index” based on “Layer Relevance” (NSILR) of multiplex network for link prediction. The performance of NSILR index is validated on each layer of seven multiplex networks in real-world systems. Experimental results show that the NSILR index can significantly improve the prediction performance compared with the traditional methods, which only consider the intralayer information. Furthermore, the more relevant the layers are, the higher the performance is enhanced.

scholarly journals Electron-Induced Chemistry in the Condensed Phase

Atoms ◽  
2019 ◽  
Vol 7 (1) ◽  
pp. 33
Author(s):  
Jan Hendrik Bredehöft
Keyword(s):  
Gas Phase ◽  
Cross Sections ◽  
Condensed Phase ◽  
Theoretical Understanding ◽  
The Past ◽  
Long Time ◽  
The Difference ◽  
Molecule Interactions ◽  
Multi Body ◽  
Molecule Interaction

Electron–molecule interactions have been studied for a long time. Most of these studies have in the past been limited to the gas phase. In the condensed-phase processes that have recently attracted attention from academia as well as industry, a theoretical understanding is mostly based on electron–molecule interaction data from these gas phase experiments. When transferring this knowledge to condensed-phase problems, where number densities are much higher and multi-body interactions are common, care must be taken to critically interpret data, in the light of this chemical environment. The paper presented here highlights three typical challenges, namely the shift of ionization energies, the difference in absolute cross-sections and branching ratios, and the occurrence of multi-body processes that can stabilize otherwise unstable intermediates. Examples from recent research in astrochemistry, where radiation driven chemistry is imminently important are used to illustrate these challenges.

scholarly journals Green Fluorescent Protein and Phase-Contrast Image Fusion via Generative Adversarial Networks

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Wei Tang ◽  
Yu Liu ◽  
Chao Zhang ◽  
Juan Cheng ◽  
Hu Peng ◽  
...  
Keyword(s):  
Phase Contrast ◽  
Fluorescent Protein ◽  
Structural Information ◽  
Generative Adversarial Networks ◽  
Phase Contrast Image ◽  
Functional Information ◽  
Adversarial Networks ◽  
Fused Image ◽  
Green Fluorescent ◽  
Contrast Image

In the field of cell and molecular biology, green fluorescent protein (GFP) images provide functional information embodying the molecular distribution of biological cells while phase-contrast images maintain structural information with high resolution. Fusion of GFP and phase-contrast images is of high significance to the study of subcellular localization, protein functional analysis, and genetic expression. This paper proposes a novel algorithm to fuse these two types of biological images via generative adversarial networks (GANs) by carefully taking their own characteristics into account. The fusion problem is modelled as an adversarial game between a generator and a discriminator. The generator aims to create a fused image that well extracts the functional information from the GFP image and the structural information from the phase-contrast image at the same time. The target of the discriminator is to further improve the overall similarity between the fused image and the phase-contrast image. Experimental results demonstrate that the proposed method can outperform several representative and state-of-the-art image fusion methods in terms of both visual quality and objective evaluation.

scholarly journals Features of the secondary structure of a protein molecule from powder diffraction data

2010 ◽  
Vol 66 (7) ◽  
pp. 756-761 ◽  
Author(s):  
Sebastian Basso ◽  
Céline Besnard ◽  
Jonathan P. Wright ◽  
Irene Margiolaki ◽  
Andrew Fitch ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Powder Diffraction ◽  
De Novo ◽  
Structural Information ◽  
Heavy Atom ◽  
Protein Molecule ◽  
Lattice Parameter ◽  
Egg White Lysozyme ◽  
Replacement Method ◽  
Isomorphous Replacement

Protein powder diffraction is shown to be suitable for obtainingde novosolutions to the phase problem at low resolutionviaphasing methods such as the isomorphous replacement method. Two heavy-atom derivatives (a gadolinium derivative and a holmium derivative) of the tetragonal form of hen egg-white lysozyme were crystallized at room temperature. Using synchrotron radiation, high-quality powder patterns were collected in which pH-induced anisotropic lattice-parameter changes were exploited in order to reduce the challenging and powder-specific problem of overlapping reflections. The phasing power of two heavy-atom derivatives in a multiple isomorphous replacement analysis enabled molecular structural information to be obtained up to approximately 5.3 Å resolution. At such a resolution, features of the secondary structure of the lysozyme molecule can be accurately located using programs dedicated to that effect. In addition, the quoted resolution is sufficient to determine the correct hand of the heavy-atom substructure which leads to an electron-density map representing the protein molecule of proper chirality.

scholarly journals Lignin-based resistance to Cuscuta campestris parasitism in Heinz resistant tomato cultivars

2019 ◽  
Author(s):  
Min-Yao Jhu ◽  
Moran Farhi ◽  
Li Wang ◽  
Richard N. Philbrook ◽  
Michael S. Belcher ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Expression Patterns ◽  
Protein Molecule ◽  
Negative Regulator ◽  
Broad Host Range ◽  
Key Factors ◽  
Resistant Lines ◽  
Cuscuta Campestris ◽  
Tomato Cultivars ◽  
Transient Overexpression

AbstractCuscuta species (dodders) are common agriculturally destructive parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts. Cuscuta campestris has a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible to C. campestris infestations. However, some Heinz tomato hybrid cultivars exhibit resistance to this parasite. The stem cortex in these resistant lines responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. We compared gene expression patterns under C. campestris infestation in resistant and susceptible cultivars and identified LIF1 (Lignin Induction Factor 1, an AP2-like transcription factor), SlMYB55, and CuRLR1 (Cuscuta R-gene for Lignin-based Resistance 1, a CC-NBS-LRR) as key factors conferring host resistance. Transient overexpression results suggest that SlMYB55 and LIF1 directly regulate cortical lignification. We also identified SlWRKY16, a transcription factor that is upregulated in all tested tomato cultivars upon C. campestris attachment. SlWRKY16 acts as a negative regulator of LIF1 function. Moreover, CuRLR1 responds to a large protein molecule from C. campestris extracts and may play a role in signaling or function as a receptor for receiving C. campestris signals to regulate lignification-based resistance.One-sentence summaryFour key regulators confer lignin accumulation in the tomato stem cortex blocking C. campestris host penetration upon infection.

scholarly journals Dihedral Angle Measurements for Structure Determination by Biomolecular Solid-State NMR Spectroscopy

2021 ◽  
Vol 8 ◽  
Author(s):  
Patrick C. A. van der Wel
Keyword(s):  
Solid State ◽  
Structure Determination ◽  
Solid State Nmr ◽  
Structural Information ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Distance Measurements ◽  
Challenges And Opportunities ◽  
Molecule Interactions ◽  
Angle Spinning

In structural studies of immobilized, aggregated and self-assembled biomolecules, solid-state NMR (ssNMR) spectroscopy can provide valuable high-resolution structural information. Among the structural restraints provided by magic angle spinning (MAS) ssNMR the canonical focus is on inter-atomic distance measurements. In the current review, we examine the utility of ssNMR measurements of angular constraints, as a complement to distance-based structure determination. The focus is on direct measurements of angular restraints via the judicious recoupling of multiple anisotropic ssNMR parameters, such as dipolar couplings and chemical shift anisotropies. Recent applications are highlighted, with a focus on studies of nanocrystalline polypeptides, aggregated peptides and proteins, receptor-substrate interactions, and small molecule interactions with amyloid protein fibrils. The review also examines considerations of when and where ssNMR torsion angle experiments are (most) effective, and discusses challenges and opportunities for future applications.

scholarly journals Unsupervised Negative Link Prediction in Signed Social Networks

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Pengfei Shen ◽  
Shufen Liu ◽  
Ying Wang ◽  
Lu Han
Keyword(s):  
Link Prediction ◽  
Nonnegative Matrix Factorization ◽  
Structural Information ◽  
Nonnegative Matrix ◽  
Sociological Study ◽  
Negative Interaction ◽  
Signed Social Networks ◽  
Real World Datasets ◽  
Negative Links ◽  
Negative Link

It has been proved in a number of applications that it is useful to predict unknown social links, and link prediction has played an important role in sociological study. Although there has been a surge of pertinent approaches to link prediction, most of them focus on positive link prediction while giving few attentions to the problem of inferring unknown negative links. The inherent characteristics of negative relations present great challenges to traditional link prediction: (1) there are very few negative interaction data; (2) negative links are much sparser than positive links; (3) social data is often noisy, incomplete, and fast-evolved. This paper intends to address this novel problem by solely leveraging structural information and further proposes the UN-PNMF framework based on the projective nonnegative matrix factorization, so as to incorporate network embedding and user’s property embedding into negative link prediction. Empirical experiments on real-world datasets corroborate their effectiveness.

Sign in / Sign up

Export Citation Format

Share Document