Comparison of COVID-19 incidence and mortality between rural and urban areas in Catalonia

Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona.Treballs Pràctics de l' Assignatura de Salut Pública del Grau de Farmàcia. Treballs Curs: 2021-2022, Tutora: Maria Grau Magaña[eng] Background. COVID-19 has had a different impact on multiple aspects, depending on the county or region where it has been studied. Therefore, in this study we have established the differences in terms of the variables of incidence and mortality between the regions of “La Garrotxa” and “Barcelonès”. Methods. This analytical and observational study compares incidence and mortality between “La Garrotxa” and “Barcelonès” regions due to COVID-19 during the period March 1, 2020 - September 30, 2021. To this end, we have standardized the data by age and sex distribution using the direct method to calculate the cumulative incidence and the indirect method to determine the mortality ratio. Results. The cumulative incidence of COVID-19 is higher in the region of “La Garrotxa” (139 / 1,000 inhabitants in men and 142 / 1,000 inhabitants in women) than in that of “Barcelonès” (125 / 1,000 inhabitants and 109 / 1,000 inhabitants, respectively). On the other hand, mortality ratio due to COVID-19 is higher in “Barcelonès” (1,226 in men and 1,891 in women) than in “La Garrotxa” (0.990 in men and 1,498 in women). Conclusion. The incidence of COVID-19 is higher in “La Garrotxa” than in “Barcelonès” and the mortality due to COVID-19 is higher in “Barcelonès”. For this reason, prevention measures for the disease should be implemented taking into account the individual characteristics of each population, such as the distribution by age and sex.[cat] Antecedents. La COVID-19 ha tingut un impacte diferent en diversos aspectes, segons la comarca o regió en la que ha estat estudiada. Per consegüent, en aquest estudi hem establert quines són les diferències en quant a les variables d’incidència i mortalitat entre les comarques de la Garrotxa i el Barcelonès. Mètodes. Aquest estudi analític i observacional compara la incidència i la mortalitat entre la comarca de la Garrotxa i el Barcelonès degudes a la COVID-19 durant el període 1 març de 2020 - 30 setembre de 2021. Amb aquest objectiu, per una banda hem estandarditzat les dades per distribució d’edat i sexe utilitzant el mètode directe per calcular la incidència acumulada i el mètode indirecte, per determinar la raó de mortalitat. Resultats. La incidència acumulada de COVID-19 és major en la comarca de la Garrotxa (139/1.000 habitants en homes i 142/1.000 habitants en dones) que en la del Barcelonès (125/ 1.000 habitants i 109/1.000 habitants, respectivament). Per contra, la raó de mortalitat deguda a la COVID-19 és major al Barcelonès (1,226 en homes i 1,891 en dones) que a la Garrotxa (0,990 en homes i 1,498 en dones). Conclusions. La incidència de COVID-19 és major a la Garrotxa que al Barcelonès i la mortalitat deguda a la COVID-19 és major al Barcelonès. Per aquest motiu, les mesures de prevenció de la malaltia s’haurien d’implantar tenint en compte les característiques individuals de cada població, com serien la distribució per edat i sexe

Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

BACKGROUND: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. RESULTS: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F(ST) between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. CONCLUSIONS: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0216-x) contains supplementary material, which is available to authorized users

Famílies botàniques de plantes medicinals

Facultat de Farmàcia, Universitat de Barcelona. Ensenyament: Grau de Farmàcia, Assignatura: Botànica Farmacèutica, Curs: 2013-2014, Coordinadors: Joan Simon, Cèsar Blanché i Maria Bosch.Els materials que aquí es presenten són els recull de 175 treballs d’una família botànica d’interès medicinal realitzats de manera individual. Els treballs han estat realitzat per la totalitat dels estudiants dels grups M-2 i M-3 de l’assignatura Botànica Farmacèutica durant els mesos d’abril i maig del curs 2013-14. Tots els treballs s’han dut a terme a través de la plataforma de GoogleDocs i han estat tutoritzats pel professor de l’assignatura i revisats i finalment co-avaluats entre els propis estudiants. L’objectiu principal de l’activitat ha estat fomentar l’aprenentatge autònom i col·laboratiu en Botànica farmacèutica

Evolució cromosòmica en mamífers: cariotips ancestrals i punts de trencament evolutius

Per a poder entendre la dinàmica evolutiva dels genomes és imprescindible conèixer com estan organitzats els cromosomes de les diferents espècies i determinar quins tipus de reorganitzacions cromosòmiques estan implicades en els processos d’especiació i en esdeveniments macroevolutius que afecten als grans grups taxonòmics. És per això que en aquesta tesi ens hem plantejat definir el cariotip ancestral de mamífers, amniotes i tetràpodes per a poder determinar les regions conservades (Homologous Syntenic Blocks, HSBs) i les regions de trencament evolutiu (Evolutionary Breakpoint Regions, EBRs) partint del genoma humà com a referència. Gràcies a la inclusió del genoma d’espècies outgroup (granota i gall), hem pogut millorar el cariotip ancestral de tetràpodes i amniotes, definint noves associacions sintèniques com a caràcters sinapomòrfics dels amniotes i dels mamífers. Igualment, hem analitzat la distribució de les EBRs en el genoma humà, veient que aquestes regions no estan distribuïdes a l’atzar i un 20% d’elles han estat re-utilitzades al llarg de l’evolució. Hem relacionat la distribució de les EBRs amb l’abundància de seqüències repetitives en el genoma humà, trobant un enriquiment de repeticions en tàndem en aquestes EBRs i una co-localització amb certs elements mòbils o transponibles (AAAT-Alus). A més a més, hem estudiat el paper del constrenyiment selectiu sobre el manteniment de les regions conservades i hem vist que certes reorganitzacions cromosòmiques no es troben en la natura ja que disrupcions en les regions afectades provocarien canvis d’expressió gènica possiblement letals per la progènie. Finalment, hem estudiat el paper de les reorganitzacions cromosòmiques en el procés d’especiació, on hem posat de manifest que regions genòmiques implicades en inversions són regions de baixa recombinació en relació a les regions no reorganitzades i per tant podrien donar lloc a un procés d’aïllament reproductiu per l’acúmul d’incompatibilitats genètiques en els híbrids. Per poder explicar les nostres observacions hem proposat un model on la presència d’heterocariotips flotants en el node d’especiació provocaria una supressió de recombinació en les regions invertides encara observable en les espècies actuals.The study of the genome organization as well as how chromosomal reorganizations are involved in speciation and adaptation processes are the key points to better understand the evolutionary dynamics of vertebrate genomes and their inter- and intra-specific phylogenetic relationships. In this thesis we described the ancestral karyotype for mammals, amniotes and tetrapods in order to determine the homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in the human genome. Using the chicken and frog genomes as outgroups, we were able to improved previously described ancestral karyotypes for tetrapods and amniotes and we defined new syntenic associations as an amniote or mammal synapomoprhies. We also analysed the distribution of EBRs in the human genome, showing that EBRs are not randomly distributed and 20% are reused during the evolutionary period. The distribution of EBRs is related to the abundance of repetitive sequences, exhibiting an enrichment of specific tandem repeats in EBRs and co-localizing with mobile elements (AAAT-Alu). Furthermore, we studied the selective constrain on the maintenance of conserved regions. We observed that certain reorganizations are not found in natural populations because disruptions of the regions involved in reorganizations would lead to changes in gene expression probably lethal for the progeny. Finally, we studied the relation between chromosomal reorganizations and speciation. We showed that regions affected by reorganizations have lower recombination rates than regions not rearranged, thus, an increase of genic incompatibilities in these regions could lead to reproductive isolation by the existence of a barrier of gen flow. In order to explain our observations we proposed the floating heterokaryotypes model, where the presence of heterokaryotypes in the speciation node resulted on a suppression of recombination in the rearranged regions, which is still detected on the extant species

Recombination rates and genomic shuffling in human and chimpanzee : a new twist in the chromosomal speciation theory

A long-standing question in evolutionary biology concerns the effect of recombination in shaping the genomic architecture of organisms and, in particular, how this impacts the speciation process. Despite efforts employed in the last decade, the role of chromosomal reorganizations in the human-chimpanzee speciation process remains unresolved. Through whole-genome comparisons, we have analyzed the genome-wide impact of genomic shuffling in the distribution of human recombination rates during the human-chimpanzee speciation process. We have constructed a highly refined map of the reorganizations and evolutionary breakpoint regions in the human and chimpanzee genomes based on orthologous genes and genome sequence alignments. The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes. In fact, rearranged chromosomes presented significantly lower recombination rates than chromosomes that have been maintained since the ancestor of great apes, and this was related with the lineage in which they become fixed. Importantly, inverted regions had lower recombination rates than collinear and noninverted regions, independently of the effect of centromeres. Our observations have implications for the chromosomal speciation theory, providing new evidences for the contribution of inversions in suppressing recombination in mammals

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions

By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution. We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages. Our data suggest that adaptive alleles - in this case, genes involved in the immune response - might have been favored by genome rearrangements in the macaque lineage. The online version of this article (doi:10.1186/1471-2164-15-530) contains supplementary material, which is available to authorized users

In silico reconstruction of chromosomal rearrangements and an avian ancestral karyotype

The recent availability of whole genome assemblies for multiple bird species has changed the way we can detect and describe patterns of avian genome evolution. Coupled with conventional cytogenetic techniques, in silico comparison and alignment of bird chromosome assemblies offer exciting opportunities for reconstructing chromosomal rearrangement events that occurred in various avian and ancestral lineages. These can later be correlated with the variety of phenotypes observed in birds. We are testing this approach using the chromosome assemblies of zebra finch, turkey, duck, and green anole lizard (as an outgroup genome); analysis of further genomes is in progress. The approach first involves identification of multi-species homologous synteny blocks and reconstruction of a tentative avian ancestral genome from contiguous ancestral regions (CARs) using the multiple genome rearrangement and ancestors tool (MGRA). Secondly, manual comparative analysis of the CARs to reveal the most likely scenarios of inter- and intrachromosomal events in separate avian lineages is performed. Finally, we compare the rearrangement rates in each lineage. We frequently observe that species with the fewest number of chromosomal rearrangements exhibit phenotypes considered being ancestral for birds. In contrast, an increased rate of chromosomal rearrangements often correlates with higher degree of phenotypic variation, diversification, and adaptation

Assessing the role of tandem repeats in shaping the genomic architecture of great apes

Background: Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal. Methodology and Principal Findings: Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements. Significance: Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements

Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia

Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints

Glossari il·lustrat de morfologia botànica bàsica. Racons verds: aportació al coneixement morfològic dels espermatòfits

Els resultats s’emmarquen en el projecte d’innovació docent «Innovació en l’ambientalització curricular de la Botànica en el grau de Farmàcia: Jardins per a la Salut» (codi 2018PID-UB/034) del Grup d’Innovació Docent de Botànica Aplicada a les Ciències Farmacèutiques (GIBAF).Facultat de Farmàcia, Universitat de Barcelona. Ensenyament: Grau de Farmàcia. Assignatura: Botànica farmacèutica. Curs: 2017-2018. Coordinadors: Cèsar Blanché, Carles Benedí, Maria Bosc i Joan SimonProjecte: 2018PID-UB/034Es presenta a continuació un glossari il·lustrat realitzat per 35 estudiants de l’assignatura Botànica Farmacèutica del grau de Farmàcia. Els resultats s’emmarquen en el projecte d’innovació docent «Innovació en l’ambientalització curricular de la Botànica en el grau de Farmàcia: Jardins per a la Salut» (codi 2018PID-UB/034) del Grup d’Innovació Docent de Botànica Aplicada a les Ciències Farmacèutiques (GIBAF). El glossari s’ha il·lustrat a partir de fotografies dels estudiants sobre detalls morfològics de les espècies del jardí de la Facultat de Farmàcia que s’ha inclòs en els «Racons Verds de la UB». El resultat ha estat la descripció i il·lustració de 80 caràcters d’organografia vegetativa i reproductora i constitueixen un nou recurs docent en obert realitzat pels propis estudiants. El treball dut a terme s’ha realitzat de forma voluntària, tutoritzada i restringida en tres grups de teoria (M2, M3 i T3) de l'assignatura troncal de Botànica Fermacèutica del grau de Farmàcia. Els resultats hanrepercutit fins a 0,5 punts sobre la nota final un cop s’ha superat l’assignatura.Grup d'Innovació Docent en Botànica Aplicada a les Ciències Farmacèutiques (GIBAF