scholarly journals In Silico Identification of Novel Immunogenic Secreted Proteins of Mycoplasma bovis from Secretome Data and Experimental Verification

Pathogens ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 770
Author(s):  
Ihsanullah Shirani ◽  
Hui Zhang ◽  
Gang Zhao ◽  
Siyi Lu ◽  
Marawan A Marawan ◽  
...  
Keyword(s):  
In Silico ◽  
Interferon Γ ◽  
Extracellular Proteins ◽  
Control Measures ◽  
Effective Control ◽  
Mycoplasma Bovis ◽  
T Cell Epitopes ◽  
Label Free ◽  
Bovine Respiratory Diseases ◽  
Immunogenic Proteins

Mycoplasma bovis is a major pathogen, responsible for bovine respiratory diseases worldwide. The present lack of effective control measures leaves cattle owners at considerable perpetual risk of M. bovis outbreaks. In this study, we identified M. bovis secreted immunogenic proteins in silico as potential candidates for novel diagnostic agents and vaccines. We used immunoinformatics to analyze 438 M. bovis proteins previously identified with a label-free proteomics analysis of virulent M. bovis HB0801 (P1) and its attenuated P150 strains. The subcellular localization of these proteins was preliminarily screened and 59 proteins were found to be secreted extracellular proteins. Twenty-seven of these proteins contained a large number of predictive T-cell epitopes presented by major histocompatibility complex (MHC) class I and II molecules. Twenty-two of these 27 proteins had a high number of conformational B-cell epitopes, predicted from the corresponding 3D structural templates, including one unique to P1, two unique to P150, and 19 common to both strains. Five proteins were selected for further validation, and two of these, MbovP274 and MbovP570, were successfully expressed and purified. Both were confirmed to be secretory and highly immunogenic proteins that induced a mouse antibody response, reacted with cattle serum positive for M. bovis infection, and significantly increased the production of interleukin 8 (IL-8), IL-12 and interferon γ (IFN-γ) during the secretion of these three cytokines by both M. bovis mutants of these genes. These results should be useful in the development of novel immunological agents against M. bovis infection.

In silico approach for designing a novel recombinant fusion protein as a Candidate Vaccine against HPV

2020 ◽  
Vol 17 ◽  
Author(s):  
Mohsen Sisakht ◽  
Amir Mahmoodzadeh ◽  
Mohammadsaeid Zahedi ◽  
Davood Rostamzadeh ◽  
Amin Moradi Hasan-Abad ◽  
...  
Keyword(s):  
Immune Responses ◽  
Fusion Protein ◽  
In Silico ◽  
Precancerous Lesions ◽  
Candidate Vaccine ◽  
T Cell Epitopes ◽  
Binding Interaction ◽  
Hpv16 E6 ◽  
E7 Proteins

Background: Human papillomavirus (HPV) is the main biological agent causing sexually transmitted diseases (STDs), including precancerous lesions and several types of prevalent cancers. To date, numerous types of vaccines are designed to prevent high-risk HPV. However, their prophylactic effect is not the same and does not clear previous infections. Therefore, there is an urgent need for developing therapeutic vaccines that trigger cell-mediated immune responses for the treatment of HPV. The HPV16 E6 and E7 proteins are ideal targets for vaccine therapy against HPV. Fusion protein vaccines, which include both immunogenic interest protein and an adjuvant for augmenting the immunogenicity effects, are theoretically capable of guarantee the power of the immune system against HPV. Method: A vaccine construct, including HPV16 E6/E7 proteins along with a heat shock protein GP96 (E6/E7-NTGP96 construct), was designed using in silico methods. By the aid of the SWISS-MODEL server, the optimal 3D model of the designed vaccine was selected, followed by physicochemical and molecular parameters were performed using bioinformatics tools. Docking studies were done to evaluate the binding interaction of the vaccine. Allergenicity, immunogenicity, B, and T cell epitopes of the designed construct were predicted. Results: Immunological and structural computational results illustrated that our designed construct is potentially proper for stimulation of cellular and humoral immune responses against HPV. Conclusion: Computational studies showed that the E6/E7-NTGP96 construct is a promising candidate vaccine that needs further in vitro and in vivo evaluations.

In Silico Identification and Molecular Characterization of Extracellular Cathepsin L Proteases from Giardia duodenalis

2020 ◽  
Vol 17 (4) ◽  
pp. 342-351
Author(s):  
Sergio A. Durán-Pérez ◽  
José G. Rendón-Maldonado ◽  
Lucio de Jesús Hernandez-Diaz ◽  
Annete I. Apodaca-Medina ◽  
Maribel Jiménez-Edeza ◽  
...  
Keyword(s):  
In Silico ◽  
Cathepsin L ◽  
Three Dimensional ◽  
Giardia Duodenalis ◽  
Evolutionary Genetics ◽  
Extracellular Proteins ◽  
In Silico Identification ◽  
Dimensional Models ◽  
Three Dimensional Models

Background: The protozoan Giardia duodenalis, which causes giardiasis, is an intestinal parasite that commonly affects humans, mainly pre-school children. Although there are asymptomatic cases, the main clinical features are chronic and acute diarrhea, nausea, abdominal pain, and malabsorption syndrome. Little is currently known about the virulence of the parasite, but some cases of chronic gastrointestinal alterations post-infection have been reported even when the infection was asymptomatic, suggesting that the cathepsin L proteases of the parasite may be involved in the damage at the level of the gastrointestinal mucosa. Objective: The aim of this study was the in silico identification and characterization of extracellular cathepsin L proteases in the proteome of G. duodenalis. Methods: The NP_001903 sequence of cathepsin L protease from Homo sapienswas searched against the Giardia duodenalisproteome. The subcellular localization of Giardia duodenaliscathepsin L proteases was performed in the DeepLoc-1.0 server. The construction of a phylogenetic tree of the extracellular proteins was carried out using the Molecular Evolutionary Genetics Analysis software (MEGA X). The Robetta server was used for the construction of the three-dimensional models. The search for possible inhibitors of the extracellular cathepsin L proteases of Giardia duodenaliswas performed by entering the three-dimensional structures in the FINDSITEcomb drug discovery tool. Results: Based on the amino acid sequence of cathepsin L from Homo sapiens, 8 protein sequences were identified that have in their modular structure the Pept_C1A domain characteristic of cathepsins and two of these proteins (XP_001704423 and XP_001704424) are located extracellularly. Threedimensional models were designed for both extracellular proteins and several inhibitory ligands with a score greater than 0.9 were identified. In vitrostudies are required to corroborate if these two extracellular proteins play a role in the virulence of Giardia duodenalisand to discover ligands that may be useful as therapeutic targets that interfere in the mechanism of pathogenesis generated by the parasite. Conclusion: In silicoanalysis identified two proteins in the Giardia duodenalisprotein repertoire whose characteristics allowed them to be classified as cathepsin L proteases, which may be secreted into the extracellular medium to act as virulence factors. Three-dimensional models of both proteins allowed the identification of inhibitory ligands with a high score. The results suggest that administration of those compounds might be used to block the endopeptidase activity of the extracellular cathepsin L proteases, interfering with the mechanisms of pathogenesis of the protozoan parasite Giardia duodenalis.

Characterizing the effectiveness of COVID-19 mitigation measures: A data-centric approach (Preprint)

2020 ◽  
Author(s):  
Lukman Olagoke ◽  
Ahmet E. Topcu
Keyword(s):  
Control Measure ◽  
Control Measures ◽  
World Health ◽  
Mitigation Measures ◽  
Effective Control ◽  
The World ◽  
Decision Making Processes ◽  
And Performance ◽  
Health Organization ◽  
The Impact

BACKGROUND COVID-19 represents a serious threat to both national health and economic systems. To curb this pandemic, the World Health Organization (WHO) issued a series of COVID-19 public safety guidelines. Different countries around the world initiated different measures in line with the WHO guidelines to mitigate and investigate the spread of COVID-19 in their territories. OBJECTIVE The aim of this paper is to quantitatively evaluate the effectiveness of these control measures using a data-centric approach. METHODS We begin with a simple text analysis of coronavirus-related articles and show that reports on similar outbreaks in the past strongly proposed similar control measures. This reaffirms the fact that these control measures are in order. Subsequently, we propose a simple performance statistic that quantifies general performance and performance under the different measures that were initiated. A density based clustering of based on performance statistic was carried out to group countries based on performance. RESULTS The performance statistic helps evaluate quantitatively the impact of COVID-19 control measures. Countries tend show variability in performance under different control measures. The performance statistic has negative correlation with cases of death which is a useful characteristics for COVID-19 control measure performance analysis. A web-based time-line visualization that enables comparison of performances and cases across continents and subregions is presented. CONCLUSIONS The performance metric is relevant for the analysis of the impact of COVID-19 control measures. This can help caregivers and policymakers identify effective control measures and reduce cases of death due to COVID-19. The interactive web visualizer provides easily digested and quick feedback to augment decision-making processes in the COVID-19 response measures evaluation. CLINICALTRIAL Not Applicable

scholarly journals In silico design and in vitro expression of novel multiepitope DNA constructs based on HIV-1 proteins and Hsp70 T-cell epitopes

2021 ◽  
Author(s):  
Elahe Akbari ◽  
Kimia Kardani ◽  
Ali Namvar ◽  
Soheila Ajdary ◽  
Esmat Mirabzadeh Ardakani ◽  
...  
Keyword(s):  
T Cell ◽  
In Silico ◽  
T Cell Epitopes ◽  
In Vitro Expression ◽  
In Silico Design ◽  
Hiv 1

scholarly journals Effectiveness of Epidemic Preventive Policies and Hospital Strategies in Combating COVID-19 Outbreak in Taiwan

2021 ◽  
Vol 18 (7) ◽  
pp. 3456
Author(s):  
Ting Wan Tan ◽  
Han Ling Tan ◽  
Man Na Chang ◽  
Wen Shu Lin ◽  
Chih Ming Chang
Keyword(s):  
Mortality Rate ◽  
Incidence Rate ◽  
Risk Ratio ◽  
Early Stage ◽  
Control Measures ◽  
Polymerase Chain Reaction Test ◽  
Effective Control ◽  
Nasopharyngeal Swab ◽  
Preventive Strategies ◽  
Epidemic Control

(1) Background: The implementation of effective control measures in a timely fashion is crucial to control the epidemic outbreak of COVID-19. In this study, we aimed to analyze the control measures implemented during the COVID-19 outbreak, as well as evaluating the responses and outcomes at different phases for epidemic control in Taiwan. (2) Methods: This case study reviewed responses to COVID-19 and the effectiveness of a range of control measures implemented for epidemic control in Taiwan and assessed all laboratory-confirmed cases between 11 January until 20 December 2020, inclusive of these dates. The confirmation of COVID-19 infection was defined as the positive result of a reverse-transcriptase–polymerase-chain-reaction test taken from a nasopharyngeal swab. Test results were reported by the Taiwan Centers for Disease Control. The incidence rate, mortality rate, and testing rate were compiled, and the risk ratio was provided to gain insights into the effectiveness of prevention measures. (3) Results and Discussion: This study presents retrospective data on the COVID-19 incidence rate in Taiwan, combined with the vital preventive control measures, in a timeline of the early stage of the epidemic that occurred in Taiwan. The implementation of multiple strategy control measures and the assistance of technologies to control the COVID-19 epidemic in Taiwan led to a relatively slower trend in the outbreak compared to the neighboring countries. In Taiwan, 766 confirmed patients were included, comprised of 88.1% imported cases and 7.2% local transmission cases, within the studied period. The incidence rate of COVID-19 in Taiwan during the studied period was 32 per million people, with a mortality rate of 0.3 per million people. Our analysis showed a significantly raised incidence risk ratio in the countries of interest in comparison to Taiwan during the study period; in the range of 1.9 to 947.5. The outbreak was brought under control through epidemic policies and hospital strategies implemented by the Taiwan Government. (4) Conclusion: Taiwan’s preventive strategies resulted in a drastically lower risk for Taiwan nationals of contracting COVID-19 when new pharmaceutical drug or vaccines were not yet available. The preventive strategies employed by Taiwan could serve as a guide and reference for future epidemic control strategies.

scholarly journals Molecular Identification of Mushroom Species in Italy: An Ongoing Project Aimed at Reinforcing the Control Measures of an Increasingly Appreciated Sustainable Food

2020 ◽  
Vol 13 (1) ◽  
pp. 238
Author(s):  
Alice Giusti ◽  
Enrica Ricci ◽  
Laura Gasperetti ◽  
Marta Galgani ◽  
Luca Polidori ◽  
...  
Keyword(s):  
Selection Process ◽  
Winning Strategy ◽  
Control Measures ◽  
Effective Control ◽  
Mushroom Poisoning ◽  
Clinical Samples ◽  
Similar Species ◽  
Mushroom Species ◽  
Ongoing Research ◽  
Genotypic Analysis

Proper investment in mushroom production (farming and wild mushroom picking activities) may represent a winning strategy for many countries, including Italy, to better face the problems of food security and environmental impact, and to break away from imports, enhancing the local products. However, the risk related to the consumption of poisoning species requires governments to implement or reinforce effective control measures to protect consumers. Mushroom identification by phenotype observation is hardly applicable if morphologically-similar species, non-whole specimens, or clinical samples are involved. Genotypic analysis is a valid alternative. An ongoing research project involving the Experimental Zooprophylactic Institute of Lazio and Tuscany, the regional Mycological Inspectorate, the Tuscany Mycological Groups Association, and the Department of Veterinary Sciences of the University of Pisa aims to reinforce the collaboration among institutions for the management of mushroom poisoning. The core’s project aims to develop an internal genetic database to support the identification of wild and cultivated mushroom species in the Italian territory. The database will include Internal Transcribed Spacer (ITS) sequences retrieved from official databases (the NCBI GenBank and the BOLD system) which are considered to be reliable, after a proper selection process, and sequences from specimens collected directly and identified by expert mycologists. Once it is validated, the database will be available and further implementable by the official network of national laboratories.

scholarly journals Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 607
Author(s):  
Nadeem Ullah ◽  
Ling Hao ◽  
Jo-Lewis Banga Ndzouboukou ◽  
Shiyun Chen ◽  
Yaqi Wu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Control Strategies ◽  
Multidrug Resistant ◽  
Differentially Expressed ◽  
Effective Control ◽  
Drug Resistant ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Candidate Target

Rifampicin (RIF) is one of the most important first-line anti-tuberculosis (TB) drugs, and more than 90% of RIF-resistant (RR) Mycobacterium tuberculosis clinical isolates belong to multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. In order to identify specific candidate target proteins as diagnostic markers or drug targets, differential protein expression between drug-sensitive (DS) and drug-resistant (DR) strains remains to be investigated. In the present study, a label-free, quantitative proteomics technique was performed to compare the proteome of DS, RR, MDR, and XDR clinical strains. We found iniC, Rv2141c, folB, and Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS strain. In addition, lprF, mce2R, mce2B, and Rv2627c were specifically expressed in the three DR strains, and 41 proteins were not detected in the DS strain. Functional category showed that these differentially expressed proteins were mainly involved in the cell wall and cell processes. When compared to the RR strain, Rv2272, smtB, lpqB, icd1, and folK were up-regulated, while esxK, PPE19, Rv1534, rpmI, ureA, tpx, mpt64, frr, Rv3678c, esxB, esxA, and espL were down-regulated in both MDR and XDR strains. Additionally, nrp, PPE3, mntH, Rv1188, Rv1473, nadB, PPE36, and sseA were specifically expressed in both MDR and XDR strains, whereas 292 proteins were not identified when compared to the RR strain. When compared between MDR and XDR strains, 52 proteins were up-regulated, while 45 proteins were down-regulated in the XDR strain. 316 proteins were especially expressed in the XDR strain, while 92 proteins were especially detected in the MDR strain. Protein interaction networks further revealed the mechanism of their involvement in virulence and drug resistance. Therefore, these differentially expressed proteins are of great significance for exploring effective control strategies of DR-TB.

scholarly journals Timing and Route of Contamination of Patient Rooms With Healthcare-Associated Pathogens

2020 ◽  
Vol 41 (S1) ◽  
pp. s412-s412
Author(s):  
Sarah Redmond ◽  
Jennifer Cadnum ◽  
Basya Pearlmutter ◽  
Natalia Pinto Herrera ◽  
Curtis Donskey
Keyword(s):  
Acute Care Hospital ◽  
Current Control ◽  
Pathogen Transmission ◽  
Control Measures ◽  
Effective Control ◽  
Portable Devices ◽  
Care Hospital ◽  
Spa Typing ◽  
Persistent Problem ◽  
Healthcare Associated

Background: Transmission of healthcare-associated pathogens such as Clostridioides difficile and methicillin-resistant Staphylococcus aureus (MRSA) is a persistent problem in healthcare facilities despite current control measures. A better understanding of the routes of pathogen transmission is needed to develop effective control measures. Methods: We conducted an observational cohort study in an acute-care hospital to identify the timing and route of transfer of pathogens to rooms of newly admitted patients with negative MRSA nares results and no known carriage of other healthcare-associated pathogens. Rooms were thoroughly cleaned and disinfected prior to patient admission. Interactions of patients with personnel and portable equipment were observed, and serial cultures for pathogens were collected from the skin of patients and from surfaces, including those observed to come in contact with personnel and equipment. For MRSA, spa typing was used to determine relatedness of patient and environmental isolates. Results: For the 17 patients enrolled, 1 or more environmental cultures became positive for MRSA in rooms of 10 patients (59%), for C. difficile in rooms of 2 patients (12%) and for vancomycin-resistant enterococci (VRE) in rooms of 2 patients (12%). The patients interacted with an average of 2.4 personnel and 0.6 portable devices per hour of observation. As shown in Figure 1, MRSA contamination of the floor occurred rapidly as personnel entered the room. In a subset of patients, MRSA was subsequently recovered from patients’ socks and bedding and ultimately from the high-touch surfaces in the room (tray table, call button, bedrail). For several patients, MRSA isolates recovered from the floor had the same spa type as isolates subsequently recovered from other sites (eg, socks, bedding, and/or high touch surfaces). The direct transfer of healthcare-associated pathogens from personnel or equipment to high-touch surfaces was not detected. Conclusions: Healthcare-associated pathogens rapidly accumulate on the floor of patient rooms and can be transferred to the socks and bedding of patients and to high-touch surfaces. Healthcare facility floors may be an underappreciated source of pathogen dissemination not addressed by current infection control measures.Funding: NoneDisclosures: None

scholarly journals Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cui Zhang ◽  
Cihan Oguz ◽  
Sue Huse ◽  
Lu Xia ◽  
Jian Wu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Malaria Parasite ◽  
Vaccine Development ◽  
De Novo ◽  
Gene Families ◽  
Plasmodium Yoelii ◽  
Control Measures ◽  
Effective Control ◽  
Malaria Parasites ◽  
Rodent Malaria

Abstract Background Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii 17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated. Results We performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains. Conclusions The genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria.

Isolation and characterization of Hena1 – a novel Erwinia amylovora bacteriophage

2020 ◽  
Vol 367 (9) ◽  
Author(s):  
Natalya V Besarab ◽  
Artur E Akhremchuk ◽  
Maryna A Zlatohurska ◽  
Liudmyla V Romaniuk ◽  
Leonid N Valentovich ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Fire Blight ◽  
Antimicrobial Agents ◽  
Erwinia Amylovora ◽  
Gc Content ◽  
Control Measures ◽  
Effective Control ◽  
Lytic Phage ◽  
Trna Genes ◽  
Isolation And Characterization

ABSTRACT Fire blight, caused by plant pathogenic bacterium Erwinia amylovora, is one of the most important diseases of Rosaceae plants. Due to the lack of effective control measures, fire blight infections pose a recurrent threat on agricultural production worldwide. Recently, bacterial viruses, or bacteriophages, have been proposed as environmentally friendly natural antimicrobial agents for fire blight control. Here, we isolated a novel bacteriophage Hena1 with activity against E. amylovora. Further analysis revealed that Hena1 is a narrow-host-range lytic phage belonging to Myoviridae family. Its genome consists of a linear 148,842 bp dsDNA (48.42% GC content) encoding 240 ORFs and 23 tRNA genes. Based on virion structure and genomic composition, Hena1 was classified as a new species of bacteriophage subfamily Vequintavirinae. The comprehensive analysis of Hena1 genome may provide further insights into evolution of bacteriophages infecting plant pathogenic bacteria.

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