scholarly journals Non-Synonymous Mutation Analysis in SARS-CoV-2 Variants Isolated from Humans and Prediction of Conserved Linear Antibody Epitopes for Use in Country-wise Epitope-Based Vaccine Development

2020 ◽  
Author(s):  
Pankaj Kumar ◽  
Kunal Sharma ◽  
Naima Noor Khan ◽  
Hamza Bin Sana ◽  
Mohammad Ali Khan
Keyword(s):  
Large Scale ◽  
Vaccine Development ◽  
Time Window ◽  
High Rate ◽  
Synonymous Mutation ◽  
Large Outbreak ◽  
Therapeutic Development ◽  
Sporadic Cases ◽  
Potential Vaccine ◽  
Antibody Epitopes

COVID-19 pandemic has caused a large-scale havoc in almost every country across the globe, putting major challenges for the healthcare system in many parts of the world. Several of the laboratories are running in the race with undying efforts for developing potential vaccine, drugs or therapeutics to treat or prevent the infection. However, with the limited time window and high rate of infection, the task is very big for humanity to find a cure. With hundreds of genomic data of SARS-CoV-2 virus isolates from humans are being submitted almost every day, it is coming into knowledge that virus is mutating, slower in countries with sporadic cases, but higher in countries experiencing large outbreak. These types of mutations in virus may bring challenges in vaccine or therapeutic development for use in each and every country, as each hotspot region may have their own pattern of mutations in virus with ongoing outbreak. In our current study, we retrieved non-synonymous mutation data of around 12,225 SARS-CoV-2 virus samples isolated from humans globally, and discovered all mutations that are collectively happening in antibody epitope regions of the virus country-wise. We found a few numbers of epitope regions in SARS-CoV-2 that are highly conserved collectively in all variants and may be used for epitope-based vaccine development for whole world. We also found epitope regions that are conserved collectively in SARS-CoV-2 variants country-wise and can be used for customized epitope-based vaccine development in each different country.

scholarly journals Profiling the Immune Vulnerability Landscape of the 2019 Novel Coronavirus

2020 ◽  
Author(s):  
James Zhu ◽  
Jiwoong Kim ◽  
Xue Xiao ◽  
Yunguan Wang ◽  
Danni Luo ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Peptide Vaccine ◽  
Immune Clearance ◽  
Clearance Mechanism ◽  
Therapeutic Development ◽  
Antiviral Antibody ◽  
Research Outcome ◽  
The Moment ◽  
Novel Coronavirus ◽  
Antibody Epitopes

The outbreak of the 2019 Novel Coronavirus (2019-nCoV) has rapidly spread from Wuhan, China to multiple countries, causing staggering number of infections and deaths. A systematic profiling of the immune vulnerability landscape of 2019-nCoV is lacking, which can bring critical insights into the immune clearance mechanism, peptide vaccine development, and antiviral antibody development. In this study, we predicted the potential of all the 2019-nCoV viral proteins to induce class I and II MHC presentation and form linear antibody epitopes. We showed that the enrichment for T cell and B cell epitopes is not uniform on the viral genome, with several focused regions that generate abundant epitopes and may be more targetable. We showed that genetic variations in 2019-nCoV, though fewer for the moment, already follow the pattern of mutations in related coronaviruses, and could alter the immune vulnerability landscape of this virus, which should be considered in the development of therapies. We create an online database to broadly share our research outcome. Overall, we present an immunological resource for 2019-nCoV that could significantly promote both therapeutic development and mechanistic research.

scholarly journals Computational Vaccinology: An Important Strategy to Discover New PotentialS. mansoniVaccine Candidates

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Carina S. Pinheiro ◽  
Vicente P. Martins ◽  
Natan R. G. Assis ◽  
Bárbara C. P. Figueiredo ◽  
Suellen B. Morais ◽  
...  
Keyword(s):  
Schistosoma Mansoni ◽  
Large Scale ◽  
Vaccine Development ◽  
Control Strategies ◽  
Schistosomiasis Control ◽  
Vaccine Candidates ◽  
The Past ◽  
Important Field ◽  
Potential Vaccine

The flatwormSchistosoma mansoniis a blood fluke parasite that causes schistosomiasis, a debilitating disease that occurs throughout the developing world. Current schistosomiasis control strategies are mainly based on chemotherapy, but many researchers believe that the best long-term strategy to control schistosomiasis is through immunization with an antischistosomiasis vaccine combined with drug treatment. Several papers onSchistosoma mansonivaccine and drug development have been published in the past few years, representing an important field of study. The advent of technologies that allow large-scale studies of genes and proteins had a remarkable impact on the screening of new and potential vaccine candidates in schistosomiasis. In this postgenomic scenario, bioinformatic technologies have emerged as important tools to mine transcriptomic, genomic, and proteomic databases. These new perspectives are leading to a new round of rational vaccine development. Herein, we discuss different strategies to identify potentialS. mansonivaccine candidates using computational vaccinology.

scholarly journals High-Rate Transition Metal-based Cathode Materials for Battery-Supercapacitor Hybrid Devices

2021 ◽  
Author(s):  
Cong Wang ◽  
Zehao Song ◽  
Pei Shi ◽  
Lin Lv ◽  
Houzhao Wan ◽  
...  
Keyword(s):  
Large Scale ◽  
Rapid Development ◽  
Electronic Devices ◽  
High Rate ◽  
Specific Power ◽  
Energy Storage Devices ◽  
Storage Devices ◽  
Electrochemical Devices ◽  
Hybrid Devices ◽  
Scale Grid

With the rapid development of portable electronic devices, electric vehicles and large-scale grid energy storage devices, it needs to reinforce specific energy and specific power of related electrochemical devices meeting...

scholarly journals mRNA-Based Vaccines

Vaccines ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 390
Author(s):  
Frank Kowalzik ◽  
Daniel Schreiner ◽  
Christian Jensen ◽  
Daniel Teschner ◽  
Stephan Gehring ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Vaccine Development ◽  
Effective Means ◽  
Cost Effective ◽  
Clinical Applications ◽  
Cell Mediated Immunity ◽  
Healthy Individuals ◽  
Emerging Pathogens ◽  
Cell Genome

Increases in the world’s population and population density promote the spread of emerging pathogens. Vaccines are the most cost-effective means of preventing this spread. Traditional methods used to identify and produce new vaccines are not adequate, in most instances, to ensure global protection. New technologies are urgently needed to expedite large scale vaccine development. mRNA-based vaccines promise to meet this need. mRNA-based vaccines exhibit a number of potential advantages relative to conventional vaccines, namely they (1) involve neither infectious elements nor a risk of stable integration into the host cell genome; (2) generate humoral and cell-mediated immunity; (3) are well-tolerated by healthy individuals; and (4) are less expensive and produced more rapidly by processes that are readily standardized and scaled-up, improving responsiveness to large emerging outbreaks. Multiple mRNA vaccine platforms have demonstrated efficacy in preventing infectious diseases and treating several types of cancers in humans as well as animal models. This review describes the factors that contribute to maximizing the production of effective mRNA vaccine transcripts and delivery systems, and the clinical applications are discussed in detail.

scholarly journals SARS-CoV-2 vaccines strategies: a comprehensive review of phase 3 candidates

npj Vaccines ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Nikolaos C. Kyriakidis ◽  
Andrés López-Cortés ◽  
Eduardo Vásconez González ◽  
Alejandra Barreto Grimaldos ◽  
Esteban Ortiz Prado
Keyword(s):  
Neutralizing Antibodies ◽  
Large Scale ◽  
Vaccine Development ◽  
Rna Virus ◽  
Protein S ◽  
Effective Vaccine ◽  
Phase 3 ◽  
Vaccine Candidates ◽  
Advantages And Disadvantages ◽  
The World

AbstractThe new SARS-CoV-2 virus is an RNA virus that belongs to the Coronaviridae family and causes COVID-19 disease. The newly sequenced virus appears to originate in China and rapidly spread throughout the world, becoming a pandemic that, until January 5th, 2021, has caused more than 1,866,000 deaths. Hence, laboratories worldwide are developing an effective vaccine against this disease, which will be essential to reduce morbidity and mortality. Currently, there more than 64 vaccine candidates, most of them aiming to induce neutralizing antibodies against the spike protein (S). These antibodies will prevent uptake through the human ACE-2 receptor, thereby limiting viral entrance. Different vaccine platforms are being used for vaccine development, each one presenting several advantages and disadvantages. Thus far, thirteen vaccine candidates are being tested in Phase 3 clinical trials; therefore, it is closer to receiving approval or authorization for large-scale immunizations.

scholarly journals Hydrology influences breeding time in the white-throated dipper

BMC Ecology ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Anna L. K. Nilsson ◽  
Thomas Skaugen ◽  
Trond Reitan ◽  
Jan Henning L’Abée-Lund ◽  
Marlène Gamelon ◽  
...  
Keyword(s):  
Climate Change ◽  
River Discharge ◽  
Large Scale ◽  
Time Window ◽  
River System ◽  
Open Water ◽  
Local Conditions ◽  
Environmental Indices ◽  
Groundwater Levels ◽  
Breeding Time

Abstract Background Earlier breeding is one of the strongest responses to global change in birds and is a key factor determining reproductive success. In most studies of climate effects, the focus has been on large-scale environmental indices or temperature averaged over large geographical areas, neglecting that animals are affected by the local conditions in their home ranges. In riverine ecosystems, climate change is altering the flow regime, in addition to changes resulting from the increasing demand for renewable and clean hydropower. Together with increasing temperatures, this can lead to shifts in the time window available for successful breeding of birds associated with the riverine habitat. Here, we investigated specifically how the environmental conditions at the territory level influence timing of breeding in a passerine bird with an aquatic lifestyle, the white-throated dipper Cinclus cinclus. We relate daily river discharge and other important hydrological parameters, to a long-term dataset of breeding phenology (1978–2015) in a natural river system. Results Dippers bred earlier when winter river discharge and groundwater levels in the weeks prior to breeding were high, and when there was little snow in the catchment area. Breeding was also earlier at lower altitudes, although the effect dramatically declined over the period. This suggests that territories at higher altitudes had more open water in winter later in the study period, which permitted early breeding also here. Unexpectedly, the largest effect inducing earlier breeding time was territory river discharge during the winter months and not immediately prior to breeding. The territory river discharge also increased during the study period. Conclusions The observed earlier breeding can thus be interpreted as a response to climate change. Measuring environmental variation at the scale of the territory thus provides detailed information about the interactions between organisms and the abiotic environment.

scholarly journals Rapid evolution at the Drosophila telomere: transposable element dynamics at an intrinsically unstable locus

Genetics ◽  
2020 ◽  
Vol 217 (2) ◽  
Author(s):  
Michael P McGurk ◽  
Anne-Marie Dion-Côté ◽  
Daniel A Barbash
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Insertion Site ◽  
Rapid Evolution ◽  
Interspecific Variation ◽  
High Rate ◽  
Evolutionary Strategy ◽  
Control Mechanisms ◽  
Genetic Conflict ◽  
Number Variation

AbstractDrosophila telomeres have been maintained by three families of active transposable elements (TEs), HeT-A, TAHRE, and TART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85  Drosophila melanogaster genomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we instead suggest that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than one-third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes, with niche specialization and telomere instability being previously underappreciated and likely predominant.

Neurofeedback for Opioid Dependent Patients in an Outpatient Setting: A Pilot Feasibility Study

2021 ◽  
Author(s):  
Helena A. Rempala ◽  
Justin A. Barterian
Keyword(s):  
Large Scale ◽  
The United States ◽  
Outpatient Setting ◽  
Opioid Use Disorder ◽  
High Rate ◽  
Treatment Center ◽  
Opioid Use ◽  
Treatment As Usual ◽  
Factors Affecting ◽  
Study Approach

Abstract Background: Neurofeedback (NF) has been described as “probably efficacious” when used in conjunction with other interventions for substance use disorders, including the most recent studies in population of individuals with opioid use disorder. Despite these promising outcomes, the seriousness of the opioid epidemic, and the high rate of relapse even with the most effective medication-assisted maintenance treatments NF continues to be an under-researched treatment modality. This article explores factors that affected the feasibility of adding Alpha/Theta Neurofeedback to treatment as usual for opioid dependence in an outpatient urban treatment center. The study strived to replicate previous research completed in Iran that found benefits of NF for opioid dependence.Methods: Out of approximately two dozen patients eligible for Alpha/Theta NF, about 60% (n=15) agreed to participate; however, only 2 participants completed treatment. The rates of enrollment in response to active treatment were monitored. Results: The 4 factors affecting feasibility were: 1) the time commitment required of participants, 2) ineffectiveness of standard incentives to promote participation, 3) delayed effects of training, and 4) the length and number of treatments required.Conclusion: The findings indicate a large scale study examining the use of NF for the treatment of opioid use disorder in the United States will likely be difficult to accomplish without modification to the traditional randomized control study approach and suggests challenges to the implementation of this treatment in an outpatient setting.

Sign in / Sign up

Export Citation Format

Share Document