scholarly journals alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein–Protein Interactions Revealing the Molecular Features of the Disease-Causing Bacteria

2021 ◽  
Vol 22 (15) ◽  
pp. 8342
Author(s):  
Raghav Kataria ◽  
Rakesh Kaundal
Keyword(s):  
Pseudomonas Syringae ◽  
Protein Interactions ◽  
The United States ◽  
Successful Implementation ◽  
Protein Protein Interactions ◽  
Forage Crops ◽  
Stem Blight ◽  
Molecular Features ◽  
Search Tool ◽  
Wide Adaptation

Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by Pseudomonas syringae pv. syringae ALF3) in alfalfa has caused around 50% yield losses in the United States. Studies are being conducted to decipher the roles of the key genes and pathways regulating the disease, but due to the sparse knowledge about the infection mechanisms of Pseudomonas, the development of resistant cultivars is hampered. The database alfaNET is an attempt to assist researchers by providing comprehensive Pseudomonas proteome annotations, as well as a host–pathogen interactome tool, which predicts the interactions between host and pathogen based on orthology. alfaNET is a user-friendly and efficient tool and includes other features such as subcellular localization annotations of pathogen proteins, gene ontology (GO) annotations, network visualization, and effector protein prediction. Users can also browse and search the database using particular keywords or proteins with a specific length. Additionally, the BLAST search tool enables the user to perform a homology sequence search against the alfalfa and Pseudomonas proteomes. With the successful implementation of these attributes, alfaNET will be a beneficial resource to the research community engaged in implementing molecular strategies to mitigate the disease. alfaNET is freely available for public use at http://bioinfo.usu.edu/alfanet/.

scholarly journals Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery

2015 ◽  
Vol 20 (5) ◽  
pp. 563-576 ◽  
Author(s):  
Andrew D. Foster ◽  
James D. Ingram ◽  
Eilidh K. Leitch ◽  
Katherine R. Lennard ◽  
Eliot L. Osher ◽  
...  
Keyword(s):  
Protein Interactions ◽  
High Throughput Screening ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Peptide Libraries ◽  
Successful Implementation ◽  
Protein Protein Interactions ◽  
Lead Discovery ◽  
Small Molecule Libraries ◽  
The Creation

The identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for screening libraries of macromolecules created using chemical biology approaches. Not only can the production of the library be directly interfaced with a cell-based assay, but these libraries also require significantly fewer resources to generate and maintain. In this context, cyclic peptides are increasingly viewed as ideal scaffolds and have proven capability against challenging targets such as protein-protein interactions. Here we discuss a range of methods used for the creation of cyclic peptide libraries and detail examples of their successful implementation.

scholarly journals ‘Candidatus Phytoplasma mali’ Genome Encodes a Protein that Functions as an E3 Ubiquitin Ligase and Could Inhibit Plant Basal Defense

2019 ◽  
Vol 32 (11) ◽  
pp. 1487-1495 ◽  
Author(s):  
Alisa Strohmayer ◽  
Mirko Moser ◽  
Azeddine Si-Ammour ◽  
Gabi Krczal ◽  
Kajohn Boonrod
Keyword(s):  
Pseudomonas Syringae ◽  
Protein Interactions ◽  
E3 Ligase ◽  
Effector Proteins ◽  
Protein Protein Interactions ◽  
Candidatus Phytoplasma Mali ◽  
Proteolytic Pathway ◽  
Ubiquitin Conjugating Enzymes ◽  
First Time

Phytoplasmas are the causative agent of numerous diseases of plant species all over the world, including important food crops. The mode by which phytoplasmas multiply and behave in their host is poorly understood and often based on genomic data. We used yeast two-hybrid screening to find new protein–protein interactions between the causal agent of apple proliferation ‘Candidatus Phytoplasma mali’ and its host plant. Here, we report that the ‘Ca. P. mali’ strain PM19 genome encodes a protein PM19_00185 that interacts with at least six different ubiquitin-conjugating enzymes (UBC; E2) of Arabidopsis thaliana. An in vitro ubiquitination assay showed that PM19_00185 is enzymatically active as E3 ligase with A. thaliana E2 UBC09 and Malus domestica E2 UBC10. We show that a nonhost bacteria (Pseudomonas syringae pv. tabaci) can grow in transgenic A. thaliana plant lines expressing PM19_00185. A connection of phytoplasma effector proteins with the proteasome proteolytic pathway has been reported before. However, this is, to our knowledge, the first time that a phytoplasma effector protein with E3 ligase activity has been reported.

scholarly journals Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods

2019 ◽  
Vol 39 (4) ◽  
Author(s):  
Shulong Zhang ◽  
Quan Wang ◽  
Qi Han ◽  
Huazhong Han ◽  
Pinxiang Lu
Keyword(s):  
Gene Expression ◽  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Protein Interactions ◽  
Disease Free Survival ◽  
Gene Expression Omnibus ◽  
Receptor Interaction ◽  
Papillary Thyroid ◽  
Protein Protein Interactions ◽  
Search Tool

AbstractThe molecular mechanism of the occurrence and development of papillary thyroid carcinoma (PTC) has been widely explored, but has not been completely elucidated. The present study aimed to identify and analyze genes associated with PTC by bioinformatics methods. Two independent datasets were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between PTC tissues and matched non-cancerous tissues were identified using GEO2R tool. The common DEGs in the two datasets were screened out by VennDiagram package, and analyzed by the following tools: KOBAS, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Search tool for the retrieval of interacting genes/proteins (STRING), UALCAN and Gene expression profiling interactive analysis (GEPIA). A total of 513 common DEGs, including 259 common up-regulated and 254 common down-regulated genes in PTC, were screened out. These common up-regulated and down-regulated DEGs were most significantly enriched in cytokine–cytokine receptor interaction and metabolic pathways, respectively. Protein–protein interactions (PPI) network analysis showed that the up-regulated genes: FN1, SDC4, NMU, LPAR5 and the down-regulated genes: BCL2 and CXCL12 were key genes. Survival analysis indicated that the high expression of FN1 and NMU genes significantly decreased disease-free survival of patients with thyroid carcinoma. In conclusion, the genes and pathways identified in the current study will not only contribute to elucidating the pathogenesis of PTC, but also provide prognostic markers and therapeutic targets for PTC.

scholarly journals Identification of Significant Proteins Associated with Diabetes Mellitus Using Network Analysis of Protein-Protein Interactions

2019 ◽  
Vol 8 (1) ◽  
pp. 41-52
Author(s):  
Muhammad Syafiuddin Usman ◽  
Wisnu Ananta Kusuma ◽  
Farit Mochamad Afendi ◽  
Rudi Heryanto
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Close Relation ◽  
Mendelian Inheritance ◽  
Protein Protein Interactions ◽  
Topology Analysis ◽  
Protein Protein Interaction ◽  
Search Tool ◽  
Dm Type 2

Computation approach to identify significance of proteins related with disease was proposed as one of the solutions from the problem of experimental method application which is generally high cost and time consuming. The case of study was conducted on Diabetes Melitus (DM) type 2 diseases. Identification of significant proteins was conducted by constructing protein-protein interactions network and then analyzing the network topology. Dataset was obtained from Online Mendelian Inheritance in Man (OMIM) and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) which provided protein data related with a disease and Protein-Protein Interaction (PPI), respectively. The results of topology analysis towards Protein-Protein Interaction (PPI) showed that there were 21 significant protein associated with DM where INS as a network center protein and AKTI, TCF7L2, KCNJ11, PPARG, GCG, INSR, IAPP, SOCS3 were proteins that had close relation directly with INS.

scholarly journals Identification of Core Prognosis-Related Candidate Genes in Cervical Cancer via Integrated Bioinformatical Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Jianxia Wei ◽  
Yang Wang ◽  
Kejian Shi ◽  
Ying Wang
Keyword(s):  
Gene Expression ◽  
Cervical Cancer ◽  
Protein Interactions ◽  
Gene Expression Omnibus ◽  
Venn Diagram ◽  
Protein Protein Interactions ◽  
Normal Tissues ◽  
Interactive Analysis ◽  
Kaplan Meier ◽  
Search Tool

Purposes. Cervical cancer (CC) is one of the highest frequently occurred malignant gynecological tumors with high rates of morbidity and mortality. Here, we aimed to identify significant genes associated with poor outcome. Materials and methods. Differentially expressed genes (DEGs) between CC tissues and normal cervical tissues were picked out by GEO2R tool and Venn diagram software. Database for Annotation, Visualization and Integrated Discovery (DAVID) was performed to analyze gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway. The protein-protein interactions (PPIs) of these DEGs were visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). Afterwards, Kaplan-Meier analysis was applied to analyze the overall survival among these genes. The Gene Expression Profiling Interactive Analysis (GEPIA) was applied for further validation of the expression level of these genes. Results. The mRNA expression profile datasets of GSE63514, GSE27678, and GSE6791 were downloaded from the Gene Expression Omnibus database (GEO). In total, 76 CC tissues and 35 normal tissues were collected in the three profile datasets. There were totally 73 consistently expressed genes in the three datasets, including 65 up-regulated genes and 8 down-regulated genes. Of PPI network analyzed by Molecular Complex Detection (MCODE) plug-in, all 65 up-regulated genes and 4 down-regulated genes were selected. The results of the Kaplan-Meier survival analysis showed that 3 of the 65 up-regulated genes had a significantly worse prognosis, while 3 of the 4 down-regulated genes had a significantly better outcome. For validation in GEPIA, 4 of 6 genes (PLOD2, ANLN, AURKA, and AR) were confirmed to be significantly deregulated in CC tissues compared to normal tissues. Conclusion. We have identified three up-regulated (PLOD2, ANLN, and AURKA) and a down-regulated DEGs (AR) with poor prognosis in CC on the basis of integrated bioinformatical methods, which could be regarded as potential therapeutic targets for CC patients.

Protein-protein interactions of the p53 family with the Bcl-2 family in hepatocellular carcinoma

2011 ◽  
Vol 49 (08) ◽  
Author(s):  
LC König ◽  
M Meinhard ◽  
C Sandig ◽  
MH Bender ◽  
A Lovas ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
P53 Family

The First Decade of Effort: Progress Toward a Hospital Information System at the UCLA Hospital, Los Angeles, California

1970 ◽  
Vol 09 (02) ◽  
pp. 75-80
Author(s):  
B. G. Lamson ◽  
W. S. Russell ◽  
J. Fullmore ◽  
W. E. Nix
Keyword(s):  
Los Angeles ◽  
Medical Record ◽  
Communication Systems ◽  
The United States ◽  
Computer Applications ◽  
Record Management ◽  
Successful Implementation ◽  
Accounting System ◽  
Accrual Accounting ◽  
Medical Specialties

Total information and communication systems within hospitals have been designed, but successful complete implementation, to date, has not been achieved. Limited applications with both patient medical data, notably in the clinical laboratories, and in the hospital accounting offices have been numerous. Although total programs are not yet a reality, it is apparent that the computer will serve ultimately many communication requirements, both medical and financial, within the hospital.Sound hospital management requires that costs of all component operations be known in order that value judgments concerning worth and efficiency may be made. Accrual accounting systems which match revenue and expense over the same time period are a prerequisite. Cash and modified cash hospital accounting cannot provide current reliable data for sound decision making.Costs of hospital operations cannot be evaluated unless related to the characteristics of the patient service load. Average per diem costs mean little except when large similar populations of patients are being compared. A modern hospital accrual accounting system should be able to provide information concerning the costs of caring for specific diseases in patients with known age and sex and disease severity characteristics. Without information of this type, it will not be possible to objectively evaluate alternative systems of financing and organizing patient care.Medical record management offers the promise of prospective use of patient disease information in the planning and scheduling of facilities. The prose content of medical record summaries, such as diagnostic statements in tissue pathology, radiology, and admission and discharge diagnoses, may be susceptible to non-coded, full prose input into computer controlled diagnostic files. Thesauri in the several medical specialties will be necessary for this achievement.There is little immediate prospect for complete hospital communication systems that can be made available as a package to any hospital without substantial local alteration. Pilot projects in teaching centers should be viewed for the time being as opportunities to define objectives, evaluate feasibility, and determine degree of risk and expense.A brief survey of applications in the United States which have been successfully implemented or which appear suitable for successful implementation is recorded.Eleven general principles which have been associated with successful implementation of computer applications within the UCLA Hospital are enumerated.

Partial Purification of a Specific Plasminogen Activator from Porcine Parotid Glands

1974 ◽  
Vol 31 (03) ◽  
pp. 403-414 ◽  
Author(s):  
Terence Cartwright
Keyword(s):  
Nucleic Acid ◽  
Salivary Glands ◽  
Plasminogen Activator ◽  
Protein Interactions ◽  
Partial Purification ◽  
Protein Protein Interactions ◽  
Parotid Glands ◽  
Two Stage ◽  
Preliminary Characterization ◽  
Specific Inhibitors

SummaryA method is described for the extraction with buffers of near physiological pH of a plasminogen activator from porcine salivary glands. Substantial purification of the activator was achieved although this was to some extent complicated by concomitant extraction of nucleic acid from the glands. Preliminary characterization experiments using specific inhibitors suggested that the activator functioned by a similar mechanism to that proposed for urokinase, but with some important kinetic differences in two-stage assay systems. The lack of reactivity of the pig gland enzyme in these systems might be related to the tendency to protein-protein interactions observed with this material.

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