scholarly journals A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicole Balasco ◽  
Gianluca Damaggio ◽  
Luciana Esposito ◽  
Flavia Villani ◽  
Rita Berisio ◽  
...  
Keyword(s):  
Structure Function ◽  
Global Analysis ◽  
First Year ◽  
Virus Structure ◽  
Hydrophobic Residues ◽  
Viral Genomes ◽  
Substitution Matrices ◽  
Great Relevance ◽  
Three Stages ◽  
Amino Acid Mutations

AbstractThe ability of SARS-CoV-2 to rapidly mutate represents a remarkable complicancy. Quantitative evaluations of the effects that these mutations have on the virus structure/function is of great relevance and the availability of a large number of SARS-CoV-2 sequences since the early phases of the pandemic represents a unique opportunity to follow the adaptation of the virus to humans. Here, we evaluated the SARS-CoV-2 amino acid mutations and their progression by analyzing publicly available viral genomes at three stages of the pandemic (2020 March 15th and October 7th, 2021 February 7th). Mutations were classified in conservative and non-conservative based on the probability to be accepted during the evolution according to the Point Accepted Mutation substitution matrices and on the similarity of the encoding codons. We found that the most frequent substitutions are T > I, L > F, and A > V and we observe accumulation of hydrophobic residues. These findings are consistent among the three stages analyzed. We also found that non-conservative mutations are less frequent than conservative ones. This finding may be ascribed to a progressive adaptation of the virus to the host. In conclusion, the present study provides indications of the early evolution of the virus and tools for the global and genome-specific evaluation of the possible impact of mutations on the structure/function of SARS-CoV-2 variants.

scholarly journals Gamificação no ensino de astronomia

2020 ◽  
Vol 4 (4) ◽  
pp. 623-639
Author(s):  
Roger Broetto Rocha ◽  
Lucio Martins Fassini Da Silva ◽  
Cleiton Kenup Piumbini ◽  
Luiz Otavio Buffon ◽  
Marconi Frank Barros
Keyword(s):  
High School ◽  
First Year ◽  
The Third ◽  
Third Stage ◽  
The Subject ◽  
Three Stages ◽  
The City

Resumo: Este trabalho tem por objetivo relatar uma atividade didática, realizada no Programa Institucional de Bolsas de Iniciação à Docência (PIBID), envolvendo o ensino de Astronomia numa turma do primeiro ano do ensino médio de uma escola do município de Vitória, ES. A atividade foi planejada e executada pelo subprojeto do Curso de Licenciatura em Física do IFES – Campus Cariacica. A metodologia foi baseada na Gamificação aplicada ao ensino-aprendizagem. A intervenção ocorreu em três etapas, sendo a primeira realizada em dois encontros, através de apresentações dialogadas sobre Astronomia usando slides e gifs, a segunda consistiu na aplicação da Gamificação através de um jogo e finalizando com a terceira etapa, foi aplicado um pequeno questionário. Ao final houve um momento de avaliação e as análises constataram que o ensino de Astronomia através da atividade gamificada do jogo conseguiu motivar os alunos, despertar o interesse pelo assunto e produzir indícios de aprendizagem.Palavras-chave: Gamificação em sala de aula; Ensino de Astronomia; PIBID. Gamification in astronomy teachingAbstract: This work aims to report on a didactic activity, carried out in the Institutional Program for Teaching Initiation Scholarships (PIBID), involving the teaching of Astronomy in a class of the first year of high school at a school in the city of Vitória, ES. The activity was carried out by the subproject of the Physics Degree Course at IFES - Campus Cariacica. The intervention took place in three stages, the first being in two meetings, through dialogued presentations on Astronomy using slides and gifs, the second consisted of the application of Gamification through a game and ending with the third stage, a small questionnaire was applied. At the end there was a moment of evaluation and the analyzes found that the teaching of Astronomy through the gamified activity of the game managed to motivate students, arouse interest in the subject and produce evidence of learning.Keywords: Gamification activity in the classroom; Astronomy teaching; PIBID. 

A Nested Analysis of Factors Affecting Bachelor's Degree Completion

2003 ◽  
Vol 4 (4) ◽  
pp. 407-435 ◽  
Author(s):  
Stephen L. DesJardins ◽  
Dong-Ok Kim ◽  
Chester S. Rzonca
Keyword(s):  
Degree Completion ◽  
College Major ◽  
Bachelor's Degree ◽  
First Year ◽  
University Of Iowa ◽  
Factors Affecting ◽  
Three Stages ◽  
The University ◽  
Nested Analysis ◽  
Sequential Nature

The main objective of this study was to examine the effects of selected factors on retention, graduation, and timely bachelor's degree completion at The University of Iowa. An additional purpose was to identify the stage-varying effects of selected variables. Reflecting the sequential nature of bachelor's degree completion, this study focused on three stages of students' progress to graduation: 1) dropout vs. persistence in the first year, 2) graduation vs. failure to graduate among first year persisters, and 3) graduation in four years or less vs. graduation in five years or more. We found that college academic performance, pre-matriculation academic achievement, and college major were the most important variables in explaining success at The University of Iowa. We also found fairly consistent results across the three models.

scholarly journals Fusion surface structure, function, and dynamics of gamete fusogen HAP2

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Juan Feng ◽  
Xianchi Dong ◽  
Jennifer Pinello ◽  
Jun Zhang ◽  
Chafen Lu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Function ◽  
Surface Structure ◽  
Outer Surface ◽  
Fold Axis ◽  
Hydrogen Deuterium Exchange ◽  
Apical Portion ◽  
Gamete Fusion ◽  
Hydrophobic Residues ◽  
Hydrogen Deuterium

HAP2 is a class II gamete fusogen in many eukaryotic kingdoms. A crystal structure of Chlamydomonas HAP2 shows a trimeric fusion state. Domains D1, D2.1 and D2.2 line the 3-fold axis; D3 and a stem pack against the outer surface. Surprisingly, hydrogen-deuterium exchange shows that surfaces of D1, D2.2 and D3 closest to the 3-fold axis are more dynamic than exposed surfaces. Three fusion helices in the fusion loops of each monomer expose hydrophobic residues at the trimer apex that are splayed from the 3-fold axis, leaving a solvent-filled cavity between the fusion loops in each monomer. At the base of the two fusion loops, Arg185 docks in a carbonyl cage. Comparisons to other structures, dynamics, and the greater effect on Chlamydomonas gamete fusion of mutation of axis-proximal than axis-distal fusion helices suggest that the apical portion of each monomer could tilt toward the 3-fold axis with merger of the fusion helices into a common fusion surface.

scholarly journals Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 516 ◽  
Author(s):  
Kentaro Tohma ◽  
Michael Kulka ◽  
Suzie Coughlan ◽  
Kim Y. Green ◽  
Gabriel I. Parra
Keyword(s):  
Evolutionary Dynamics ◽  
Age Groups ◽  
Similar Rate ◽  
Full Length ◽  
Phylogenetic Clustering ◽  
Sequencing Platform ◽  
Viral Genomes ◽  
Amino Acid Mutations ◽  
Genomic Regions ◽  
Full Length Genome

Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.

scholarly journals Internalizing Client-Centredness in Occupational Therapy Students

2014 ◽  
Vol 4 (2) ◽  
Author(s):  
Jacquie Ripat ◽  
Pamela Wener ◽  
Kendra Dobinson ◽  
Cynthia Yamamoto
Keyword(s):  
Health Care ◽  
Occupational Therapy ◽  
Interprofessional Education ◽  
Interprofessional Collaboration ◽  
First Year ◽  
Health Care Students ◽  
The Core ◽  
Occupational Therapy Students ◽  
Three Stages ◽  
Push And Pull

Background: Pre-licensure interprofessional education prepares students for collaborative client-centred practice. However, most interprofessional educational efforts are aimed at developing the collaborative component of practice. The purpose of this article is to share the findings of a study that explored occupational therapy students’ client-centred development, in order to inform other pre-licensure educators about integrating client-centredness into uni- and interprofessional education contexts.Methods and Findings: Twenty-nine participants were recruited from each of three stages assumed to be representative of occupational therapy client-centred development in each of the two years of the educational program and during the first year of practice. Semi-structured focus groups were used to capture the participants’ experiences. The core emergent theme, internalizing client-centredness, included three main processes: identifying occupational therapy as a client-centred profession, engaging in the push and pull of client-centredness, and defining self as a client-centred practitioner.Conclusions: Educators of pre-licensure health care students should deliberately focus on client-centredness in their uni- and interprofessional education curricula; the authors offer examples of curricular opportunities focused on internalizing client-centredness. Enabling health care students to internalize client-centredness may be an important aspect of developing practitioners who are prepared to enact interprofessional collaboration for client-centred practice.

scholarly journals A Global Analysis of Evolutionary Conservation among Known and Predicted Gammaherpesvirus MicroRNAs

2009 ◽  
Vol 84 (2) ◽  
pp. 716-728 ◽  
Author(s):  
Nicole Walz ◽  
Thomas Christalla ◽  
Uwe Tessmer ◽  
Adam Grundhoff
Keyword(s):  
Global Analysis ◽  
Japanese Macaque ◽  
Computational Prediction ◽  
Evolutionary Conservation ◽  
Viral Genomes ◽  
Small Noncoding Rnas ◽  
Barr Virus ◽  
Large Numbers ◽  
Evolutionarily Conserved ◽  
Epstein Barr

ABSTRACT MicroRNAs (miRNAs) are small, noncoding RNAs which posttranscriptionally regulate gene expression. The current release of the miRNA registry lists 16 viruses which encode a total of 146 miRNA hairpins. Strikingly, 139 of these are encoded by members of the herpesvirus family, suggesting an important role for miRNAs in the herpesvirus life cycle. However, with the exception of 7 miRNA hairpins known to be shared by Epstein-Barr virus (EBV) and the closely related rhesus lymphocryptovirus (rLCV), the known herpesvirus miRNAs show little evidence of evolutionary conservation. We have performed a global analysis of miRNA conservation among gammaherpesviruses which is not limited to family members known to encode miRNAs but includes also those which have not been previously analyzed. For this purpose, we have performed a computational prediction of miRNA candidates of all fully sequenced gammaherpesvirus genomes, followed by sequence/structure alignments. Our results indicate that gammaherpesvirus miRNA conservation is limited to two pairs of viral genomes. One is the already-known case of EBV and rLCV. These viruses, however, share significantly more miRNAs than previously thought, as we identified and experimentally verified 10 novel conserved as well as 7 novel nonconserved rLCV pre-miRNA hairpins. The second case consists of rhesus rhadinovirus (RRV), which is predicted to share at least 9 pre-miRNAs with the closely related Japanese macaque herpesvirus (JMHV). Although several other gammaherpesviruses are predicted to encode large numbers of clustered miRNAs at conserved genomic loci, no further examples of evolutionarily conserved miRNA sequences were found.

Viral endomyocardial infection in the 1st year post transplant is associated with persistent inflammation in children who have undergone cardiac transplant

2013 ◽  
Vol 24 (2) ◽  
pp. 331-336
Author(s):  
Kimberly Molina ◽  
Susan Denfield ◽  
Yuxin Fan ◽  
Mousumi Moulik ◽  
Jeffrey Towbin ◽  
...  
Keyword(s):  
Graft Loss ◽  
Resistance Index ◽  
First Year ◽  
Cardiac Transplant ◽  
Viral Genomes ◽  
Post Transplant ◽  
Persistent Inflammation ◽  
Pulmonary Vascular Resistance Index ◽  
Early Graft ◽  
Texas Heart Institute

AbstractBackground: Viral genome in cardiac allograft has been associated with early graft loss in children who have undergone cardiac transplant from unknown mechanisms. Methods: This study is a retrospective review of children who have undergone cardiac transplant at a single institution from 1/2004 to 5/2008. Patients underwent cardiac catheterisations with endomyocardial biopsies to evaluate for rejection – graded on Texas Heart Institute scale – and the presence of virus by polymerase chain reaction. Patients with virus identified during the first year post transplant were compared at 1 year post transplant with virus-free patients. Results: The cohort comprised 59 patients, and the median age at transplant was 5.1 years. Viral genomes were isolated from 18 (31%) patients. The PCR + group had increased inflammation on endomyocardial biopsies, with a median score of 4 (ISHLT IR) versus 1 (ISHLT 1R) in the PCR – group (p = 0.014). The PCR + group had a similar cardiac index (median 3.7 ml/min/m2), pulmonary capillary wedge pressure (median 10 mmHg), and pulmonary vascular resistance index (median 1.7 U m2) comparatively. PCR + patients were more likely to have experienced an episode of rejection (p = 0.004). Conclusions: Children who developed viral endomyocardial infections after a cardiac transplant have increased allograft inflammation compared with virus-free patients. However, the haemodynamic profile is similar between the groups. The ongoing subclinical inflammation may contribute to the early graft loss associated with these patients.

scholarly journals Emergence of norovirus strains: A tale of two genes

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Gabriel I Parra
Keyword(s):  
Mammalian Species ◽  
Point Mutations ◽  
Viral Genomes ◽  
Low Levels ◽  
Amino Acid Mutations ◽  
Capsid Protein Vp1 ◽  
Different Strains ◽  
Host Virus Interactions ◽  
Virus Interactions ◽  
Limited Duration

Abstract Noroviruses are a very diverse group of viruses that infect different mammalian species. In humans, norovirus is a major cause of acute gastroenteritis. Multiple norovirus infections can occur in a lifetime as the result of limited duration of acquired immunity and cross-protection among different strains. A combination of advances in sequencing methods and improvements on surveillance has provided new insights into norovirus diversification and emergence. The generation of diverse norovirus strains has been associated with (1) point mutations on two different genes: ORF1, encoding the non-structural proteins, and ORF2, encoding the major capsid protein (VP1); and (2) recombination events that create chimeric viruses. While both mechanisms are exploited by all norovirus strains, individual genotypes utilize each mechanism differently to emerge and persist in the human population. GII.4 noroviruses (the most prevalent genotype in humans) present an accumulation of amino acid mutations on VP1 resulting in the chronological emergence of new variants. In contrast, non-GII.4 noroviruses present co-circulation of different variants over long periods with limited changes on their VP1. Notably, genetic diversity of non-GII.4 noroviruses is mostly related to the high number of recombinant strains detected in humans. While it is difficult to determine the precise mechanism of emergence of epidemic noroviruses, observations point to multiple factors that include host-virus interactions and changes on two regions of the genome (ORF1 and ORF2). Larger datasets of viral genomes are needed to facilitate comparison of epidemic strains and those circulating at low levels in the population. This will provide a better understanding of the mechanism of norovirus emergence and persistence.

scholarly journals Understanding Transmedia Music on YouTube through Disney Storytelling

2021 ◽  
Vol 13 (7) ◽  
pp. 3667
Author(s):  
Arantxa Vizcaíno-Verdú ◽  
Ignacio Aguaded ◽  
Paloma Contreras-Pulido
Keyword(s):  
Social Media ◽  
Statistical Test ◽  
Human Interaction ◽  
Cultural Industries ◽  
Contemporary Society ◽  
Transmedia Storytelling ◽  
Great Relevance ◽  
Three Stages ◽  
Original Story ◽  
The Impact

Transmedia storytelling has been integrated into contemporary society through social media, where influencers have enabled the building of worlds. Within this environment of human-interaction, fiction and converging social realities have become an essential tool to tell stories. On YouTube, storytelling has expanded to music, where cover videos take on great relevance. The aim of this study is to understand the transmedia music phenomenon due to the impact of music on the platform. To this end, we applied a methodology that stemmed from Grounded Theory principles in the analysis of 300 Disney animation song covers in three stages: (1) deductive and inductive codebook development; (2) social network analysis; and (3) statistical test. The results showed that youtubers highlight specific audiovisual codes from the film and cultural industries. Furthermore, we observed these productions often display configurations that expand the original story through performance, location, costumes, make-up, among others. We argue that, on the digital sphere, a sustainable transmedia music paradigm is developing, where performers construct more meaningful and valuable stories.

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