1,721,042 research outputs found
Stalking influenza by vaccination with pre-fusion headless HA mini-stem for broadly reactive antibodies
No full textBackground: Influenza vaccine has been available for over 70 years, yet influenza still causes epidemics or pandemic with substantial morbidity and mortality. The protective responses induced by current human influenza vaccines still primarily depend on vaccine-induced neutralizing antibodies
(nAbs) against the HA head. However, the continually evolving influenza virus evades herd immunity induced through natural infection and vaccination by means of antigenic drift and shift. These antigenic drift and shift events render vaccine stockpiling unviable in case of an outbreak or pandemic. In addition, a major shortcoming of current influenza vaccines is its long production time because of existing egg-based or cell-based vaccine manufactory pipelines. Thus, these factors combined necessitate the development of novel influenza vaccine with increased breadth of protection and potential for rapid production and deployment.
Method: Recent studies indicated the conserved stem domain contains a greater proportion of vulnerable sites targeted by broadly neutralizing antibodies. Importantly, anti-stem broadly neutralizing antibodies are detectable in some individuals at a low level, suggesting they can be induced
naturally by infection and optimized by vaccination. Here, we reported the design of a bacterially expressed polypeptide that mimics a H5 HA stem (i.e. group 1 HA) in the pre-fusion conformation by protein minimization.
Results: The absent of HA head domain of this protein could focus host’s antibody responses toward the HA stem. The HA mini-stem folded as a trimer and it was resistant to thermal/chemical stress. It bound to various broadly neutralizing HA stem-specific antibodies with high affinity. Mice vaccinated
with the group 1 HA mini-stems were protected from morbidity and mortality against lethal challenge by group 1 and group 2 influenza viruses, the first report of cross-group protection. Vaccine-induced antibodies showed broad HA reactivity and no antibody-dependent enhancement activity. Protection
from lethal infection was attributed to a broadly reactive antibody response that was able to provide passive protection.
Conclusion: The HA mini-stem vaccination can elicit cross-reactive antibody responses that confer robust protection against lethal heterologous influenza A virus challenge from both group 1 and 2 viruses. The recombinant protein is highly stable at room temperature and it can be readily produced in large scale. Our study provides a promising foundation for developing a HA stem-based ‘universal’ influenza vaccine
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Vaccine induced selection pressure on seasonal influenza virus in mice
No full textInfluenza viruses are characterised by their ability to overcome species barriers and evade host immunity, at times with devastating consequences. Within individuals, influenza virus populations exist as a closely related quasispecies that may evolve to exhibit diverse antigenicity. Protection conferred by seasonal influenza vaccines against disease is punctuated by rapid accumulation of genetic changes in the surface antigens that leads to emergence of novel subtypes disparate to the vaccine seed strains. Next generation universal vaccines designed to target conserved viral epitopes can potentially offer broad protection against diverse circulating and emerging subtypes. Host immune pressure resulting from widespread vaccine usage on a population wide level has been implied to accelerate the process of antigenic diversification, leading to inherent concern for the emergence of escape phenotypes that can circumvent universal protection.
This study characterises temporal genome wide evolution of influenza viruses as a function of intra-host adaptation, and further defines the impact of heterosubtypic immune pressure in driving variant formation within a mouse model. Mapping of minor variant landscape over distal timepoints revealed both transient and fixed changes in the consensus sequence. Fixation events of functional variants were found to be accelerated by vaccine induced heterosubtypic immune selection, although inherent drift occurring within major immunodominant regions was not dependent on the immune status of the host. Emergence of escape phenotypes that encompassed the ability to ablate vaccine mediated protection from mortality and exhibited a high level of host directed virulence was associated with sustained adaptation under heterosubtypic immune selection, of which productive display of virulent characteristics was attributed to polygenic alterations. Importantly, genotypic markers associated with host-specific virulence unique to heterosubtypic immune escape phenotypes were identified within the polymerase encoding segments. Using structural based approaches, a functional residue involved in mediating template directed nucleotide addition that exhibited distinctive side chain flexibility was identified in the polymerase active site. Alterations at the residue was found to impact transcription fidelity of the RdRp machinery. Preliminary investigations on approaches to engineer attenuated vaccines by structural manipulation within the RdRp were explored at this residue.
This study addresses the impact of broadly protective vaccines on short-term viral evolution within the context of natural infection using a combination of molecular, virological and deep sequencing approaches, which contributes to defining larger evolutionary patterns of influenza virus under selection pressure. Findings from this study provide a basis for informing the design of next generation vaccines that can confer broad, cross-subtype protection and impart preliminary assessments of the potential of universal vaccine driven escape. Importantly, results from this study can serve as a mechanistic framework for future generation of assessment platforms that can be used for efficient identification of emerging antigenically novel viral subtypes that pose inherent threats to the greater population.published_or_final_versionPublic HealthDoctoralDoctor of Philosoph
The expression, function and potential mechanism of long non-coding RNA in the context of influenza virus infection
No full textInfluenza virus leads to contagious respiratory-related diseases, posing threats to public health.
The molecular interplay between viruses and host cells determines the progression of influenza
virus infection. Robust cellular reactions are triggered during influenza virus infection to
activate and synthesize antiviral molecules that target influenza virus replication in multiple
stages; meanwhile, host molecules can also be exploited to facilitate virus infection. As a
deeper understanding of virus-host interaction has been gained during recent years, diverse
types of novel molecules that play a crucial role in influenza virus infection have been
discovered. Long non-coding RNAs (lncRNAs) is a class of RNA transcripts that is encoded
from non-coding genes with limited protein-coding capacity, showing its significance in
influenza virus infection. However, the understanding of lncRNAs in influenza virus infection
remains preliminary.
This study revealed the profile landscape of lncRNAs and identified lncRNAs candidates that
are universally differentially expressed in influenza virus infection. Moreover, the study
unveiled Interferon Sensitive Response Element (ISRE)-dependent lncRNAs, lncRNAs
carrying ISRE-like motifs in the promoter region, may act as a vital regulator in influenza
virus-induced immune responses. To study the biological effect of lncRNAs, two lncRNA
candidates were investigated in detail. USP30-AS1 was identified as a universally differentially
expressed ISRE-dependent lncRNA in influenza virus infection. Knocking out of USP30-AS1
enhanced influenza virus replication via promoting viral protein synthesis without affecting
viral RNA transcription and replication. The activation of USP30-AS1 was JAK-STAT
signaling pathway dependent and USP30-AS1 was engaged in the regulation of inflammatory
response. Loss of USP30-AS1 switches a balanced immune response into acute inflammatory
reaction. Furthermore, BCAR4 was identified as another highly universally differentially
expressed lncRNA that carries out its biological activity through an immune-independent
manner during influenza virus infection. Deletion of BCAR4 inhibited influenza virus
replication via suppressing viral RNA transcription and replication, as well as subsequent viral
protein synthesis. The activation of BCAR4 was achieved through a potential promoter-enhancer
interaction in response to influenza virus infection and was associated with impeded
spliceosomes function.
This study reveals the profile signatures of lncRNAs in influenza virus infection and identifies
novel ISRE-dependent lncRNAs, providing more information and laying a solid foundation for
further studies. Elaborate study in USP30-AS1 reveals that influenza virus infection triggers
immune effectors, as well as immune regulators, which plays an equally critical role to
maintain a fine-tuned immune response. Moreover, the study of USP30-AS1 provides an
possible explanation for tissue damage caused by HPAIs induced acute inflammatory response,
implying USP30-AS1 may serve as a potential therapeutic target for attenuating severe
inflammation induced by HPAIs infection. The study of BCAR4 gains key clues that influenza
virus may trigger BCAR4-dependent emergency splicing working mode in cells by inducing
cell stresses and that this BCAR4-dependent splicing machinery is required for influenza virus
replication. The study also indicates that USP30-AS1 and BCAR4 is universally triggered under
different biological processes during influenza virus infection and highlights that the potential
value of USP30-AS1 and BCAR4 for prospective clinical application.published_or_final_versionPublic HealthDoctoralDoctor of Philosoph
Viral sequence features of influenza A viruses and coronaviruses
No full textViral genomes are shaped by different selection forces in evolution, and the resulting synonymous mutations and non-synonymous mutations can gradually accumulate and lead to changes in the phenotype. Although synonymous mutations in the nucleic acid sequence do not change the amino acid sequence, they can have significant effects on viral fitness. To date, several viral sequence features that can be caused by synonymous mutations have been identified, such as codon usage, dinucleotide usage and RNA secondary structures. The origins and outcomes of these sequence features are largely unexplored due to a lack of appropriate experimental settings that can control most of the confounding factors. The objective of this doctoral work is to identify patterns of different sequence features in influenza A viruses (IAV) and coronaviruses, and to develop and apply bioinformatic tools for guiding further experimental studies on sequence features. Results showed that dinucleotide preference, codon usage bias and direct RNA-RNA interaction were identified or predicted in viral genomes, and viral fitness was changed after introducing synonymous mutations into corresponding genomic regions.
Codon usage bias of different coronaviruses was studied by different types of correspondence analyses. Different patterns of codon usage between different virus genera were observed. While the novel SARS-CoV-2 virus was found to be similar to bat and human SARSr-CoVs at the amino acid usage level, its synonymous codon usage was most similar to bat RaTG13 virus and pangolin P1E virus. Besides codon usage bias, dinucleotide usage preference was also demonstrated to be significant in viral genomes. Dinucleotides CpG, UpA, UpG and CpA were found to be significantly under-represented or over-represented in the genomes of IAV, and evidence for dinucleotide preference directly resulting in synonymous codon usage bias was observed. These results revealed the interacting nature between codon usage and dinucleotide usage, and opened up new areas for studying mutations in viruses while controlling both codon usage and dinucleotide usage.
An R package SynMut was developed for directional reprogramming of viral genomes with specific codon usage patterns and extreme dinucleotide usage, while not affecting the original amino acid sequence or known important genomic signals. The mutant viruses designed by this tool aided in studying different effects between codon usage and dinucleotide usage to viral fitness. Another bioinformatic tool was developed to design mutant viruses for studying direct RNA-RNA interactions between viral segments in IAV. This tool minimizes the complementary base pairing in predicted RNA-RNA interacting regions by
introducing synonymous mutations. Some of the mutated viruses were significantly attenuated in different cells. These results constituted important evidence on critical synonymous mutations in IAV.
Bioinformatic analysis on codon usage and dinucleotide usage in coronaviruses and influenza A viruses was conducted in this thesis. Computational methods and tools for designing mutant viruses for studying codon usage, dinucleotide usage and RNA-RNA interactions were developed. The discovery of critical synonymous mutations by experiments opens up potential future research directions on synonymous mutations in viral genomes.published_or_final_versionPublic HealthDoctoralDoctor of Philosoph
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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