Prediction of protein-protein interactions between viruses and human by an SVM model

<p>Abstract</p> <p>Background</p> <p>Several computational methods have been developed to predict protein-protein interactions from amino acid sequences, but most of those methods are intended for the interactions within a species rather than for interactions across different species. Methods for predicting interactions between homogeneous proteins are not appropriate for finding those between heterogeneous proteins since they do not distinguish the interactions between proteins of the same species from those of different species.</p> <p>Results</p> <p>We developed a new method for representing a protein sequence of variable length in a frequency vector of fixed length, which encodes the relative frequency of three consecutive amino acids of a sequence. We built a support vector machine (SVM) model to predict human proteins that interact with virus proteins. In two types of viruses, human papillomaviruses (HPV) and hepatitis C virus (HCV), our SVM model achieved an average accuracy above 80%, which is higher than that of another SVM model with a different representation scheme. Using the SVM model and Gene Ontology (GO) annotations of proteins, we predicted new interactions between virus proteins and human proteins.</p> <p>Conclusions</p> <p>Encoding the relative frequency of amino acid triplets of a protein sequence is a simple yet powerful representation method for predicting protein-protein interactions across different species. The representation method has several advantages: (1) it enables a prediction model to achieve a better performance than other representations, (2) it generates feature vectors of fixed length regardless of the sequence length, and (3) the same representation is applicable to different types of proteins.</p

Uniaxial and Mixed Orientations of Poly(ethylene oxide) in Nanoporous Alumina Studied by X-ray Pole Figure Analysis

The orientation of polymers under confinement is a basic, yet not fully understood phenomenon. In this work, the texture of poly(ethylene oxide) (PEO) infiltrated in nanoporous anodic alumina oxide (AAO) templates was investigated by X-ray pole figures. The influence of geometry and crystallization conditions, such as pore diameter, aspect ratio, and cooling rates, was systematically examined. All the samples exhibited a single, volume-dependent crystallization temperature (Tc) at temperatures much lower than that exhibited by bulk PEO, indicating “clean” microdomains without detectable heterogeneous nucleation. An “orientation diagram” was established to account for the experimental observations. Under very high cooling rates (quenching), crystallization of PEO within AAO was nucleation-controlled, adopting a random distribution of crystallites. Under low cooling rates, growth kinetics played a decisive role on the crystal orientation. A relatively faster cooling rate (10 °C/min) and/or smaller pores lead to the * ║ pore axis (n⃗) mode (uniaxial orientation). When the cooling rate was lower (1 °C/min), and/or the pores were larger, a mixed orientation, with a coexistence of * ║ n⃗ and * ║ n⃗ , was observed. The results favor the kinetic model where the fastest growth direction tends to align parallel to the pore axis.This work is supported by the National Natural Science Foundation of China (NSFC, 21873109, 51820105005, 21274156). G. L. is grateful to the Youth Innovation Promotion Association of the Chinese Academy of Sciences (2015026). G. L., D. W., and A. J. M. also acknowledge European funding by the RISE BIODEST project (H2020-MSCA-RISE-2017-778092). The authors thank Dr. Zhongkai Yang for assistance with pole figure measurement

An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program for finding cliques and near-cliques in a protein-protein interaction network. Analysis of the interaction network of yeast proteins using the algorithm demonstrates that 59% of the near-cliques identified by our algorithm have at least one function shared by all the proteins within a near-clique, and that 56% of the near-cliques show a good agreement with the experimentally determined protein complexes catalogued in MIPS

Knockout of CAFFEOYL-COA 3-O-METHYLTRANSFERASE 6/6L enhances the S/G ratio of lignin monomers and disease resistance in Nicotiana tabacum

BackgroundNicotiana tabacum is an important economic crop, which is widely planted in the world. Lignin is very important for maintaining the physiological and stress-resistant functions of tobacco. However, higher lignin content will produce lignin gas, which is not conducive to the formation of tobacco quality. To date, how to precisely fine-tune lignin content or composition remains unclear.ResultsHere, we annotated and screened 14 CCoAOMTs in Nicotiana tabacum and obtained homozygous double mutants of CCoAOMT6 and CCoAOMT6L through CRSIPR/Cas9 technology. The phenotype showed that the double mutants have better growth than the wild type whereas the S/G ratio increased and the total sugar decreased. Resistance against the pathogen test and the extract inhibition test showed that the transgenic tobacco has stronger resistance to tobacco bacterial wilt and brown spot disease, which are infected by Ralstonia solanacearum and Alternaria alternata, respectively. The combined analysis of metabolome and transcriptome in the leaves and roots suggested that the changes of phenylpropane and terpene metabolism are mainly responsible for these phenotypes. Furthermore, the molecular docking indicated that the upregulated metabolites, such as soyasaponin Bb, improve the disease resistance due to highly stable binding with tyrosyl-tRNA synthetase targets in Ralstonia solanacearum and Alternaria alternata.ConclusionsCAFFEOYL-COA 3-O-METHYLTRANSFERASE 6/6L can regulate the S/G ratio of lignin monomers and may affect tobacco bacterial wilt and brown spot disease resistance by disturbing phenylpropane and terpene metabolism in leaves and roots of Nicotiana tabacum, such as soyasaponin Bb

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

余剰活性汚泥のミミズ堆肥過程における抗生物質耐性遺伝子の挙動と微生物群集との関連性の解明

博士(工学)岐阜大学(Gifu University

A Hybrid Path-Oriented Code Assignment CDMA-Based MAC Protocol for Underwater Acoustic Sensor Networks

Due to the characteristics of underwater acoustic channel, media access control (MAC) protocols designed for underwater acoustic sensor networks (UWASNs) are quite different from those for terrestrial wireless sensor networks. Moreover, in a sink-oriented network with event information generation in a sensor field and message forwarding to the sink hop-by-hop, the sensors near the sink have to transmit more packets than those far from the sink, and then a funneling effect occurs, which leads to packet congestion, collisions and losses, especially in UWASNs with long propagation delays. An improved CDMA-based MAC protocol, named path-oriented code assignment (POCA) CDMA MAC (POCA-CDMA-MAC), is proposed for UWASNs in this paper. In the proposed MAC protocol, both the round-robin method and CDMA technology are adopted to make the sink receive packets from multiple paths simultaneously. Since the number of paths for information gathering is much less than that of nodes, the length of the spreading code used in the POCA-CDMA-MAC protocol is shorter greatly than that used in the CDMA-based protocols with transmitter-oriented code assignment (TOCA) or receiver-oriented code assignment (ROCA). Simulation results show that the proposed POCA-CDMA-MAC protocol achieves a higher network throughput and a lower end-to-end delay compared to other CDMA-based MAC protocols