The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily ...longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, ...subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait.
Microbial communities that inhabit the mosquito body play an import role in host biology and may have potential for mosquito control. However, the forces that shape these microbial communities are ...poorly understood.
To gain a better understanding of how host location influences the composition and diversity of mosquito microbiota, we performed a survey of microbial communities in mosquito samples collected from six USA states using HiSeq sequencing of the 16S rRNA gene.
A total of 284 bacterial operational taxonomic units (OTUs) belonging to 14 phyla were detected in nine mosquito species, with Proteobacteria, Firmicutes and Actinobacteria accounting for 95% of total sequences. OTU richness varied markedly within and between mosquito species. The microbial composition and diversity was heavily influenced by the site of mosquito collection, suggesting that host location plays an important role in shaping the mosquito microbiota.
Variation in microbial composition and diversity between mosquitoes from different locations may have important implications on vector competence and transmission dynamics of mosquito-borne pathogens. Future studies should investigate the environmental factors responsible for these variations and the role of key bacteria characterized in this study on mosquito biology and their potential application in symbiotic control of mosquito-borne diseases.
Influenza A virus (IAV) populations harbor large subpopulations of defective-interfering particles characterized by internally deleted viral genomes. These internally deleted genomes have ...demonstrated the ability to suppress infectivity and boost innate immunity, rendering them promising for therapeutic and immunogenic applications. In this study, we aimed to investigate the diversity and complexity of the internally deleted IAV genomes within a panel of plaque-purified avian influenza viruses selected for their enhanced interferon-inducing phenotypes. Our findings unveiled that the abundance and diversity of internally deleted viral genomes were contingent upon the viral subculture and plaque purification processes. We observed a heightened occurrence of internally deleted genomes with distinct junctions in viral clones exhibiting enhanced interferon-inducing phenotypes, accompanied by additional truncation in the nonstructural 1 protein linker region (NS1Δ76-86). Computational analyses suggest the internally deleted IAV genomes can encode a broad range of carboxy-terminally truncated and intrinsically disordered proteins with variable lengths and amino acid composition. Further research is imperative to unravel the underlying mechanisms driving the increased diversity of internal deletions within the genomes of viral clones exhibiting enhanced interferon-inducing capacities and to explore their potential for modulating cellular processes and immunity.
Voltage-gated and ligand-gated ion channels are used in eukaryotic organisms for the purpose of electrochemical signaling. There are prokaryotic homologues to major eukaryotic channels of these ...sorts, including voltage-gated sodium, potassium, and calcium channels, Ach-receptor and glutamate-receptor channels. The prokaryotic homologues have been less well characterized functionally than their eukaryotic counterparts. In this study we identify likely prokaryotic functional counterparts of eukaryotic glutamate receptor channels by comprehensive analysis of the prokaryotic sequences in the context of known functional domains present in the eukaryotic members of this family. In particular, we searched the nonredundant protein database for all proteins containing the following motif: the two sections of the extracellular glutamate binding domain flanking two transmembrane helices. We discovered 100 prokaryotic sequences containing this motif, with a wide variety of functional annotations. Two groups within this family have the same topology as eukaryotic glutamate receptor channels. Group 1 has a potassium-like selectivity filter. Group 2 is most closely related to eukaryotic glutamate receptor channels. We present analysis of the functional domain architecture for the group of 100, a putative phylogenetic tree, comparison of the protein phylogeny with the corresponding species phylogeny, consideration of the distribution of these proteins among classes of prokaryotes, and orthologous relationships between prokaryotic and human glutamate receptor channels. We introduce a construct called the Evolutionary Domain Network, which represents a putative pathway of domain rearrangements underlying the domain composition of present channels. We believe that scientists interested in ion channels in general, and ligand-gated ion channels in particular, will be interested in this work. The work should also be of interest to bioinformatics researchers who are interested in the use of functional domain-based analysis in evolutionary and functional discovery.
Se analizan los hallazgos de una investigación sobre representaciones sociales del proceso de restablecimiento de derechos de un grupo de adolescentes que lo habían vivido tras ser víctimas de ...explotación sexual comercial en la ciudad de Medellín, Colombia. Se realizó una investigación exploratoria descriptiva cualitativa basada en la teoría de las representaciones sociales. Participaron 5 jóvenes con antecedentes de cursar el proceso administrativo de restablecimiento de derechos por explotación sexual comercial. Los resultados evidencian como núcleo central de la representaciones sociales sobre el proceso administrativo de restablecimiento de derechos, que la institución especializada donde se realiza el proceso -el internado- se equipara al proceso mismo; el sistema periférico devela tensiones respecto: 1. al reconocimiento de la explotación sexual comercial como vulneración de derechos y, 2. a las formas de relacionamiento entre adultos y niñas, niños y adolescentes en las instituciones de protección. Se concluye que el reconocimiento de la explotación sexual comercial como vulneración de derechos y las relaciones de confianza y de afecto intergeneracionales constituyen un motivo para resultados exitosos en el proceso administrativo de restablecimiento de derechos.
This article seeks to contribute to the emerging body of research on learning to teach a second language (L2). Specijcally, it examines the learning‐to‐teach experience of a preservice German ...language teacher from her own perspective illuminating the contextual, biographical, academic, and cognitive factors affecting her development (Freeman G Johnson, 1998; Freeman 6 Richards, 1996; Richards G Nunan, 1990). Multiple data collection instruments that generated relevant and rich data were used. They included open‐ended interviews, participant observation, class videotaping and stimulus recall procedures, and lesson plans. Analysis of the data revealed that the interplay of factors, such as the learning background the participant brought with her added to her knowledge of the subject matter, her level of commit ment, and an effective mentoring relationship contributed to the participant's success ful, productive, and meaningful experience.
: This study draws from sociocultural theory to examine how biographical factors interplay with contextual factors to shape the professional identity of a Spanish language teacher candidate. ...Specifically, it explores the student teaching experience of Marcos, a 30‐year‐old language teacher candidate from South America. Analysis of the data reveals that in forging his professional identity, the participant appropriates discourses that place high value on native speakerness and male authority. While this allows him to claim legitimacy as a Spanish language teacher, it also leads him to assume a taken‐for‐granted view of both subject matter knowledge and classroom management skills, precluding his development as a teacher. Implications derived from this study call for a critical language teacher education that provides tools for examining unquestioned assumptions about language and gender ideologies, expanding identity options, and fostering professional agency.
This paper intends to make a contribution to the study of the spread of the English language in Colombia. To characterize this social and cultural context, I draw a sociolinguistic profile following ...the framework provided by Berns (1990, 1992). Although English has no official status in Colombia and its functional range is still restricted, it has expanded at a pace not experienced before. There is a growing consensus that English has a role to play in Colombia's social and economical advancement in the international arena. This is evidenced in the educational policies and programs contributing to securing a prominent position for English in the national curriculum as well as in the unprecedented boom of the English language teaching industry.
The paper begins by providing an overview of Colombia and its linguistic makeup, briefly tracing the presence of the English language from the eighteenth century to date. Then it goes on to characterize the users and uses of English documenting how the interpersonal, instrumental, and creative/innovative functions are manifested in this particular setting. Next, the paper describes the attitudinal range towards the English language, its speakers, and its study as well as the process of borrowing, adaptation, and innovation. It concludes by highlighting the need for additional research to further define this particular socio–cultural milieu of learning and use of English. It is argued that further research has a central role in informing the determination of relevant and appropriate models for language teaching in Colombia.
Identification of bacterial and archaeal counterparts to eukaryotic ion channels has greatly facilitated studies of structural biophysics of the channels. Often, searches based only on sequence ...alignment tools are inadequate for discovering such distant bacterial and archaeal counterparts. We address the discovery of bacterial and archaeal members of the Pentameric Ligand-Gated Ion Channel (pLGIC) family by a combination of four computational methods. One domain-based method involves retrieval of proteins with pLGIC-relevant domains by matching those domains to previously established domain templates in the InterPro family of databases. The second domain-based method involves searches using ungapped de-novo motifs discovered by MEME which were trained with well characterized members of the pLGIC family. The third and fourth methods involve the use of two sequence alignment search algorithms BLASTp and psiBLAST respectively. The sequences returned from all methods were screened by having the correct topology for pLGIC's, and by returning an annotated member of this family as one of the first ten hits using BLASTp against a comprehensive database of eukaryotic proteins. We found the domain based searches to have high specificity but low sensitivity, while the sequence alignment methods have higher sensitivity but lower specificity. The four methods together discovered 69 putative bacterial and archaeal members of the pLGIC family. We ranked and divide the 69 proteins into groups according to the similarity of their domain compositions with known eukaryotic pLGIC's. One especially notable group is more closely related to eukaryotic pLGIC's than to any other known protein family, and has the overall topology of pLGIC's, but the functional domains they contain are sufficiently different from those found in known pLGIC's that they do not score very well against the pLGIC domain templates. We conclude that multiple methods used in a coordinated fashion outperform any single method for identifying likely distant bacterial and archaeal proteins that may provide useful models for important eukaryotic channel function. We note also that the methods used here are largely standard and readily accessible. The novelty is in the effectiveness of a strategy that combines these methods for identifying bacterial and archea relatives of this family. Therefore the paper may serve as a template for a broad group of workers to reliably identify bacterial and archaeal counterparts to eukaryotic proteins.
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