A diferenciação morfo-fisiológica entre rainhas e operárias de Apis mellifera decorre da alimentação recebida durante o desenvolvimento larval. Dentre as diferenças morfológicas entre as duas castas encontram-se estruturas especializadas para a coleta de pólen e própolis, localizadas nas pernas metatorácicas das operárias, ausentes nas pernas de rainhas. Os padrões de expressão de Ultrabithorax (Ubx) durante o desenvolvimento de operárias e rainhas estão associados aos padrões de cerdas das pernas de fêmeas adultas. Pernas mesotorácicas de operárias apresentam estruturas descritas como importantes na coleta de pólen, ausentes em rainhas. Por outro lado, as asas não possuem estruturas casta-específicas. No presente trabalho, análises globais de transcrição gênica por hibridação de lâminas de microarrays a partir de RNA total de pernas metatorácicas de operárias e rainhas em três estágios do desenvolvimento mostram 1952 genes diferencialmente expressos. Discos de pernas metatorácicas de larvas no início do quinto estágio larval, quando comparados aos de estágios mais tardios no desenvolvimento, têm alto níveis de transcritos de ativadores de Ubx, o qual está 25 vezes mais expresso em estágios subseqüentes do desenvolvimento. Buscas por motivos de ligação de fatores de transcrição nos promotores dos grupos de genes diferencialmente expressos revelam que os motivos para ligação de Ubx, Zeste e Twist estão super-representados em um dos conjuntos analisados. Dentro deste grupo, estão presentes genes cujos ortólogos em Drosophila são controlados por Ubx, como o caso do gene lola. Análises do processamento do mRNA de Ubx em pernas e asas de ambas as castas mostram que são produzidas três isoformas diferentes quanto à presença de dois microéxons (m1 and m2), que contêm 42 nt and 53 nt, respectivamente. A isoforma IIa-like, que contém o m2, entretanto, parece não ser capaz de produzir uma proteína Hox, já que possui um códon de terminação antes do homeodomínio. O perfil de transcrição diferencial de Ubx entre as castas está associado a apêndices que apresentam diferenças morfológicas, sendo Ubx mais transcrito em pernas meso e metatorácicas de operárias que rainhas. Quando analisadas as porcentagens de expressão de cada isoforma nos apêndices, claramente a isoforma IVa-like, sem microéxons, é a mais transcrita em todos os tecidos. Entretanto, nota-se que nas asas anteriores, onde há menos Ubx, a isoforma IIa-like é proporcionalmente mais transcrita que II nos outros apêndices. Destaca-se uma tendência à inclusão do microéxon m1 (isoforma IIIa-like) ao mRNA de Ubx transcrito em asas posteriores e pernas de rainhas em comparação a operárias, em detrimento da isoforma IVa-like. Análises do uso da região 3UTR em pupas de operárias mostram que há um microssatélite transcrito na porção distal da região 3UTR deUbx. A estrutura secundária predita agrupa separadamente as regiões codificadora e as regiões 3UTR proximal e distal. Análises de seqüenciamento de última geração revelaram que oito dos 51 microRNAs com sítios-alvo preditos na região 3UTR de Ubx estão mais expressos em asas anteriores, e outros dois em asas posteriores. Assim, nossos resultados mostram que o controle da expressão diferencial de Ubx é dada pela ativação desse gene por fatores de transcrição que se ligam ao promotor, controle do splicing alternativo, e expressão de microRNAs diferencial em cada casta e apêndice, controlando, assim, a morfogênese diferencial dos apêndices de fêmeas observada em A. mellifera. / Along with differences in physiological and behavioral characteristics, workers and queens of Apis mellifera also differ in appendage morphology. Some appendage specializations in the hind legs of honeybee workers, which are highly specialized pollinators, deserve special attention. The hind tibia of the worker has an expanded bristle-free region used for carrying pollen and propolis, the corbicula. In queens, this structure is absent. Although these morphological differences have been well characterized, the genetic inputs triggering the development of this alternative morphology have remained unknown. Through microarray analysis, we detected 1,952 genes that are differentially expressed during worker versus queen hind leg development. The gene expression signatures of the two castes have similar patterns of genes controlling development. At the beginning of the last larval instar, Ultrabithorax (Ubx) activators are more strongly expressed than in prepupae and early pupae; at this time Ubx expression is approximately 25 times higher. Within the gene expression signature, we identified a cluster formed by genes in which Ubx, Twist and Zeste binding sites are over-represented. This cluster includes genes for which Drosophila orthologs are known to be bound by Ubx, as in the case of lola. We also tested the extent of Ubx mRNA processing during wing and leg development. Unexpectedly, we found Ubx alternative splicing in both workers and queens; there were two microexons (m1 and m2) encoding 42 nt and 53 nt, respectively, arguing against the hypothesis that alternative splicing occurs exclusively within the Diptera. Inclusion of the m2 exon inserts a stop codon upstream from the exon containing the homeodomain, producing a truncated protein. Moreover, these bee microexons conserve the nucleotides known to be important for alternative splicing in Drosophila. During bee wing development, Ubx mRNA isoforms are transcribed in similar amounts in both castes; however, during leg development, queens produce 60% of the Ubx levels transcribed by workers. Analysis of 3UTR usage during bee development revealed a microsatellite region transcribed within the Ubx 3UTR. The predicted secondary structure locations separated the coding region into three branches and the proximal and the distal 3UTR regions. Deep-sequencing analysis revealed that eight out of 51 miRNAs predicted to target the Ubx mRNA are more highly expressed in worker forewings and two are more expressed in the hindwings. Therefore, we conclude that Ubx differential expression is activated by transcription factors that bind to its promoter, by control of alternative splicing, and moreover by microRNAs differentially expressed according to tissue and caste, resulting in differential morphogenesis of the hind leg in honeybee females.

Um dos desafios atuais da pesquisa em frutíferas tropicais é incorporar abordagens baseadas em marcadores moleculares nos programas convencionais de melhoramento. O maracujá-doce (Passiflora alata) é uma espécie diploide, de fecundação cruzada e pouco explorada. Recentemente, nosso grupo construiu um mapa de ligação de P. alata composto de diferentes tipos de marcadores moleculares. Além disso, dispõe-se de um conjunto de transcritos de Passiflora edulis, obtidos a partir de duas bibliotecas de expressão: forward e reverse onde foram isolados transcritos diferencialmente expressos na planta inoculada com Xanthomonas axonopodis (Xap) (672) e na planta controle, não inoculada (310), respectivamente. Assim, neste estudo, este conjunto de transcritos foi explorado visando ao desenvolvimento de marcadores SSR e SNP com o intuito de enriquecer, posteriormente, o mapa de ligação de P. alata com marcadores funcionais putativos. Para o desenvolvimento dos marcadores SSRs, as 672 sequências da biblioteca forward foram investigadas e em 91 delas foram encontrados 115 SSRs. Como esperado, a classe de repetições trinucleotídicas foi a mais abundante, sendo o motivo (AG)n o mais comum entre as repetições dinucleotídicas. Desenhou-se primers para amplificar 42 desses SSRs. Dois acessos de P. edulis e seis indivíduos da população de mapeamento de P. alata foram usados nos testes de transferibilidade e avaliação do polimorfismo. Trinta e quatro pares de primers apresentaram bom padrão de amplificação, porém apenas 10 deles revelaram polimorfismo em P. alata. Para o desenvolvimento dos marcadores SNPs, 118 sequências selecionadas das bibliotecas de expressão forward e reverse foram usadas para o desenho de primers; 37 delas foram usadas para avaliar o polimorfismo no mesmo set de indivíduos de P. alata. Foram encontrados 34 locos contendo SNPs bialélicos em 16 fragmentos gênicos, cujas sequencias variaram em tamanho de 332 a 872 pb. Considerando todos os fragmentos gênicos (16), foi analisado um total de 10.003 pb; a frequência de SNPs foi estimada como sendo 1 a cada 294 pb. Observou-se a mesma ocorrência de SNPs (50%, 17/34) em regiões codantes e não-codantes. Uma função putativa pôde ser atribuída a todos os fragmentos gênicos de P. alata, sendo que 82% mostraram homologia com as mesmas proteínas das sequências de origem, isoladas de P. edulis. No geral, os locos marcadores apresentaram baixo nível de polimorfismo molecular. Este é o primeiro trabalho sobre o desenvolvimento de locos marcadores funcionais putativos em Passiflora usando transcritos expressos em resposta à Xap. / One of the current challenges of tropical fruit research is to incorporate molecular marker-based approaches into conventional breeding programs. The sweet passion fruit (Passiflora alata) is a diploid, outcrossing and underexploited species. Recently, our group has constructed a P. alata linkage map consisted of different types of molecular markers. Moreover, we have a set of transcripts of Passiflora edulis obtained from two expression libraries: the forward and the reverse where differentially expressed transcripts were isolated from a plant inoculated with Xanthomonas axonopodis (Xap) (672), and from the control plant, uninoculated (310), respectively. Thus, in this study, this set of transcripts were exploited aiming at the development of SNP and SSR markers for future enrichment of the P. alata linkage map with putative functional markers. For the development of SSR markers, the 672 sequences from the forward library were investigated and 91 of them were found to have 115 SSRs. As expected, the trinucleotide class of repeats was the most abundant, and the (AG)n motif was the most common among the dinucleotide repeats. Primers were designed to amplify 42 of these SSRs. Transferability tests and polymorphism investigation were carried out using two accessions of P. edulis and six individuals of the mapping population of P. alata. Thirty-four primer pairs showed a good amplification pattern but only 10 loci revealed polymorphism in P. alata. For the development of SNP markers, 118 sequences selected from forward and reverse expression libraries were used for designing primers; 37 were used to assess the polymorphism in the same set of individuals of P. alata. Thirty-four biallelic SNPs were found in 16 gene fragment sequences that ranged in size from 332 to 872 bp. Considering all gene fragments, a total of 10,003 bp was obtained; the frequency of SNPs was estimated to be 1 every 294 bp. The same prevalence of SNPs (50%, 17/34) was observed within coding and non-coding regions. A putative function was assigned to all gene fragments of P. alata; 82% of them have shown homology to the original protein sequences isolated from P. edulis. Overall, the marker loci showed a low level of molecular polymorphism. This is the first report on the development of putative functional marker loci in Pasiflora using transcripts induced in response to Xap.

Abiotic stress is a major constraint for crop productivity worldwide. To better understand the common biological mechanisms of abiotic stress responses in plants, we performed meta-analysis of 652 samples of RNA sequencing (RNA-Seq) data from 43 published abiotic stress experiments in Arabidopsis thaliana. These samples were categorized into eight different abiotic stresses including drought, heat, cold, salt, light and wounding. We developed a multi-step computational pipeline, which performs data downloading, preprocessing, read mapping, read counting and differential expression analyses for RNA-Seq data. We found that 5729 and 5062 genes are induced or repressed by only one type of abiotic stresses. There are only 18 and 12 genes that are induced or repressed by all stresses. The commonly induced genes are related to gene expression regulation by stress hormone abscisic acid. The commonly repressed genes are related to reduced growth and chloroplast activities. We compared stress responsive genes between any two types of stresses and found that heat and cold regulate similar set of genes. We also found that high light affects different set of genes than blue light and red light. Interestingly, ABA regulated genes are different from those regulated by other stresses. Finally, we found that membrane related genes are repressed by ABA, heat, cold and wounding but are up regulated by blue light and red light. The results from this work will be used to further characterize the gene regulatory networks underlying stress responsive genes in plants. / Master of Science / Abiotic stress is a major constraint for crop productivity worldwide. To better understand the common biological mechanisms of abiotic stress responses in plants, we performed analysis of 652 samples of RNA sequencing data from 43 published abiotic stress experiments in Arabidopsis thaliana. These samples were collected from eight different abiotic stresses including drought, heat, cold, salt, light and wounding. We identified genes that were induced or repressed by each of these stresses. We found that 5729 and 5062 genes are induced or repressed by only one type of abiotic stresses. There are only 18 and 12 genes that are induced or repressed by all stresses. The commonly induced genes are related to gene expression regulation by stress hormone. The commonly repressed genes are related to reduced growth. We compared stress responsive genes between any two types of stresses and found that heat and cold regulate similar set of genes. We also found that high light affects different set of genes than blue light and red light. Finally, we found that membrane related genes are repressed by stress hormone, heat, cold and wounding but are up regulated by blue light and red light. The results from this work will be used to further characterize the gene regulations underlying stress responsive genes in plants.

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No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) dissertacao_marcelo_nogueira_do_amaral.pdf: 2321866 bytes, checksum: 813c57b5a855e4f2470433f907cc1a61 (MD5) Previous issue date: 2015-03-04 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / O arroz (Oryza sativa L.) é o segundo cereal mais cultivado no mundo, sendo o Brasil o 9º maior produtor. Apesar dos bons níveis de produtividade, acredita-se que estes números sejam insuficientes para suprir o requerimento populacional no mundo, sendo necessário um aumento na produção. Entretanto, diversos estresses abióticos, como salinidade, toxidez por ferro e baixa temperatura, limitam a produtividade do arroz mundialmente. A resposta das plantas às condições estressantes é um fenômeno complexo, envolvendo alterações morfológicas, fisiológicas, bioquímicas e moleculares. Assim, o conhecimento do transcriptoma e análise fotossintética de plantas de arroz submetidas a estes estresses, pode auxiliar a elucidar quais vias metabólicas são alteradas e quais são as principais respostas bioquímicas e fisiológicas das plantas em tais condições. Desta forma, o objetivo desse trabalho foi analisar os genes diferencialmente expressos (DEGs), através da metodologia de RNA-Seq e quantificar as trocas gasosas em folhas de arroz (cv. BRS Querência), no estádio V3, submetidas aos estresses por frio, ferro e sal durante o período de 24 horas. Um intervalo entre 41 - 51 milhões de reads foram submetidas ao alinhamento, sendo que deste total um intervalo entre 88,47 - 89,21% foram mapeadas no genoma de referência. Foi observado 5.506 genes diferencialmente expressos para o estresse por frio, 1.808 para o sal e 630 para o ferro, sendo que 330 DEGs foram comuns aos três estresses. A anotação funcional através do software MapMan demonstrou que o estresse por frio promoveu maiores alterações no metabolismo em geral. O estresse salino apresentou uma rede de interação de termos de Ontologia Gênica (GOs) sobre-representados mais complexa que os demais estresses. Nos parâmetros de trocas gasosas, a taxa assimilatória liquida foi a única que apresentou diferença significativa, com o estresse por frio apresentando a menor média. A partir dos resultados obtidos foi possível concluir que o estresse por baixa temperatura apresenta um maior número de genes diferencialmente expressos e que há uma maior relação entre o estresse salino e por ferro. Além disso, o estresse por frio é o que afeta mais drasticamente a fotossíntese, tanto em nível molecular quanto fisiológico, e apesar de reduções na taxa assimilatória liquida, a cultivar BRS Querência demonstrou menores alterações nos estresses salino e por excesso de ferro. / Rice (Oryza sativa L.) is the second most cultivated cereal in the world; Brazil is the ninth biggest producer. Despite the high levels of productivity, it is believed that these numbers are insufficient to meet the population requirement in the world, demanding an increase in its production. However, various abiotic stresses, such as salinity, toxicity by iron and low temperature, limit the productivity of rice worldwide. The response of plants to stressful conditions is a complex phenomenon involving morphological, physiological, biochemical and molecular changes. Thus, the knowledge of the transcriptome and photosynthetic analysis of rice plants subjected to these stresses can help to elucidate which metabolic pathways are changed and what are the main biochemical and physiological responses of plants under such conditions. Thus, the objective of this study was to analyze the differentially expressed genes (DEGs), through the methodology of RNA-Seq and quantify gas exchanges in rice leaves (cv. BRS Querência) in V3 stage, under cold, iron and salt stress during 24 hours. A range from 41 to 51 million reads was submitted to alignment, in which a range from 88.47 to 89.21% has been mapped in the reference genome. 5,506 differentially expressed genes under cold stress were observed, as well as, 1,808 for salt and 630 for iron stress; 330 of them were similar to the three DEGs stresses. Functional annotation by MapMan software showed that, usually, cold stress promoted major changes in the metabolism. The saline stress presented a network of interaction of Gene Ontology terms (GOs) over-represented are more complex than the other stresses. In the parameters of gas exchange, the net assimilation rate was the only one significant difference, with stress by cold presenting the lowest average. From the results obtained it was possible to conclude that the low temperature stress has a greater number of differentially expressed genes and that there is a greater relationship between salt and iron stress. In addition, the cold stress is affecting more drastically photosynthesis, either in molecular-level and physiological, and despite reductions in net assimilation rate, BRS Querência showed minor changes in the salt stress and excess iron.

No description available.

Face à la rapidité des changements climatiques, les arbres doivent faire preuve de plasticité phénotypique. Les mécanismes épigénétiques font partie des pistes de recherche actuelles pour expliquer la plasticité phénotypique. Cette thèse visait à évaluer le rôle de la méthylation de l’ADN dans la plasticité phénotypique d’un organisme pérenne séquencé, le peuplier, en réponse à des variations de disponibilité en eau du sol. Les travaux, combinant écophysiologie et épigénomique, se sont focalisés sur le méristème apical caulinaire, centre de la morphogenèse de la tige feuillée. Trois résultats majeurs sont issus de cette thèse : i) Chaque état hydrique est associé à un méthylome et un transcriptome spécifiques, ii) Certaines régions différentiellement méthylées sont conservées dans le temps et entre contextes environnementaux, iii) Des lignées RNAi hypométhylées soumises à différents contextes hydriques présentent une réponse modifiée. Les résultats acquis lors de cette thèse appuient une contribution de la méthylation de l’ADN à la plasticité phénotypique et suggèrent un rôle des mécanismes épigénétiques dans la mémoire d’un stress chez les arbres. / Due to rapid climate changes, trees must exhibit phenotypic plasticity. Epigenetic mechanisms are part of current research to explain phenotypic plasticity. This thesis aimed to evaluate the role of DNA methylation in phenotypic plasticity of a perennial sequenced organism, poplar, in response to variations in soil water availability. The work, combining ecophysiology and epigenomics, focused on the shoot apical meristem, the center of morphogenesis of the leafy stem. Three major results emerge from this thesis: (i) Each hydric state is associated with a specific methylome and transcriptome, (ii) Some differentially methylated regions are conserved in time and between environmental contexts, (iii) Hypomethylated RNAi lines subjected to different contexts show a modified response. The results obtained during this thesis support a contribution of DNA methylation to phenotypic plasticity and suggest a role of epigenetic mechanisms in stress memory in trees.

Les invasions biologiques dans les agroécosystèmes engendrent de lourdes pertes économiques. Parmi les nombreuses espèces en cause, on retrouve les nématodes phytoparasites, vers microscopiques s’attaquant principalement aux racines. Présent dans tous les principaux pays producteurs de soya, le nématode à kyste du soya (NKS), Heterodera glycines, serait à lui seul responsable annuellement de plusieurs milliards de dollars de pertes. La rotation avec des cultivars résistants est le moyen le plus efficace de contrôler les populations de NKS, mais la surutilisation des mêmes lignées a conduit à la sélection d’individus virulents et mené à leur inefficacité. À ce jour, les mécanismes ainsi que les gènes de virulence associés au contournement de la résistance continuent de mystifier les scientifiques. Dans cette thèse, les effets des changements climatiques sur la reproduction et l’établissement du NKS ainsi que sur la phénologie de son hôte, le soya, ont été étudiés. Le premier modèle bioclimatique simulant le cycle de vie du NKS et du soya a été développé. Il a démontré que le nématode peut déjà se reproduire dans toutes les régions du Québec et que la hausse attendue des températures dans le futur proche (2041-2070) permettrait au NKS de pratiquement doubler le nombre de générations produites par saison de croissance dans toutes les régions. De plus, la production de soya issu du groupe de maturité I pourrait s’étendre à toutes les régions du Québec d’ici 2070. Une étude sur la distribution de la variabilité génétique entre 64 populations américaines et ontariennes et les gènes associés à diverses composantes bioclimatiques et leur rôle dans l’adaptation a également été réalisée. Celle-ci a révélé que la diversité génétique était très élevée entre les populations et qu’un flux de gène continu aurait facilité l’adaptation du NKS à diverses conditions bioclimatiques et son établissement dans toutes les régions nord-américaines où l’on produit du soya. Finalement, cette thèse présente l’analyse des génotypes du NKS et des gènes différentiellement exprimés sur des plants de soya résistant (Peking et PI88788) et sensible (Essex). En plus d’identifier plusieurs protéines liées à la virulence, cette étude a permis de mettre en évidence une région génomique sous forte pression évolutive. Cet îlot génique contient plusieurs répétitions en tandem qui ont divergé et dont certaines sont maintenant utilisées de façon sélective pour le contournement de différents types de résistance. / Biological invasions in agroecosystems are a major cause of economic losses. Plant parasitic nematodes are among the many species causing significant crop damages. The soybean cyst nematode (SCN) is causing billions of dollars of losses in all areas where soybean is produced. Rotation with resistant cultivars is the most effective mean of controlling SCN populations, but the overuse of the same lines has led to the selection of virulent individuals and the ineffectiveness of resistance. To this day, the virulence genes and mecanisms associated with the circumvention of resistance continue to mystify scientists. In this thesis, I explored the effects of climate change on the reproduction and establishment of SCN as well as on the phenology of its host, soybean. I have demonstrated that the nematode can already reproduce in all regions of Québec and that the expected rise in temperatures in the near future (2041-2070) will allow the development of more generations per growing season in all regions. In addition, I have demonstrated that the area suitable for the production of soybean from maturity group I will expand toward the north by 2070, further facilitating the expansion of SCN. I have also explored the genetic variability among more than 64 SCN populations from North America and analyzed the genes associated with various bioclimatic components and their role in adaptation. These analyses revealed that the genetic diversity was very high among SCN populations. This diversity associated with a continuous gene flow between populations has facilitated the adaptation of SCN to various bioclimatic conditions and its establishment in all US and Canadian soybean producing regions. Finaly, this thesis presents an analysis of the SCN genotypes and the differentially expressed genes associated with virulence in two resistant soybean lines (Peking and PI88788) and susceptible Essex. This work has identified several proteins associated with virulence and allowed the discovery of a genomic region under strong evolutionary pressure. This island contains several genes in tandem duplications that have diverged and are now used selectively for overcoming different sources of resistance.

Indiana University-Purdue University Indianapolis (IUPUI) / Colon rectal cancer (CRC) is one of the most common cancers worldwide. It is characterized by the successive accumulation of mutations in genes controlling epithelial cell growth and differentiation leading to genomic in-stability. This results in the activation of proto-oncogene(K-ras), loss of tumor suppressor gene activity and ab-normality in DNA repair genes. Targeted therapy is a new generation of cancer treatment in which drugs attack targets which are specific for the cancer cell and are critical for its survival or for its malignant behavior. Survival of metastatic CRC patients has approximately doubled due to the development of new combinations of stan-dard chemotherapy, and the innovative targeted therapies, such as monoclonal antibodies against epidermal growth factor receptor (EGFR) or monoclonal antibodies against vascular endothelial growth factor (VEGFR).The study is to exhibit the need for right drug-right target and provides a proof of principle for potent efficacy of molecular targeted therapy for CRC. We have performed the weighted gene co-expression network analysis for three different patient cohort treated with different targeted therapy drugs. The results demonstrates the variation across different treatment regime in context of transcription factor networks. New significant tran-scription factors have been identified as potential biomarker for CRC cancer including EP300, STAT6, ATF3, ELK1, HNF4A, JUN, TAF1, IRF1, TP53, ELF1 and YY1. The results provides guidance for future omic study on CRC and additional validation work for potent biomarker for CRC.

Patients not responding to therapy as expected is one of the most pressing healthcare concerns of today. It causes economical, medical and societal issues along with suffering for patients. This project aimed to address this problem and evaluate how to find the best suited drug treatments for individual patients to treat Covid-19. This project was carried out in collaboration with the company AB Mavatar, that have two networks, one experimental and one predicted, which produce drug treatment rankings differently. Different methods are used to connect drug targets to disease associated genes and thus evaluate what drugs are best suited for specific patients to treat Covid-19. The aim of this project is to examine how network, method and drug category affect the ranking of a drug treatment for four mapped Covid-19 patients. Which drug category a drug belongs to did not seem to significantly affect the drug ranking. Yet, certain drug subcategories were closely correlated. However, these subcategories were not those that are typically associated with Covid-19. The method used to connect drug targets to disease associated genes heavily impacts the ranking of the drug treatment. The methods should be further evaluated to see if some should be excluded or weighted less in drug ranking calculations. The two networks are similar in how they rank different drugs, especially in severely ill patients. Through this project and the evaluation of the impact of method choice, one can start to figure out what should be prioritized among disease related changes. Also, important parameters for personalized treatment can be evaluated. / Patienter som inte svarar på terapi som förväntat är en av de största utmaningarna inom hälso- och sjukvård idag. Det orsakar ekonomiska, medicinska och samhälleliga problem samt lidande för patienter. Det här projektet adresserade detta problem och evaluerade hur man kan hitta det bäst lämpade läkemedlet för specifika patienter för att behandla Covid-19. Projektet gjordes tillsammans med företaget AB Mavatar, som har två interaktom, en experimentell och en datadriven, som rangordnar läkemedelsrekommendationer på olika sätt. Olika metoder används för att koppla samman läkemedelsmål med sjukdomsrelaterade gener och således evaluera vilka läkemedel som är bäst lämpade för specifika patienter för behandling av Covid-19. Syftet med projektet var att undersöka hur nätverk, metod och läkemedelskategori påverkar hur läkemedel rangordnas för fyra kartlagda Covid-19-patienter.  Vilken läkemedelskategori ett läkemedel tillhör tycks inte märkbart påverka läkemedelsrangordning. Trots detta var vissa läkemedelsunderkategorier nära korrelerade. Dock var dessa underkategorier inte typiskt associerade med Covid-19. Metoden för att koppla samman läkemedelsmål med sjukdomsassocierade gener påverkade läkemedelsrangordningen väsentligt. Metoderna borde dock evalueras ytterligare för att eventuellt exkludera eller vikta vissa mindre i uträkningar av läkemedelsrang. De två nätverken är lika i hur de rangordnar olika läkemedel, särskilt för svårt sjuka patienter. Genom detta projekt och genom evaluering av metodvalets påverkan kan man börja begripa hur man borde priorita bland sjukdomsrelaterade förändringar. Dessutom kunde viktiga parametrar inom personlig behandling evalueras.

<p dir="ltr">The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects but does not necessarily indicate the initial point of interference within a network. The objective of this project is to take advantage of large scale and genome-wide perturbational or Perturb-Seq datasets by using them to pre-train a generalist machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of single cell RNA sequencing data collected from CRISPR knock out screens in cell culture. The advent of generative machine learning algorithms, particularly transformers, make it an ideal time to re-assess large scale data libraries in order to grasp cell and even organism-wide genomic expression motifs. By tailoring an algorithm to learn the downstream effects of the genetic perturbations, we present a pre-trained generalist model capable of predicting the effects of multiple perturbations in combination, locating points of origin for perturbation in new datasets, predicting the effects of known perturbations in new datasets, and annotation of large-scale network motifs. We demonstrate the utility of this model by identifying key perturbational signatures in RNA sequencing data from spaceflown biological samples from the NASA Open Science Data Repository.</p>