scholarly journals VirionFinder: Identification of Complete and Partial Prokaryote Virus Virion Protein From Virome Data Using the Sequence and Biochemical Properties of Amino Acids

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhencheng Fang ◽  
Hongwei Zhou
Keyword(s):  
Amino Acids ◽  
Functional Annotation ◽  
Recognition Rate ◽  
Biochemical Properties ◽  
Metagenomic Data ◽  
Virion Protein ◽  
Species Classification ◽  
Viral Community ◽  
Benchmark Datasets ◽  
Virus Proteins

Viruses are some of the most abundant biological entities on Earth, and prokaryote virus are the dominant members of the viral community. Because of the diversity of prokaryote virus, functional annotation cannot be performed on a large number of genes from newly discovered prokaryote virus by searching the current database; therefore, the development of an alignment-free algorithm for functional annotation of prokaryote virus proteins is important to understand the viral community. The identification of prokaryote virus proteins (PVVPs) is a critical step for many viral analyses, such as species classification, phylogenetic analysis and the exploration of how prokaryote virus interact with their hosts. Although a series of PVVP prediction tools have been developed, the performance of these tools is still not satisfactory. Moreover, viral metagenomic data contains fragmented sequences, leading to the existence of some incomplete genes. Therefore, a tool that can identify partial prokaryote virus proteins is also needed. In this work, we present a novel algorithm, called VirionFinder, to identify the complete and partial PVVPs from non-prokaryote virus virion proteins (non-PVVPs). VirionFinder uses the sequence and biochemical properties of 20 amino acids as the mathematical model to encode the protein sequences and uses a deep learning technique to identify whether a given protein is a PVVP. Compared with the state-of-the-art tools using artificial benchmark datasets, the results show that under the same specificity (Sp), the sensitivity (Sn) of VirionFinder is approximately 10–34% much higher than the Sn of these tools on both complete and partial proteins. When evaluating related tools using real virome data, the recognition rate of PVVP-like sequences of VirionFinder is also much higher than that of the other tools. We expect that VirionFinder will be a powerful tool for identifying novel virion proteins from both complete prokaryote virus genomes and viral metagenomic data. VirionFinder is freely available at https://github.com/zhenchengfang/VirionFinder.

scholarly journals SCMTHP: A New Approach for Identifying and Characterizing of Tumor-Homing Peptides Using Estimated Propensity Scores of Amino Acids

Pharmaceutics ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 122
Author(s):  
Phasit Charoenkwan ◽  
Wararat Chiangjong ◽  
Chanin Nantasenamat ◽  
Mohammad Ali Moni ◽  
Pietro Lio’ ◽  
...  
Keyword(s):  
Amino Acids ◽  
Propensity Scores ◽  
Nearest Neighbor ◽  
Biochemical Properties ◽  
Least Squares Regression ◽  
K Nearest Neighbor ◽  
Accurate Identification ◽  
Major Drawback ◽  
Benchmark Datasets ◽  
Tumor Homing

Tumor-homing peptides (THPs) are small peptides that can recognize and bind cancer cells specifically. To gain a better understanding of THPs’ functional mechanisms, the accurate identification and characterization of THPs is required. Although some computational methods for in silico THP identification have been proposed, a major drawback is their lack of model interpretability. In this study, we propose a new, simple and easily interpretable computational approach (called SCMTHP) for identifying and analyzing tumor-homing activities of peptides via the use of a scoring card method (SCM). To improve the predictability and interpretability of our predictor, we generated propensity scores of 20 amino acids as THPs. Finally, informative physicochemical properties were used for providing insights on characteristics giving rise to the bioactivity of THPs via the use of SCMTHP-derived propensity scores. Benchmarking experiments from independent test indicated that SCMTHP could achieve comparable performance to state-of-the-art method with accuracies of 0.827 and 0.798, respectively, when evaluated on two benchmark datasets consisting of Main and Small datasets. Furthermore, SCMTHP was found to outperform several well-known machine learning-based classifiers (e.g., decision tree, k-nearest neighbor, multi-layer perceptron, naive Bayes and partial least squares regression) as indicated by both 10-fold cross-validation and independent tests. Finally, the SCMTHP web server was established and made freely available online. SCMTHP is expected to be a useful tool for rapid and accurate identification of THPs and for providing better understanding on THP biophysical and biochemical properties.

scholarly journals A Filovirus-Unique Region of Ebola Virus Nucleoprotein Confers Aberrant Migration and Mediates Its Incorporation into Virions

2008 ◽  
Vol 82 (13) ◽  
pp. 6190-6199 ◽  
Author(s):  
Wei Shi ◽  
Yue Huang ◽  
Mark Sutton-Smith ◽  
Berangere Tissot ◽  
Maria Panico ◽  
...  
Keyword(s):  
Amino Acids ◽  
Ebola Virus ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Biochemical Properties ◽  
Virion Protein ◽  
Unique Region ◽  
Syncytial Virus ◽  
Viruslike Particles ◽  
Acidic Region

ABSTRACT The Ebola virus nucleoprotein (NP) is an essential component of the nucleocapsid, required for filovirus particle formation and replication. Together with virion protein 35 (VP35) and VP24, this gene product gives rise to the filamentous nucleocapsid within transfected cells. Ebola virus NP migrates aberrantly, with an apparent molecular mass of 115 kDa, although it is predicted to encode an ∼85-kDa protein. In this report, we show that two domains of this protein determine this aberrant migration and that this region mediates its incorporation into virions. These regions, amino acids 439 to 492 and amino acids 589 to 739, alter the mobility of Ebola virus NP by sodium dodecyl sulfate-polyacrylamide gel electrophoresis by 5 and 15 kDa, respectively, and confer similar effects on a heterologous protein, LacZ, in a position-independent fashion. Furthermore, when coexpressed with VP40, VP35, and VP24, this region mediated incorporation of NP into released viruslike particles. When fused to chimeric paramyxovirus NPs derived from measles or respiratory syncytial virus, this domain directed these proteins into the viruslike particle. The COOH-terminal NP domain comprises a conserved highly acidic region of NP with predicted disorder, distinguishing Ebola virus NPs from paramyxovirus NPs. The acidic character of this domain is likely responsible for its aberrant biochemical properties. These findings demonstrate that this region is essential for the assembly of the filamentous nucleocapsids that give rise to filoviruses.

scholarly journals Non-Intrusive Load Disaggregation Based on a Multi-Scale Attention Residual Network

2020 ◽  
Vol 10 (24) ◽  
pp. 9132
Author(s):  
Liguo Weng ◽  
Xiaodong Zhang ◽  
Junhao Qian ◽  
Min Xia ◽  
Yiqing Xu ◽  
...  
Keyword(s):  
Smart Grids ◽  
Recognition Rate ◽  
Low Frequency ◽  
Attention Mechanism ◽  
Learning Ability ◽  
Residual Network ◽  
Multi Scale ◽  
Energy Disaggregation ◽  
Benchmark Datasets ◽  
Load Disaggregation

Non-intrusive load disaggregation (NILD) is of great significance to the development of smart grids. Current energy disaggregation methods extract features from sequences, and this process easily leads to a loss of load features and difficulties in detecting, resulting in a low recognition rate of low-use electrical appliances. To solve this problem, a non-intrusive sequential energy disaggregation method based on a multi-scale attention residual network is proposed. Multi-scale convolutions are used to learn features, and the attention mechanism is used to enhance the learning ability of load features. The residual learning further improves the performance of the algorithm, avoids network degradation, and improves the precision of load decomposition. The experimental results on two benchmark datasets show that the proposed algorithm has more advantages than the existing algorithms in terms of load disaggregation accuracy and judgments of the on/off state, and the attention mechanism can further improve the disaggregation accuracy of low-frequency electrical appliances.

scholarly journals META-pipe cloud setup and execution

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 2060
Author(s):  
Aleksandr Agafonov ◽  
Kimmo Mattila ◽  
Cuong Duong Tuan ◽  
Lars Tiede ◽  
Inge Alexander Raknes ◽  
...  
Keyword(s):  
Functional Annotation ◽  
High Performance ◽  
Sequence Data ◽  
Metagenomic Data ◽  
Taxonomic Profiling ◽  
Geographically Distributed ◽  
Computationally Intensive ◽  
High Performance Computing Cluster ◽  
And Storage ◽  
Performance Computing

META-pipe is a complete service for the analysis of marine metagenomic data. It provides assembly of high-throughput sequence data, functional annotation of predicted genes, and taxonomic profiling. The functional annotation is computationally demanding and is therefore currently run on a high-performance computing cluster in Norway. However, additional compute resources are necessary to open the service to all ELIXIR users. We describe our approach for setting up and executing the functional analysis of META-pipe on additional academic and commercial clouds. Our goal is to provide a powerful analysis service that is easy to use and to maintain. Our design therefore uses a distributed architecture where we combine central servers with multiple distributed backends that execute the computationally intensive jobs. We believe our experiences developing and operating META-pipe provides a useful model for others that plan to provide a portal based data analysis service in ELIXIR and other organizations with geographically distributed compute and storage resources.

scholarly journals Truncated Prosequence of Rhizopus oryzae Lipase: Key Factor for Production Improvement and Biocatalyst Stability

Catalysts ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 961 ◽  
Author(s):  
Josu López-Fernández ◽  
Juan J. Barrero ◽  
M. Dolors Benaiges ◽  
Francisco Valero
Keyword(s):  
Amino Acids ◽  
Ionic Strength ◽  
Rhizopus Oryzae ◽  
Lipase Production ◽  
Biochemical Properties ◽  
Mature Sequence ◽  
Rhizopus Oryzae Lipase ◽  
Batch Cultures ◽  
Production Improvement ◽  
Key Factor

Recombinant Rhizopus oryzae lipase (mature sequence, rROL) was modified by adding to its N-terminal 28 additional amino acids from the C-terminal of the prosequence (proROL) to obtain a biocatalyst more suitable for the biodiesel industry. Both enzymes were expressed in Pichia pastoris and compared in terms of production bioprocess parameters, biochemical properties, and stability. Growth kinetics, production, and yields were better for proROL harboring strain than rROL one in batch cultures. When different fed-batch strategies were applied, lipase production and volumetric productivity of proROL-strain were always higher (5.4 and 4.4-fold, respectively) in the best case. rROL and proROL enzymatic activity was dependent on ionic strength and peaked in 200 mM Tris-HCl buffer. The optimum temperature and pH for rROL were influenced by ionic strength, but those for proROL were not. The presence of these amino acids altered lipase substrate specificity and increased proROL stability when different temperature, pH, and methanol/ethanol concentrations were employed. The 28 amino acids were found to be preferably removed by proteases, leading to the transformation of proROL into rROL. Nevertheless, the truncated prosequence enhanced Rhizopus oryzae lipase heterologous production and stability, making it more appropriate as industrial biocatalyst.

scholarly journals Effects of Substrate-Binding Site Residues on the Biochemical Properties of a Tau Class Glutathione S-Transferase from Oryza sativa

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 25 ◽  
Author(s):  
Xue Yang ◽  
Jinchi Wei ◽  
Zhihai Wu ◽  
Jie Gao
Keyword(s):  
Amino Acids ◽  
Enzyme Activity ◽  
Abiotic Stress ◽  
Binding Site ◽  
Stress Responses ◽  
Stress Resistance ◽  
Substrate Binding ◽  
Biochemical Properties ◽  
Biotic And Abiotic Stress ◽  
Substrate Binding Site

Glutathione S-transferases (GSTs)—an especially plant-specific tau class of GSTs—are key enzymes involved in biotic and abiotic stress responses. To improve the stress resistance of crops via the genetic modification of GSTs, we predicted the amino acids present in the GSH binding site (G-site) and hydrophobic substrate-binding site (H-site) of OsGSTU17, a tau class GST in rice. We then examined the enzyme activity, substrate specificity, enzyme kinetics and thermodynamic stability of the mutant enzymes. Our results showed that the hydrogen bonds between Lys42, Val56, Glu68, and Ser69 of the G-site and glutathione were essential for enzyme activity and thermal stability. The hydrophobic side chains of amino acids of the H-site contributed to enzyme activity toward 4-nitrobenzyl chloride but had an inhibitory effect on enzyme activity toward 1-chloro-2,4-dinitrobenzene and cumene hydroperoxide. Different amino acids of the H-site had different effects on enzyme activity toward a different substrate, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. Moreover, Leu112 and Phe162 were found to inhibit the catalytic efficiency of OsGSTU17 to 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole, while Pro16, Leu112, and Trp165 contributed to structural stability. The results of this research enhance the understanding of the relationship between the structure and function of tau class GSTs to improve the abiotic stress resistance of crops.

scholarly journals Frame-Based Facial Expression Recognition Using Geometrical Features

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Anwar Saeed ◽  
Ayoub Al-Hamadi ◽  
Robert Niese ◽  
Moftah Elzobi
Keyword(s):  
Facial Expression ◽  
Prior Knowledge ◽  
State Of The Art ◽  
Recognition Rate ◽  
Human Interaction ◽  
Expression Recognition ◽  
Acoustic Data ◽  
Geometrical Features ◽  
Benchmark Datasets ◽  
Neutral Expression

To improve the human-computer interaction (HCI) to be as good as human-human interaction, building an efficient approach for human emotion recognition is required. These emotions could be fused from several modalities such as facial expression, hand gesture, acoustic data, and biophysiological data. In this paper, we address the frame-based perception of the universal human facial expressions (happiness, surprise, anger, disgust, fear, and sadness), with the help of several geometrical features. Unlike many other geometry-based approaches, the frame-based method does not rely on prior knowledge of a person-specific neutral expression; this knowledge is gained through human intervention and not available in real scenarios. Additionally, we provide a method to investigate the performance of the geometry-based approaches under various facial point localization errors. From an evaluation on two public benchmark datasets, we have found that using eight facial points, we can achieve the state-of-the-art recognition rate. However, this state-of-the-art geometry-based approach exploits features derived from 68 facial points and requires prior knowledge of the person-specific neutral expression. The expression recognition rate using geometrical features is adversely affected by the errors in the facial point localization, especially for the expressions with subtle facial deformations.

Purification of an exo-1,3-β-glucanase from Candida utilis

1976 ◽  
Vol 54 (11) ◽  
pp. 927-934 ◽  
Author(s):  
T. G. Villa ◽  
V. Notario ◽  
T. Benítez ◽  
J. R. Villanueva
Keyword(s):  
Amino Acids ◽  
Heavy Metal ◽  
Cell Wall ◽  
Heavy Metal Ions ◽  
Candida Utilis ◽  
Negative Charge ◽  
Hydrolysis Product ◽  
Culture Fluid ◽  
Biochemical Properties ◽  
Acidic Amino Acids

An exo-1,3-β-glucanase (EC 3.2.1.—) has been purified from the culture fluid of the yeast Candida utilis, and its biochemical properties have been studied. The amino acid analysis revealed a high content of acidic amino acids. The purified enzyme had 20% carbohydrate and a net negative charge showing higher affinity for laminarin than for p-nitrophenyl-β-D-glucopyranoside and yeast cell-wall 1,3-β-glucans. In addition, the enzyme hydrolyzed the substrates starting from the nonreducing ends, releasing glucose as the exclusive hydrolysis product. The enzyme activity was strongly inhibited by lactones and also by some heavy-metal ions.

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