Gene duplication in an African cichlid adaptive radiation

Background Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis “chilingali”) and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei). Results Using Astatotilapia burtoni as reference, microarray comparative genomic hybridization analysis of 5689 genes reveals 134 duplicated genes among the four cichlid species tested. Between 51 and 55 genes were identified as duplicated in each of the three species from the Lake Malawi radiation, representing a 38%–49% increase in number of duplicated genes relative to the non-radiated lineage (37 genes). Duplicated genes include several that are involved in immune response, ATP metabolism and detoxification. Conclusions These results contribute to our understanding of the abundance and type of gene duplicates present in cichlid fish lineages. The duplicated genes identified in this study provide candidates for the analysis of functional relevance with regard to phenotype and divergence. Comparative sequence analysis of gene duplicates can address the role of positive selection and adaptive evolution by gene duplication, while further study across the phylogenetic range of cichlid radiations (and more generally in other adaptive radiations) will determine whether the patterns of gene duplication seen in this study consistently accompany rapid radiation

Community socioeconomic deprivation and SARS-CoV-2 infection risk: findings from Portugal

Background: Socioeconomic differences have been observed in the risk of acquiring infectious diseases, but evidence regarding SARS-CoV-2 remains sparse. Hence, this study aimed to investigate the association between SARS-CoV-2 infection risk and socioeconomic deprivation, exploring whether this association varied according to different phases of the national pandemic response. Methods: A cross-sectional study was conducted. Data routinely collected for patients with a laboratorial result recorded in SINAVE®, between 2 March and 14 June 2020, were analysed. Socioeconomic deprivation was assessed using quintiles of the European Deprivation Index (Q1-least deprived to Q5-most deprived). Response phases were defined as before, during and after the national State of Emergency. Associations were estimated using multilevel analyses. Results: The study included 223 333 individuals (14.7% were SARS-CoV-2 positive cases). SARS-CoV-2 infection prevalence ratio increased with deprivation [PR(Q1)=Ref; PR(Q2)=1.37 (95% CI 1.19-1.58), PR(Q3)=1.48 (95% CI 1.26-1.73), PR(Q4)=1.73 (95% CI 1.47-2.04), PR(Q5)=2.24 (95% CI 1.83-2.75)]. This was observed during the State of Emergency [PR(Q5)=2.09 (95% CI 1.67-2.62)] and more pronounced after the State of Emergency [PR(Q5)= 3.43 (95% CI 2.66-4.44)]. Conclusion: The effect of socioeconomic deprivation in the SARS-CoV-2 infection risk emerged after the implementation of the first State of Emergency in Portugal, and became more pronounced as social distancing policies eased. Decision-makers should consider these results when deliberating future mitigation measures. © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the European Public Health Association.A.I.R. was supported by National Funds through FCT (Foundation for Science and Technology, Portuguese Ministry of Science, Technology and Higher Education), under the programme of 'Stimulus of Scientific Employment-Individual Support' within the contract CEECIND/02386/2018

Development, Test and Validation of a Mechatronic Device for Spasticity Quantification

Abstract Spasticity is a common pathological phenomenon in clinical practices, frequently expressed as a stroke, multiple sclerosis or cerebral palsy. The accurate quantification of spasticity allows early action to prevent the potentially irreversible consequences. The aim of this work is to develop and implement a mechatronic device for the accurate quantification of spasticity, which is able to differentiate spasticity from other motor disorders. The proposed method is based on the quantification of the tonic stretch reflex threshold (TSRT) for the assessment of the range of motion of the limb affected by spasticity. In order to validate the developed device, experimental trials have been conducted, considering the flexor muscle of the elbow joint. The developed device was tested, first in a laboratory environment with healthy subjects and secondly, in a clinical environment with the collaboration of patients with spasticity. The evaluations in th clinical environment were performed on three different days in order to evaluate the reproducibility of the obtained results. The experimental trials confirm the sensibility, reproducibility and reliability of spasticity quantification based on the TSRT method. This project has been developed in cooperation with the Hospital of Braga and Fisimaia rehabilitation clinic, both in Portugal

Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila

<p>Abstract</p> <p>Background</p> <p>Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from <it>Drosophila melanogaster </it>to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (<it>D. sechellia</it>, <it>D. simulans</it>, and <it>D. yakuba</it>). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence.</p> <p>Results</p> <p>We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (< 92% sequence identity to <it>D. melanogaster</it>) ~84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (≥ 97% identity), only 13% of genes were identified as diverged. While ~40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to <it>D. melanogaster</it>, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation.</p> <p>Conclusions</p> <p>Here we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which microarray platforms are available, comparative studies can be conducted for many interesting lineages in order to identify highly diverged genes that may be the target of natural selection.</p

Gene duplication in an African cichlid adaptive radiation

BACKGROUND: Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis “chilingali”) and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei). RESULTS: Using Astatotilapia burtoni as reference, microarray comparative genomic hybridization analysis of 5689 genes reveals 134 duplicated genes among the four cichlid species tested. Between 51 and 55 genes were identified as duplicated in each of the three species from the Lake Malawi radiation, representing a 38%–49% increase in number of duplicated genes relative to the non-radiated lineage (37 genes). Duplicated genes include several that are involved in immune response, ATP metabolism and detoxification. CONCLUSIONS: These results contribute to our understanding of the abundance and type of gene duplicates present in cichlid fish lineages. The duplicated genes identified in this study provide candidates for the analysis of functional relevance with regard to phenotype and divergence. Comparative sequence analysis of gene duplicates can address the role of positive selection and adaptive evolution by gene duplication, while further study across the phylogenetic range of cichlid radiations (and more generally in other adaptive radiations) will determine whether the patterns of gene duplication seen in this study consistently accompany rapid radiation

Social interactions through the eyes of macaques and humans

Group-living primates frequently interact with each other to maintain social bonds as well as to compete for valuable resources. Observing such social interactions between group members provides individuals with essential information (e.g. on the fighting ability or altruistic attitude of group companions) to guide their social tactics and choice of social partners. This process requires individuals to selectively attend to the most informative content within a social scene. It is unclear how non-human primates allocate attention to social interactions in different contexts, and whether they share similar patterns of social attention to humans. Here we compared the gaze behaviour of rhesus macaques and humans when free-viewing the same set of naturalistic images. The images contained positive or negative social interactions between two conspecifics of different phylogenetic distance from the observer; i.e. affiliation or aggression exchanged by two humans, rhesus macaques, Barbary macaques, baboons or lions. Monkeys directed a variable amount of gaze at the two conspecific individuals in the images according to their roles in the interaction (i.e. giver or receiver of affiliation/aggression). Their gaze distribution to non-conspecific individuals was systematically varied according to the viewed species and the nature of interactions, suggesting a contribution of both prior experience and innate bias in guiding social attention. Furthermore, the monkeys’ gaze behavior was qualitatively similar to that of humans, especially when viewing negative interactions. Detailed analysis revealed that both species directed more gaze at the face than the body region when inspecting individuals, and attended more to the body region in negative than in positive social interactions. Our study suggests that monkeys and humans share a similar pattern of role-sensitive, species- and context-dependent social attention, implying a homologous cognitive mechanism of social attention between rhesus macaques and humans

Antibodies to Toxoplasma gondii and Neospora caninum in Captive Neotropical and Exotic Wild Canids and Felids

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)This study was designed to detect antibodies to Toxoplasma gondii and Neospora caninum in wild captive carnivores maintained in Brazilian zoos. Blood samples were collected from 142 Brazilian wild felids and 19 exotic felids in zoos, and 3 European wolves (Canis lupus) and 94 Brazilian wild canids maintained in captivity in Brazilian zoos of Sao Paulo, Mato Grosso states and Federal District. One hundred and two (63.4%) and 70 (50.3%) of the 161 wild felids tested were seropositive for T gondii and N. caninum by indirect immunofluorescent assay test (IFAT), respectively. Among sampled wild canids, 49 (50.5%) and 40 (41.2%) animals were seropositive for T. gondii and N. caninum antigens by IFAT, respectively. To our knowledge, this is the first serological detection of antibodies to N. caninum in Brazilian wild captive felids and bush dogs (Speothos venaticus (Lund)).96510071009Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renovaveis (IBAMA) [S02027.002943/2005, 15901-1]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP [07/59889-6, 08/55570-8]Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renovaveis (IBAMA) [S02027.002943/2005, 15901-1