Academic literature on the topic 'Transcriptomic analysi'
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Journal articles on the topic "Transcriptomic analysi"
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Ochsner, Scott A., Christopher M. Watkins, Apollo McOwiti, Xueping Xu, Yolanda F. Darlington, Michael D. Dehart, Austin J. Cooney, David L. Steffen, Lauren B. Becnel, and Neil J. McKenna. "Transcriptomine, a web resource for nuclear receptor signaling transcriptomes." Physiological Genomics 44, no. 17 (September 1, 2012): 853–63. http://dx.doi.org/10.1152/physiolgenomics.00033.2012.
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The nuclear receptor (NR) superfamily of ligand-regulated transcription factors directs ligand- and tissue-specific transcriptomes in myriad developmental, metabolic, immunological, and reproductive processes. The NR signaling field has generated a wealth of genome-wide expression data points, but due to deficits in their accessibility, annotation, and integration, the full potential of these studies has not yet been realized. We searched public gene expression databases and MEDLINE for global transcriptomic datasets relevant to NRs, their ligands, and coregulators. We carried out extensive, deep reannotation of the datasets using controlled vocabularies for RNA Source and regulating molecule and resolved disparate gene identifiers to official gene symbols to facilitate comparison of fold changes and their significance across multiple datasets. We assembled these data points into a database, Transcriptomine ( http://www.nursa.org/transcriptomine ), that allows for multiple, menu-driven querying strategies of this transcriptomic “superdataset,” including single and multiple genes, Gene Ontology terms, disease terms, and uploaded custom gene lists. Experimental variables such as regulating molecule, RNA Source, as well as fold-change and P value cutoff values can be modified, and full data records can be either browsed or downloaded for downstream analysis. We demonstrate the utility of Transcriptomine as a hypothesis generation and validation tool using in silico and experimental use cases. Our resource empowers users to instantly and routinely mine the collective biology of millions of previously disparate transcriptomic data points. By incorporating future transcriptome-wide datasets in the NR signaling field, we anticipate Transcriptomine developing into a powerful resource for the NR- and other signal transduction research communities.
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Callaway, Edward M., Hong-Wei Dong, Joseph R. Ecker, Michael J. Hawrylycz, Z. Josh Huang, Ed S. Lein, John Ngai, et al. "A multimodal cell census and atlas of the mammalian primary motor cortex." Nature 598, no. 7879 (October 6, 2021): 86–102. http://dx.doi.org/10.1038/s41586-021-03950-0.
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AbstractHere we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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Nesterenko, Maksim, and Aleksei Miroliubov. "From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)." F1000Research 11 (May 27, 2022): 583. http://dx.doi.org/10.12688/f1000research.110492.1.
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Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, the system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into “zombies”. Despite all these amazing traits, there is no genomic and transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: externa and main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for both P. reticulata and Rhizocephala. Based on the results obtained, the spatial heterogeneity of protein-coding genes expression in different regions of P. reticulata adult female body was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans “got stuck in the metamorphosis”, even in their reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of this amazing parasites.
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Nesterenko, Maksim, and Aleksei Miroliubov. "From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)." F1000Research 11 (January 9, 2023): 583. http://dx.doi.org/10.12688/f1000research.110492.2.
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Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into “zombies”. Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: the externa, and the main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite’s body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for any rhizocephalan. Based on the results obtained, the spatial heterogeneity of protein-coding gene expression in different regions of the adult female body of P. reticulata was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans “got stuck in their metamorphosis”, even at the reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of these extraordinary parasites.
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Chen, Wanze, Orane Guillaume-Gentil, Pernille Yde Rainer, Christoph G. Gäbelein, Wouter Saelens, Vincent Gardeux, Amanda Klaeger, et al. "Live-seq enables temporal transcriptomic recording of single cells." Nature 608, no. 7924 (August 17, 2022): 733–40. http://dx.doi.org/10.1038/s41586-022-05046-9.
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AbstractSingle-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity1. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy2,3, thus allowing to couple a cell’s ground-state transcriptome to its downstream molecular or phenotypic behaviour. To benchmark Live-seq, we used cell growth, functional responses and whole-cell transcriptome read-outs to demonstrate that Live-seq can accurately stratify diverse cell types and states without inducing major cellular perturbations. As a proof of concept, we show that Live-seq can be used to directly map a cell’s trajectory by sequentially profiling the transcriptomes of individual macrophages before and after lipopolysaccharide (LPS) stimulation, and of adipose stromal cells pre- and post-differentiation. In addition, we demonstrate that Live-seq can function as a transcriptomic recorder by preregistering the transcriptomes of individual macrophages that were subsequently monitored by time-lapse imaging after LPS exposure. This enabled the unsupervised, genome-wide ranking of genes on the basis of their ability to affect macrophage LPS response heterogeneity, revealing basal Nfkbia expression level and cell cycle state as important phenotypic determinants, which we experimentally validated. Thus, Live-seq can address a broad range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.
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Gui, Yu, Xiujing He, Jing Yu, and Jing Jing. "Artificial Intelligence-Assisted Transcriptomic Analysis to Advance Cancer Immunotherapy." Journal of Clinical Medicine 12, no. 4 (February 6, 2023): 1279. http://dx.doi.org/10.3390/jcm12041279.
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The emergence of immunotherapy has dramatically changed the cancer treatment paradigm and generated tremendous promise in precision medicine. However, cancer immunotherapy is greatly limited by its low response rates and immune-related adverse events. Transcriptomics technology is a promising tool for deciphering the molecular underpinnings of immunotherapy response and therapeutic toxicity. In particular, applying single-cell RNA-seq (scRNA-seq) has deepened our understanding of tumor heterogeneity and the microenvironment, providing powerful help for developing new immunotherapy strategies. Artificial intelligence (AI) technology in transcriptome analysis meets the need for efficient handling and robust results. Specifically, it further extends the application scope of transcriptomic technologies in cancer research. AI-assisted transcriptomic analysis has performed well in exploring the underlying mechanisms of drug resistance and immunotherapy toxicity and predicting therapeutic response, with profound significance in cancer treatment. In this review, we summarized emerging AI-assisted transcriptomic technologies. We then highlighted new insights into cancer immunotherapy based on AI-assisted transcriptomic analysis, focusing on tumor heterogeneity, the tumor microenvironment, immune-related adverse event pathogenesis, drug resistance, and new target discovery. This review summarizes solid evidence for immunotherapy research, which might help the cancer research community overcome the challenges faced by immunotherapy.
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Cheon, Seongmin, Sung-Gwon Lee, Hyun-Hee Hong, Hyun-Gwan Lee, Kwang Young Kim, and Chungoo Park. "A guide to phylotranscriptomic analysis for phycologists." Algae 36, no. 4 (December 15, 2021): 333–40. http://dx.doi.org/10.4490/algae.2021.36.12.7.
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Phylotranscriptomics is the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes. Because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics, the phylotranscriptomic analysis has recently emerged as the preferred method for studying evolutionary biology. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. This study presents a protocol for phylotranscriptomic analysis to aid marine biologists unfamiliar with UNIX command-line interface and bioinformatics tools. Here, we used transcriptomes to reconstruct a molecular phylogeny of dinoflagellate protists, a diverse and globally abundant group of marine plankton organisms whose large and complex genomic sequences have impeded conventional phylogenic analysis based on genomic data. We hope that our proposed protocol may serve as practical and helpful information for the training and education of novice phycologists.
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Chaudhuri, Roy R., Lu Yu, Alpa Kanji, Timothy T. Perkins, Paul P. Gardner, Jyoti Choudhary, Duncan J. Maskell, and Andrew J. Grant. "Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome." Microbiology 157, no. 10 (October 1, 2011): 2922–32. http://dx.doi.org/10.1099/mic.0.050278-0.
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C ampylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community.
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Ortiz, Randy, Priyanka Gera, Christopher Rivera, and Juan C. Santos. "Pincho: A Modular Approach to High Quality De Novo Transcriptomics." Genes 12, no. 7 (June 22, 2021): 953. http://dx.doi.org/10.3390/genes12070953.
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Transcriptomic reconstructions without reference (i.e., de novo) are common for data samples derived from non-model biological systems. These assemblies involve massive parallel short read sequence reconstructions from experiments, but they usually employ ad-hoc bioinformatic workflows that exhibit limited standardization and customization. The increasing number of transcriptome assembly software continues to provide little room for standardization which is exacerbated by the lack of studies on modularity that compare the effects of assembler synergy. We developed a customizable management workflow for de novo transcriptomics that includes modular units for short read cleaning, assembly, validation, annotation, and expression analysis by connecting twenty-five individual bioinformatic tools. With our software tool, we were able to compare the assessment scores based on 129 distinct single-, bi- and tri-assembler combinations with diverse k-mer size selections. Our results demonstrate a drastic increase in the quality of transcriptome assemblies with bi- and tri- assembler combinations. We aim for our software to improve de novo transcriptome reconstructions for the ever-growing landscape of RNA-seq data derived from non-model systems. We offer guidance to ensure the most complete transcriptomic reconstructions via the inclusion of modular multi-assembly software controlled from a single master console.
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Macrander, Jason, Jyothirmayi Panda, Daniel Janies, Marymegan Daly, and Adam M. Reitzel. "Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data." PeerJ 6 (July 31, 2018): e5361. http://dx.doi.org/10.7717/peerj.5361.
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The advent of next-generation sequencing has resulted in transcriptome-based approaches to investigate functionally significant biological components in a variety of non-model organism. This has resulted in the area of “venomics”: a rapidly growing field using combined transcriptomic and proteomic datasets to characterize toxin diversity in a variety of venomous taxa. Ultimately, the transcriptomic portion of these analyses follows very similar pathways after transcriptome assembly often including candidate toxin identification using BLAST, expression level screening, protein sequence alignment, gene tree reconstruction, and characterization of potential toxin function. Here we describe the Python package Venomix, which streamlines these processes using common bioinformatic tools along with ToxProt, a publicly available annotated database comprised of characterized venom proteins. In this study, we use the Venomix pipeline to characterize candidate venom diversity in four phylogenetically distinct organisms, a cone snail (Conidae; Conus sponsalis), a snake (Viperidae; Echis coloratus), an ant (Formicidae; Tetramorium bicarinatum), and a scorpion (Scorpionidae; Urodacus yaschenkoi). Data on these organisms were sampled from public databases, with each original analysis using different approaches for transcriptome assembly, toxin identification, or gene expression quantification. Venomix recovered numerically more candidate toxin transcripts for three of the four transcriptomes than the original analyses and identified new toxin candidates. In summary, we show that the Venomix package is a useful tool to identify and characterize the diversity of toxin-like transcripts derived from transcriptomic datasets. Venomix is available at: https://bitbucket.org/JasonMacrander/Venomix/.
Dissertations / Theses on the topic "Transcriptomic analysi"
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Jousset, Agnès. "analyse génomique et transcriptomique de bactéries productrices de carbapénèmases." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS527.
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Le combat contre les infections bactériennes reste un enjeu majeur de santé publique notamment avec la dissémination des Entérobactéries productrices de carbapénèmases, capables d’hydrolyser l’ensemble des β-lactamines. On assiste à l’émergence de certains clones épidémiques, se distinguant par leur distribution mondiale, leur forte transmissibilité et leur capacité à persister chez les patients. L’exemple le plus parlant est le cas du clone de Klebsiella pneumoniae appartenant au « sequence type » (ST) 258 et responsable de la diffusion mondiale de la carbapénèmase KPC (Klebsiella Pneumoniae Carbapenemase) portée majoritairement par des plasmides de la famille InFIIk. Les raisons du succès de ce clone et de l’association KPC/IncFIIk/ST258 ne sont pas encore totalement élucidées. Par ailleurs, il n’existe pas de corrélation entre le niveau d’expression d’une carbapénèmase, la sensibilité in vitro de la souche vis à vis des carbapénèmes et l’efficacité clinique d’un traitement par ces molécules. Les phénomènes d’héterorésistance aux carbapénèmes sont fréquents chez les souches produisant KPC, mais l’impact clinique est inconnu. Les mécanismes de régulation de l’expression des carbapénèmases ne sont pas élucidés.Les objectifs de cette thèse résident dans l’analyse des facteurs génétiques associés à la diffusion et la persistance de clones multi-résistants ainsi que l’analyse de l’expression des β-lactamases associées.La première partie de ce travail porte sur l’analyse de l’évolution in vivo d’une souche de K. pneumoniae ST258 produisant KPC ayant persisté chez un patient pendant près de 5 ans. L’analyse comparative des génomes provenant de 17 isolats a permis de mettre en évidence une diversification génétique importante ainsi que la sélection de mutations modifiant la virulence de la souche et sa sensibilité aux antibiotiques. Afin de caractériser les raisons du succès de certains plasmides portant KPC, une analyse transcriptomique d’une souche de Escherichia coli TOP10 transformée par un plasmide multi-réplicon IncFIIk-IncFIB exprimant KPC-2, a été réalisée en présence ou non d’imipénème. Les gènes les plus exprimés dans ces conditions sont les gènes de résistance aux antibiotiques et certains gènes essentiels à la réplication du plasmide. La présence d’imipénème affecte peu la transcription des gènes plasmidiques mais induit un stress oxydatif important dans l’ensemble de la souche. Par ailleurs, l’analyse de l’expression du gène blaKPC-2 dans différentes espèces par 5’-RACE a permis de révéler que ce gène de résistance est sous la dépendance de plusieurs promoteurs, dont la force diffère selon le fond génétique. Cette caractéristique pourrait expliquer le succès de certains isoformes du transposon Tn4401 permettant une meilleure expression du gène blaKPC-2, dans certaines espèces. Les outils développés dans cette thèse ont également été appliqués à l’analyse d’un clone d’Enterobacter kobei ST125 dont la céphalosporinase naturelle ACT-28 possède une activité d’hydrolyse accrue vis à vis de l’imipénème. Enfin, l’analyse du génome de la première souche Shewanella sp. produisant une BLSE de type CTX-M-15 a permis de révéler la présence d’un nouveau variant oxacillinase chromosomique avec activité carbapénèmase, appelé OXA-535. OXA-535 est proche d’OXA-436, un autre variant carbapénèmase porté par un plasmide ayant déjà disséminé chez les Entérobactéries. L’analyse de l’environnement génétique des gènes blaOXA-535 et blaOXA-436 confirme le rôle du genre Shewanella comme progéniteur des carbapénèmases de classe D. Ce travail contribue à une meilleure compréhension de la diffusion de certains clones multi-résistants et des mécanismes contrôlant l’expression des gènes de résistance aux β-lactaminesMultidrug resistant bacteria and in particular carbapenemase-producing Enterobacteriaceae remain a major health public challenge. Some successful clones are emerging globally, due to their high transmissibility and their ability to colonize and persist in patients over time. Genomic analyses revealed that the dissemination of KPC carbapenemase is closely related to the spread of Klebsiella pneumoniae of the sequence-type (ST) 258 and to few successful plasmids linked to IncFIIk family. However, the reasons of the association between K. pneumoniae ST258, IncFIIk plasmids and KPC that led to the rapid spread of this clone are currently unknown.Furthermore, there is no correlation between expression level of a carbapenemase-encoding gene, in vitro susceptibility to carbapenems and efficiency of a carbapenem-based treatment. Most of the time, KPC-producing K. pneumoniae exhibit a heteroresistant phenotype with carbapenems, but its clinical impact remains unknown. The mechanisms underlying the regulation of carbapenemases expression remain to be explored.The objectives of the thesis are to obtain deeper insights into genomic plasticity of carbapenemase–producing clones, and into the expression of their β-lactamases.The first part of this work was dedicated to the in vivo evolution of a single strain of KPC-producing K. pneumoniae ST258 that colonized a patient for almost 5 years. Genomic comparison of 17 isolates revealed a remarkable diversification with occurrence of several mutations with impact on bacterial virulence and susceptibility to antibiotics.Several studies extensively described the genetic structures of blaKPC-carrying plasmids, but information regarding gene expression at the whole plasmid level are lacking. Accordingly, we performed RNA-seq on Escherichia coli TOP10 transformed with an IncFIIk-IncFI blaKPC-2-carrying plasmid, with or without imipenem exposure. In both conditions, plasmid-encoded genes related to antimicrobial resistance and involved in plasmid replication were the most expressed. Imipenem exposure led to a more general response with overexpression of E. coli numerous chromosome-encoded genes involved in oxidative stress response. In addition, analysis of blaKPC-2 gene expression in several species using 5’RACE revealed the presence of several promoters whose strength depends on the bacterial genetic background. This could promote higher expression of blaKPC-2 gene and explain the association of some isoforms of Tn4401 in different species. The tools developed in the frame of this work were also applied to study a single Enterobacter kobei ST125 clone whose natural cephalosporinase (ACT-28) has increased hydrolytic activity towards imipenem. Finally, genomic analysis of the first ESBL-producing Shewanella sp. was performed. It revealed the presence of blaCTX-M-15 and blaSHV-2 genes carried on an IncA/C plasmid and a new chromosomally-encoded oxacillinase variant of OXA-48 with carbapenemase activity, called OXA-535. OXA-535 was found to be closely related to OXA-436, another carbapenemase which has recently spread in Enterobacteriaceae. Analysis of the genetic environment of both blaOXA-48-like genes confirmed the role of Shewanella spp. as progenitors of class D carbapenemases.Overall, this work contributes to a better comprehension of the diffusion of multi-drug resistant clones and of the mechanisms implicated in β-lactamase expression
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Rodó, Morera Jordi. "Transcriptomic analysis of white and brown adipose tissue during non-shivering thermogenesis." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667915.
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L’obesitat i la diabetis tipus 2 (DT2) són dues malalties estretament relacionades que representen un greu problema de salut, social i econòmic per la seva alta prevalença a tot el món. Ambdues malalties també es relacionen amb altres patologies que presenten una mortalitat elevada. Les teràpies disponibles actualment no són del tot efectives. Per tant, el desenvolupament de noves estratègies terapèutiques per a l'obesitat i la DT2 és crucial.
El teixit adipós s'ha definit com un òrgan que té un paper central en el control del balanç energètic. El descobriment de funcions endocrines i termogèniques dels adipòcits han tornat a centrar l’interès en l’estudi d’aquest teixit. La termogènesi no associada a tremolor està descrita per dur-se a terme al teixit adipós marró dels ratolins, però sota certs estímuls, com l'exposició prolongada al fred, cèl·lules amb una morfologia similar als adipòcits marrons (adipòcits beix) apareixen en alguns dipòsits de teixit adipós blanc de rosegadors i humans, un procés conegut com a browning. L’activació a través de l’exposició al fred de la termogènesi no associada a tremolor en humans augmenta el consum energètic en repòs, la sensibilitat a la insulina i millora el metabolisme de la glucosa. No obstant, es necessiten més estudis d'expressió gènica per aprofundir en els mecanismes moleculars subjacents a la millora induïda per fred a través de la termogènesi no associada a tremolor, així com per determinar les diferències entre l'activació del teixit adipós marró (BAT) i el browning del teixit adipós blanc (WAT).
En aquesta tesi doctoral, es van examinar els canvis transcriptómica dels dipòsits adiposos blancs epidídimal i inguinal (eWAT i iWAT, respectivament), així com la del dipòsit adipós marró interscapular (iBAT) de ratolins exposats a 22ºC o 4ºC durant 4 dies. L’exposició al fred va augmentar l’activitat metabòlica i termogènica de l’iWAT. En aquest dipòsit, els gens relacionats amb la glucòlisi, el cicle de l'àcid tricarboxílic, la lipòlisi i la degradació d'alguns aminoàcids van presentar una expressió incrementada per mantenir la potència protonmotriu per generar calor. A més, l'expressió de gens relacionats amb la termogènesi també va augmentar molt, demostrant una inducció del browning induïda per fred en el iWAT. S'ha descrit que el dipòsit d’eWAT és resistent al browning. Per tant, l’activació metabòlica observada d’aquest dipòsit va ser suau en comparació amb la d’iWAT, i en aquest dipòsit no es va observar cap millora rellevant de la termogènesi no associada a tremolor. Finalment, l’iBAT ja presentava nivells d’expressió de gens termogènics elevats, ja que els ratolins no estaven estabulats a termo-neutralitat.
L’observació que els gens termogènics i metabòlics presentaven un patró d’expressió similar entre les mostres va recolzar l’ús d’eines d’anàlisi de patrons per descriure Atp4b i 1700040L02Rik com a nous gens potencialment implicats en la termogènesi. La sobreexpressió d’Atp4b i 1700040L02Rik en el teixit adipós mitjançant l’ús de vectors AAV va produir una reducció del guany de pes corporal, una disminució del pes de l'eWAT i del fetge, la millora de la hipertròfia dels adipòcits blancs i la reducció de la esteatosi hepàtica. Tots aquests resultats van ser potencialment fruit de la termogènesi millorada detectada en iWAT. En general, aquests resultats indiquen un possible nou paper anti-obesogènic d’aquests gens.
Els resultats d’aquesta tesi han contribuit a una millor comprensió de la inducció de la termogènesi no associada a tremolor en els dipòsits de teixit adipós de ratolins. Entre els diferents dipòsits de teixit adipos, l’anàlisi exploratori dels nivells d’expressió gènica va determinar que el iWAT era el dipòsit que va respondre de manera més significativa a l’exposició al fred. A més, tal com es va observar en l’anàlisi de l’enriquiment de vies i d’ontologia gènica, aquesta resposta va ser altament coordinada, presentant un elevat nombre de gens relacionats amb rutes metabòliques que presentaven una expressió altament incrementats. Igualment, l’estudi detallat de les vies metabòliques va destacar una gran inducció de la termogènesi no associada a tremolor, revelar que els mecanismes de producció i de consum d’energia estaven altament sincronitzats. Aquest estudi detallat del teixit adipós també va permetre la identificació de nous gens potencialment implicats en la termogènesi no associada a tremolors.Obesity and type 2 diabetes (T2D) are two closely related diseases that represent a serious health, social and economic problem due to their high prevalence worldwide. Both diseases are also associated with other pathologies that present high mortality. The currently available therapies are not entirely effective. Thus, the development of new therapeutic strategies for obesity and T2D is crucial. Adipose tissue has been defined as an organ that plays a central role in the control of energy balance. The proved endocrine and thermogenic functions of adipocytes has renewed interest in the study of this tissue. Non-shivering thermogenesis has been described as occurring in brown adipose tissue of mice, but under certain stimuli, such as prolonged cold exposure, brown fat-like cells (beige adipocytes), appear in some white adipose tissue depots of rodents and humans. The activation of non-shivering thermogenesis in humans through cold-exposure increases resting energy expenditure, whole-body glucose disposal, insulin sensitivity, and ameliorates glucose metabolism independently of BMI. However, more gene expression studies to gain insight into the molecular mechanisms underlying the cold-induced enhancement of non-shivering thermogenesis, as well as to determine differences between BAT activation and browning of WAT, are needed. In this study, the transcriptomic response of epididymal and inguinal white adipose depots (eWAT and iWAT, respectively) as well as that of the interscapular brown adipose depot (iBAT) of mice either exposed to 22ºC or 4ºC for the period of 4 days were examined. Cold exposure increased the metabolic and thermogenic activity of iWAT. In this depot, genes related to glycolysis, tricarboxylic acid cycle, lipolysis, and the degradation of some amino acids presented a high upregulation to maintain the protonmotive power to generate heat. Moreover, the expression of thermogenic-related genes was also highly increased, demonstrating a cold-induced browning of iWAT. The eWAT depot has been reported to be resilient to browning. Thus, the observed metabolic activation of this depot was mild in comparison with that of iWAT, and no relevant enhancement of non-shivering thermogenesis was observed in this depot. Finally, iBAT already presented high expression levels of thermogenic genes because mice were not housed at thermoneutrality. The observation that genes related to thermogenesis and metabolism presented a similar expression pattern among samples endorsed the utilization of pattern matching analysis tools to unravel Atp4b and 1700040L02Rik as novel genes potentially involved in thermogenesis. The overexpression of Atp4b and 1700040L02Rik in adipose tissue by means of AAV vectors produced a body weight gain reduction, decreased eWAT, and liver weight, amelioration of white adipocytes hypertrophy, and reduced hepatic steatosis potentially as a result of the detected enhanced thermogenesis in iWAT. Overall, these results indicate a new potential anti-obesogenic role for these genes. The results from this thesis contributed to a better understanding of the induction of non-shivering thermogenesis in adipose tissue depots in mice. Among the different adipose depots, exploratory data analysis of the gene expression levels of mice exposed from 22ºC to 4ºC determined that iWAT was the depot that responded most significantly to cold exposure. Moreover, as observed in the pathway enrichment and gene ontology analysis, this response was highly coordinated, presenting a high number of genes related to metabolic pathways highly affected. The detailed study of the metabolic pathways led to the detection of a high induction of non-shivering thermogenesis, revealing that both energy production and energy consumption mechanisms were highly synchronized. This in detail study of the adipose tissue also allowed the identification of novel genes potentially involved in non-shivering thermogenesis.
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Stranneheim, Henrik. "Enabling massive genomic and transcriptomic analysis." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45957.
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In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid advances have enormously expanded sequencing opportunities and applications, but also imposed heavy strains on steps prior to sequencing, as well as the subsequent handling and analysis of the massive amounts of sequence data that are generated, in order to exploit the full capacity of these novel platforms. The work presented in this thesis (based on six appended papers) has contributed to balancing the sequencing process by developing techniques to accelerate the rate-limiting steps prior to sequencing, facilitating sequence data analysis and applying the novel techniques to address biological questions. Papers I and II describe techniques to eliminate expensive and time-consuming preparatory steps through automating library preparation procedures prior to sequencing. The automated procedures were benchmarked against standard manual procedures and were found to substantially increase throughput while maintaining high reproducibility. In Paper III, a novel algorithm for fast classification of sequences in complex datasets is described. The algorithm was first optimized and validated using a synthetic metagenome dataset and then shown to enable faster analysis of an experimental metagenome dataset than conventional long-read aligners, with similar accuracy. Paper IV, presents an investigation of the molecular effects on the p53 gene of exposing human skin to sunlight during the course of a summer holiday. There was evidence of previously accumulated persistent p53 mutations in 14% of all epidermal cells. Most of these mutations are likely to be passenger events, as the affected cell compartments showed no apparent growth advantage. An annual rate of 35,000 novel sun-induced persistent p53 mutations was estimated to occur in sun-exposed skin of a human individual. Paper V, assesses the effect of using RNA obtained from whole cell extracts (total RNA) or cytoplasmic RNA on quantifying transcripts detected in subsequent analysis. Overall, more differentially detected genes were identified when using the cytoplasmic RNA. The major reason for this is related to the reduced complexity of cytoplasmic RNA, but also apparently due (at least partly) to the nuclear retention of transcripts with long, structured 5’- and 3’-untranslated regions or long protein coding sequences. The last paper, VI, describes whole-genome sequencing of a large, consanguineous family with a history of Leber hereditary optic neuropathy (LHON) on the maternal side. The analysis identified new candidate genes, which could be important in the aetiology of LHON. However, these candidates require further validation before any firm conclusions can be drawn regarding their contribution to the manifestation of LHON.QC 20111115
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Braga, D. "TRANSCRIPTOMIC ANALYSIS IN SEPTIC SHOCK PATIENTS." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/473670.
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Introduction
Septic shock, also defined as distributive shock, is a complication of sepsis, characterized by pronounced hypotension, followed by anomalous distribution of blood at vessels, organs and tissues. The hemodynamic, cellular and metabolic alterations described in septic shock patients lead to a mortality that is at present around 40%. Septic shock patients develop dysfunctions or failure to multiple organs (MOF) but the molecular mechanisms triggering tissue injury remain largely undetermined and a specific treatment for septic shock is still not available.
Aim
This work is part of the European Project ShockOmics, a multicentric, prospective, observational study, whose aim is to identify with a multiscale approach, molecular biomarkers in septic shock patients who develop acute heart failure. The specific aim of the present Research project is to investigate the modifications induced by septic shock on transcriptional profile, using blood cells as RNA source. This investigation is performed at different timepoints starting from admission of the patient to the intensive care unit (ICU).
Materials and Methods
Septic shock patients were recruited in the ICUs of Geneva and Bruxelles University Hospitals, that are Partners of ShockOmics Project. Blood samples were collected in the acute phase of the disease at ICU admission (T1), after the appropriate pharmacological intervention (T2 ) and at steady state on day 7 of the ICU stay (T3). RNA was extracted from whole blood and RNA sequencing was used to evaluate the expression level of genes, long non coding RNAs and microRNAs. We explored the dataset using PCA and unsupervised hierarchical clustering and we identified differentially expressed genes and microRNAs across conditions. Gene Ontology analysis was used to identify relevant biological processes involved in shock. We identified microRNA regulatory targets with an in silico target prediction.
Results
We identified two main gene expression profiles corresponding to the acute phase of shock and to the condition of steady state. Between the acute phase of shock (day 1) and the steady state condition (day 7) we observed in patients at day 7 a downregulation of pathways of the innate immune response (Toll-like receptor and C-type lectin receptors pathways) and of acute inflammation (IL-1 receptor family and alarmins) and the upregulation in the same patients of genes of the adaptive immunity related to B and T lymphocytes activation. A transcriptional regulation was observed also for genes with antimicrobial function and protease activity and for genes involved in carbohydrate metabolism, lipid inflammatory pathway, transport of vesicles and protein synthesis. miR-125a-5p and miR-150-5p, with a predicted regulatory role in the MAPK pathway, and miR-193a-3p were differentially expressed in the acute and steady state condition.
Conclusion
We observed a significant modulation of multiple classes of genes involved in defense response to pathogens, immunity, inflammation and metabolism. From these results it appears that in septic shock a relevant change in the transcriptomic profile of blood cells is induced, in order to counteract the pathogens and as a consequence of the hemodynamic changes underlying the circulatory failure. The transcriptomic profile of septic shock patients showed inter patient variability reflecting the complexity of the shock condition and of the individual response to treatment. Specific signatures could turn out by combining clinical data and expression profile and could be used to better classify septic shock patients.
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Loe-mie, Yann. "Contribution bioinformatique à l' analyse du transcriptome humain." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM4002/document.
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Dans la première partie j'ai analysé des jeux de données de RNA-seq de transcriptome de petits ARNs disponibles dans les bases de données publiques. J'y ai observé 2 points intrigants : - une grande partie des lectures (bien que courtes) ne peux pas être alignée sur le génome de référence sans discordance et cette fraction non-alignable est parfois majoritaire. - de nombreuses lectures ont des tailles autours de 15-18nt qui ne correspondent à aucun type de petits ARNs connues, cette fraction est également majoritaires dans certains cas. Ces expériences sont souvent conçues pour la détection des miRNAs et l'analyse bioinformatique de ces données passent toujours par un alignement sur le génome de référence ou sur des séquences connues pour donner des petits ARNs. J'ai donc simplement éliminé la contrainte d'alignement dans l'analyse de ces données et effectué un regroupement des lectures par similarité (à la manière des ESTs). Ce regroupement donne une vision différente des données dans laquelle la notion de position génomique n'est plus centrale et ouvre la possibilité d'y découvrir des phénomènes non-standard. La deuxième partie est tirée d'une collaboration avec le laboratoire U675 INSERM. J'ai fait l'analyse bioinformatique des gènes dérégulés par la répression par RNAi du gène REST dans une lignée de neuroblastome de souris (N18). Ce gène est un facteur de transcription qui réprime les gènes neuronaux dans les cellules non neuronales. Ce répertoire de gènes dérégulés est potentiellement constitué de gènes clefs dans la biologie des neuronesIn first part of this thesis I have analysed small RNA-seq transcriptome data. I have noticed : - a large fraction of reads can't be aligned perfectly on reference genome - lot of reads are very short (15-18 nt) and don't match on previously known functionnal small RNAs. These experiments are designed for miRNA discovery and bioinformatics analysis of these data use alignments on genome or on known small RNA precursors sequences. I have eliminated the alignment and I have clustered these sequences. This clustering let me to observe these data with a new view in wich the genomic location is not central and open the gate to discover unconventional events. The second part is the analysis of deregulate genes by the silencing of the gene REST/NRSF in mouse N18 cell line. This gene is a transcription factor and it works as a repressor of neuronal genes in non neuronal cells. This deregulate genes repertoire potentially contains key genes in neuron biology. We found in this repertoire a network of genes centered on SWI/SNF complex including SMARCA2. This gene was associated to schizophrenia (SZ) in association studies and structural variation studies. In this network we found another genes associated to SZ. We show that these genes exhibit positive evolution in primate compare to rodents
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Sidaway, Adam. "Transcriptomics analysis of differentiating erythroblasts." Thesis, University of Bristol, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.715794.
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Badawi, Sally. "Characterization of dynamic molecular networks in control ischemic-reperfused mouse heart." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSE1158.
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Les maladies cardiovasculaires représentent un important problème de santé publique à travers le monde. Parmi ces pathologies, l’infarctus du myocarde (IM) a fait l’objet de nombreux essais visant à diminuer sa sévérité. Néanmoins peu ont remporté leur pari. Cet échec peut avoir plusieurs composantes parmi lesquelles la méconnaissance de la complexité des mécanismes moléculaires impliqués. Notre compréhension de l’IM a cependant été nettement améliorée grâce à des méthodes utilisées pendant les dernières décennies et qui consistaient à étudier séparément un nombre limité d’acteurs moléculaires impliqués dans un mécanisme simple et linéaire. Cependant, l’échec des essais cliniques basés sur ces approches réductionnistes ont montré leurs limites. L’émergence de la biologie des systèmes, ces dernières années, a stimulé les recherches visant à mieux intégrer et comprendre la nature complexe et stochastique des réseaux moléculaires et leur dynamique dans la progression des pathologies. L’objectif général de cette thèse a consisté en le développement et l’amélioration de méthode d’analyses et de combinaison des données spatio-temporelles issus d’expériences réalisées sur un modèle d’infarctus du myocarde chez la souris. L’objectif scientifique visait à caractériser les principaux signaux dynamiques au cours de la séquence d’ischémie-reperfusion. A cet effet, nous avons tout d’abord développé une chaîne de méthode utilisant la clarification d’organe et la microscopie de fluorescence permettant de quantifier, en 3 dimensions, la zone du myocarde soumise au choc oxydant lors de la reperfusion. Dans une seconde partie, nous avons développé une nouvelle chaîne analytique pour caractériser la dynamique d’expression des transcrits. Appliquée aux animaux contrôles (soumis à la chirurgie et l’anesthésie), nous mettrons, grâce à cette chaîne de méthode, le rôle majeur de la voie de l’interleukine 6 dans le développement de la réponse immunitaire et nous concluons ainsi sur la nécessité de réaliser une analyse dynamique du modèle expérimental pour caractériser sa réponse à l’échelle moléculaire et éviter toute surinterprétation de la réponse à l’IMCardiovascular diseases represent a major health burden worldwide. According to the World Health Organization, 17 million people are dying each year by heart diseases which account to 31% of total deaths globally. Among these diseases is myocardial infarction (MI). Several efforts have been made to decrease the associated mortality rates but unfortunately, only few has succeeded to date. This failure is contributed to several factors, among them is the misunderstanding of the mechanism responsible for the progression of the disease.Our understanding of the MI pathology has been greatly improved by the approaches that have been widely used in the previous decades, relying mainly on studying molecules/pathways separately. However, this knowledge was not enough to make a difference clinically. Therefore, deciphering the interconnections between molecules has become an urge for better understanding of the diseases’ progression. In this regard, the work in this doctoral thesis involves different aspects of the MI pathology. The general aim of this work is to improve the dynamic analytical approach using systems biology tools, where new mechanistic information is decoded. Firstly, in a 3D heart model, we propose a chain of methods using clarified mouse heart and fluorescence microscopy to molecularly characterize the area at risk in the myocardium of IR and cardioprotected mice based on its redox state. In addition, we aim to develop a new analytical approach using dynamical large-scale transcriptomic data for characterizing the dynamic transcripts expression. Applying this approach on a control mouse model (mice subjected to anesthesia and surgical interventions), we show that Il-6 is a major mediator of the activated inflammatory reaction. In conclusion, this analytical approach highlights the necessity of the sapatio-temporal analysis to characterize the molecular events occurring in response to MI
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Schwalb, Björn. "Dynamic transcriptome analysis (DTA)." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-147748.
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BERTOLAZZI, Giorgio. "MicroRNA Interaction Networks." Doctoral thesis, Università degli Studi di Palermo, 2021. http://hdl.handle.net/10447/498927.
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La tesi di Giorgio Bertolazzi è incentrata sullo sviluppo di nuovi algoritmi per la predizione dei legami miRNA-mRNA. In particolare, un algoritmo di machine-learning viene proposto per l'upgrade del web tool ComiR; la versione originale di ComiR considerava soltanto i siti di legame dei miRNA collocati nella regione 3'UTR dell'RNA messaggero. La nuova versione di ComiR include nella ricerca dei legami la regione codificante dell'RNA messaggero.Bertolazzi’s thesis focuses on developing and applying computational methods to predict microRNA binding sites located on messenger RNA molecules. MicroRNAs (miRNAs) regulate gene expression by binding target messenger RNA molecules (mRNAs). Therefore, the prediction of miRNA binding is important to investigate cellular processes. Moreover, alterations in miRNA activity have been associated with many human diseases, such as cancer. The thesis explores miRNA binding behavior and highlights fundamental information for miRNA target prediction. In particular, a machine learning approach is used to upgrade an existing target prediction algorithm named ComiR; the original version of ComiR considers miRNA binding sites located on mRNA 3’UTR region. The novel algorithm significantly improves the ComiR prediction capacity by including miRNA binding sites located on mRNA coding regions.
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Crivelente, Horta Maria Augusta 1981. "Análise do transcriptoma de Trichoderma harzianum para a bioprospecção de enzimas hidrolíticas = Analysis of Trichoderma harzianum transcriptome for bioprospecting of hydrolytic enzymes." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316510.
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Orientadores: Anete Pereira de Souza, Sindélia Freitas AzzoniTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Buscando contribuir com o desenvolvimento da tecnologia de produção do etanol de segunda geração, o presente estudo analisa o transcriptoma de T. harzianum IOC-3844 utilizando técnicas de sequenciamento high-thoughput. O principal objetivo dessas análises foi identificar, caracterizar e catalogar os transcritos expressos por T. harzianum relacionados com a degradação de substratos complexos, como o bagaço de cana de açúcar, revelando o conjunto de genes envolvidos na degradação da biomassa. A análise do transcriptoma do fungo Trichoderma harzianum sob condições que induzem a degradação da biomassa permitiu a identificação de sequências de genes potencialmente eficazes no processo de biodegradação, uma etapa essencial à compreensão do processo de hidrólise enzimática. O sequenciamento resultou em 246 milhões de sequências com 72 pb, o que corresponde a 14,7 GPB analisados. Após a montagem , 32.494 contigs foram gerados, submetidos à identificação e classificados de acordo com sua identidade. Todas as sequências de contigs foram comparados com o banco de dados do NCBI, Gene Ontology (GO terms), Enciclopédia de Genes Kyoto (KEGG), Carbohydrate Active-Enzymes (CAZYmes). Foram identificados 487 CAZymes no transcriptoma, inclusive aquelas ligadas as reações químicas de despolimerização de celulose e hemicelulose. As sequências classificadas como atividade catalítica (6.975) e atividade reguladora (143) podem estar envolvidas com esse tipo de reação.A análise permitiu definir o principal conjunto de genes envolvidos na degradação da celulose e de hemicelulose do T. harzianum , e genes acessórios relativos à despolimerização de biomassa. Uma análise dos níveis de expressão permitiu determinar os conjuntos de genes diferencialmente expressos em diferentes condições de cultivo. Os resultados obtidos acrescentam conhecimento sobre a constituição do genoma, as atividades de expressão gênica do fungo Trichoderma harzianum e fornece informações importantes a respeito dos mecanismos genéticos de degradação de biomassa que o fungo utiliza. As informações obtidas poderão ser utilizadas para outras espécies de fungos filamentosos com potencial para a biodegradação
Abstract: In order to contribute to the development of second-generation ethanol technology, this study analyzes the transcriptome of T. harzianum IOC-3844 using high-thoughput sequencing techniques. The main objective of this analysis was to identify, characterize and catalog the transcripts expressed by T. harzianum related to the degradation of complex substrates such as sugar cane bagasse, revealing the set of genes involved in the degradation of biomass. The analysis of the transcriptome of the fungus Trichoderma harzianum under conditions that induce the degradation of biomass allowed the identification of genes potentially effective in the biodegradation process, an essential step for understanding the enzymatic process. Sequencing resulted in 246 million sequences with 72 bp, which corresponds to 14.7 GBP analyzed. After assembly, 32,494 contigs were generated, identified and classified according to their identity. All sequence contigs were compared with NCBI database, Gene Ontology (GO terms), Kyoto Encyclopedia of Genes (KEGG), Carbohydrate Active-Enzymes (CAZYmes). 487 CAZymes were identified in the transcriptome, including those related to reactions of cellulose and hemicellulose depolymerization. Sequences classified as catalytic activity (6,975) and regulatory activity (143) may be involved with this type of reaction. This analysis define the set of genes involved in the degradation of cellulose and hemicellulose of T. harzianum, and accessories genes related to depolymerization of the biomass. An analysis of expression levels was used to calculate the set of differentially expressed genes in different culture conditions. The results add to knowledge about the composition of the genome and gene expression activity of the fungus Trichoderma harzianum, and provides important information regarding the genetic mechanisms of biomass degradation that the fungus uses. The information obtained may be used for other species of filamentous fungi with potential for biodegradation
Doutorado
Genetica Vegetal e Melhoramento
Doutora em Genética e Biologia Molecular
Books on the topic "Transcriptomic analysi"
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Cellerino, Alessandro, and Michele Sanguanini. Transcriptome Analysis. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1.
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Wang, Yejun, and Ming-an Sun, eds. Transcriptome Data Analysis. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7710-9.
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Genome transcriptome and proteome analysis. Chichester: Wiley, 2004.
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Bernot, Alain. Genome Transcriptome and Proteome Analysis. New York: John Wiley & Sons, Ltd., 2005.
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Krizay, Daniel Kyle. Transcriptomic and Functional Analysis of Neuronal Activity and Disease. [New York, N.Y.?]: [publisher not identified], 2022.
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Lee, Albert Kim. Characterizing Immune Responses to Marburg Virus Infection in Animal Hosts Using Statistical Transcriptomic Analysis. [New York, N.Y.?]: [publisher not identified], 2018.
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Scanfeld, Daniel. Exploring the Plasmodium falciparum Transcriptome Using Hypergeometric Analysis of Time Series (HATS). [New York, N.Y.?]: [publisher not identified], 2013.
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author, Tuimala Jarno, Somervuo Panu author, Huss Mikael author, and Wong Garry author, eds. RNA-seq data analysis: A practical approach. Boca Raton: CRC Press, Taylor & Francis Group, 2015.
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Blumenberg, Miroslav, ed. Transcriptome Analysis. IntechOpen, 2019. http://dx.doi.org/10.5772/intechopen.77860.
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Transcriptome Analysis. IntechOpen, 2019.
Find full textBook chapters on the topic "Transcriptomic analysi"
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Cellerino, Alessandro, and Michele Sanguanini. "A primer on data distributions and their visualisation." In Transcriptome Analysis, 1–10. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_1.
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Cellerino, Alessandro, and Michele Sanguanini. "Next-generation RNA sequencing." In Transcriptome Analysis, 11–25. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_2.
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Cellerino, Alessandro, and Michele Sanguanini. "RNA-seq raw data processing." In Transcriptome Analysis, 27–44. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_3.
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Cellerino, Alessandro, and Michele Sanguanini. "Differentially expressed gene detection and analysis." In Transcriptome Analysis, 45–58. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_4.
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Cellerino, Alessandro, and Michele Sanguanini. "Unbiased clustering methods." In Transcriptome Analysis, 59–83. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_5.
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Cellerino, Alessandro, and Michele Sanguanini. "Knowledge-based clustering methods." In Transcriptome Analysis, 85–98. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_6.
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Cellerino, Alessandro, and Michele Sanguanini. "Network analysis." In Transcriptome Analysis, 99–119. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_7.
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Cellerino, Alessandro, and Michele Sanguanini. "Mesoscale transcriptome analysis." In Transcriptome Analysis, 121–39. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_8.
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Cellerino, Alessandro, and Michele Sanguanini. "Microscale transcriptome analysis." In Transcriptome Analysis, 141–68. Pisa: Scuola Normale Superiore, 2018. http://dx.doi.org/10.1007/978-88-7642-642-1_9.
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Yonekura-Sakakibara, Keiko, and Kazuki Saito. "Transcriptome Coexpression Analysis Using ATTED-II for Integrated Transcriptomic/Metabolomic Analysis." In Methods in Molecular Biology, 317–26. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-414-2_25.
Full textConference papers on the topic "Transcriptomic analysi"
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Collar, Giovanna Carello, Marco Antônio De Bastiani, and Eduardo R. Zimmer. "HUNTINGTON’S DISEASE AND EARLYONSET ALZHEIMER’S DISEASE SHARE A TRANSCRIPTOMIC SIGNATURE." In XIII Meeting of Researchers on Alzheimer's Disease and Related Disorders. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1980-5764.rpda082.
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Background: Neurodegenerative diseases share progressive loss of neurons and protein misfolding, which ultimately culminates in dementia; many diseases have been identified as causes of early-onset dementia (< 65 years of age) such as Huntington’s disease (HD) and early-onset Alzheimer’s disease (EOAD). Importantly, disease-specific genetic mutations have already been identified for HD and EOAD. Thus, one could suggest that the molecular link between these diseases may arise from alterations at the transcriptomic level, which is yet to be determined. Objective: We aimed at identifying transcriptome similarities between HD and EOAD. Methods: We collected data of the postmortem cerebral cortex from 1 HD and 6 AD microarray studies in the Gene Expression Omnibus. Of note, only subjects with age at death under 65 were selected (HD: n = 158, controls: n = 158; EOAD: n = 65, controls: n = 266). Differential expression and functional enrichment analyses were performed. Results: We identified 1,260 differentially expressed genes and 675 enriched gene ontology terms between HD and EOAD. Conclusion: Our results demonstrate a transcriptomic signature shared by HD and EOAD. Unveiling the similarities between these diseases at the transcriptomic level could advance our knowledge about pathogenesis and may help to develop therapeutic strategies targeting early-onset dementias.
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Kusakin, P. G., T. A. Serova, N. E. Gogoleva, Yu V. Gogolev, and V. E. Tsyganov. "Transcriptome analysis of pea (Pisum sativum L.) symbiotic nodules using laser capture microdissection." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.146.
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Olsen, E., L. Perez, B. Franca, Y. Li, R. Schluger, I. Sulaiman, J. Carpenito, B. Wu, L. N. Segal, and J. J. Tsay. "Transcriptomic Analysis of Lower Airway Dysbiosis." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a5410.
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Vetchinkina, E. P., V. Yu Gorshkov, N. E. Gogoleva, Yu V. Gogolev, and V. E. Nikitina. "Comparative analysis of transcriptomes of different morphological structures of the basidiomycete Lentinus edodes." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.270.
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A comparative analysis of transcriptomes at the vegetative and generative stages of the development of Lentinus edodes basidiomycetes was carried out. The nature of differential gene expression was described, and the activated/repressed metabolic pathways were visualized.
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Pavlenko, O. S., N. S. Sadovskaya, O. N. Mustafayev, Yu V. Akashkina, and I. V. Goldenkova-Pavlova. "Transcriptome analysis of Euonymus europaeus fruits at different stages of development." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.193.
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The transcript Euonymus europaeus was collected de novo. A comparative analysis of transcriptomes from the stage of the globular embryo and the mature fruit made it possible to identify key DGAT genes at the contrasting stages of the development of E. europaeus fruits.
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Langston, Michael A., Andy D. Perkins, Arnold M. Saxton, Jon A. Scharff, and Brynn H. Voy. "Innovative computational methods for transcriptomic data analysis." In the 2006 ACM symposium. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1141277.1141319.
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Cai, Hong, and Yufeng Wang. "Transcriptomic analysis using SVD clustering and SVM classification." In 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2011. http://dx.doi.org/10.1109/gensips.2011.6169476.
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Nurhani, A. R. Siti, A. M. Abdul Munir, S. Mohd Wahid, and A. B. Farah Diba. "A preliminary transcriptomic analysis of lichen Dirinaria sp." In THE 2013 UKM FST POSTGRADUATE COLLOQUIUM: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2013 Postgraduate Colloquium. AIP Publishing LLC, 2013. http://dx.doi.org/10.1063/1.4858665.
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Alexander-Brett, J., D. Steinberg, E. Katz, C. E. Kluender, E. Roberson, S. C. Tzeng, and B. Evans. "Proteomic and Transcriptomic Analysis of Exosomes in COPD." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4019.
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Chen, Minyu. "The Genomic and Transcriptomic Analysis of Stomach Cancer." In ICBBS 2019: 2019 8th International Conference on Bioinformatics and Biomedical Science. New York, NY, USA: ACM, 2019. http://dx.doi.org/10.1145/3369166.3369193.
Full textReports on the topic "Transcriptomic analysi"
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Hildebrand, Mark. Development of Renewable Biofuels Technology by Transcriptomic Analysis and Metabolic Engineering of Diatoms. Office of Scientific and Technical Information (OSTI), November 2013. http://dx.doi.org/10.2172/1227375.
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Tien, Ming. Transcriptome and Biochemical Analyses of Fungal Degradation of Wood. Office of Scientific and Technical Information (OSTI), March 2009. http://dx.doi.org/10.2172/1056641.
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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.
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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.
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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600013.bard.
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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped to specific genetic loci and significant quantitative-trait-loci (QTLs) can be identified that account for a major portion of the population variance. Susceptibility of apple fruit to P. expansumis dependent on the ability of the pathogen to produce LysM effectors that actively suppress primary and/or secondary resistance mechanisms in the fruit. Objectives: 1) Identify QTL(s) and molecular markers for blue mold resistance in GMAL4593 mapping population (‘Royal Gala’ X MalussieversiiPI613981), 2) Characterize the transcriptome of the host and pathogen (P. expansum) during the infection process 3) Determine the function of LysM genes in pathogenicity of P. expansum. Methods: A phenotypic evaluation of blue mold resistance in the GMAL4593 mapping population, conducted in several different years, will be used for QTL analysis (using MapQTL 6.0) to identify loci associated with blue mold resistance. Molecular markers will be developed for the resistance loci. Transcriptomic analysis by RNA-seq will be used to conduct a time course study of gene expression in resistant and susceptible apple GMAL4593 genotypes in response to P. expansum, as well as fungal responses to both genotypes. Candidate resistance genes identified in the transcriptomic study and or bioinformatic analysis will be positioned in the ‘Golden Delicious’ genome to identify markers that co-locate with the identified QTL(s). A functional analysis of LysM genes on pathogenicity will be conducted by eliminating or reducing the expression of individual effectors by heterologous recombination and silencing technologies. LysMeffector genes will also be expressed in a yeast expression system to study protein function. Expected Results: Identification of postharvest disease resistance QTLs and tightly-linked genetic markers. Increased knowledge of the role of effectors in blue mold pathogenic
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Wisniewski, Michael, Samir Droby, John Norelli, Dov Prusky, and Vera Hershkovitz. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the identification of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597928.bard.
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Use of Lqh2 mutants (produced at TAU) and rNav1.2a mutants (produced at the US side) for identifying receptor site-3: Based on the fact that binding of scorpion alpha-toxins is voltage-dependent, which suggests toxin binding at the mobile voltage-sensing region, we analyzed which of the toxin bioactive domains (Core-domain or NC-domain) interacts with the DIV Gating-module of rNav1.2a. This analysis was based on the assumption that the dissociation of toxin mutants upon depolarization would vary from that of the unmodified toxin should the substitutions affect a site of interaction with the channel Gating-module. Using a series of toxin mutants (mutations at both domains) and two channel mutants that were shown to reduce the sensitivity to scorpion alpha-toxins, and by comparison of depolarization-driven dissociation of Lqh2 derivatives off their binding site at rNav1.2a mutant channels we found that the toxin Core-domain interacts with the Gating-module of DIV. Details of the experiments and results appear in Guret al (2011). Mapping receptor site 3 at Nav1.2a by extensive channel mutagenesis (Seattle): Since previous studies with photoaffinity labeling and antibody mapping implicated domains I and IV in scorpion alpha-toxin binding, Nav1.2 channel mutants containing substitutions at these extracellular regions were expressed and tested for receptor function by whole-cell voltage clamp. Of a large number of channel mutants, T1560A, F1610A, and E1613A in domain IV had ~5.9-, ~10.7-, and ~3.9-fold lower affinities for the scorpion toxin Lqh2, respectively, and mutant E1613R had 73-fold lower affinity. Toxin dissociation was accelerated by depolarization for both wild-type and mutants, and the rates of dissociation were also increased by mutations T1560A, F1610A and E1613A. In contrast, association rates for these three mutant channels at negative membrane potentials were not significantly changed and were not voltage-dependent. These results indicated that Thr1560 in the S1-S2 loop, Phe1610 in the S3 segment, and Glu1613 in the S3-S4 loop in domain IV participate in toxin binding. T393A in the SS2-S6 loop in domain I also showed a ~3.4-fold lower affinity for Lqh2, indicating that this extracellular loop may form a secondary component of the toxin binding site. Analysis with the Rosetta-Membrane algorithm revealed a three-dimensional model of Lqh2 binding to the voltage sensor in a resting state. In this model, amino acid residues in an extracellular cleft formed by the S1-S2 and S3-S4 loops in domain IV that are important for toxin binding interact with amino acid residues on two faces of the wedge-shaped Lqh2 molecule that are important for toxin action. The conserved gating charges in the S4 transmembrane segment are in an inward position and likely form ion pairs with negatively charged amino acid residues in the S2 and S3 segments (Wang et al 2011; Gurevitz 2012; Gurevitzet al 2013).
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Katzir, Nurit, James Giovannoni, Marla Binzel, Efraim Lewinsohn, Joseph Burger, and Arthur Schaffer. Genomic Approach to the Improvement of Fruit Quality in Melon (Cucumis melo) and Related Cucurbit Crops II: Functional Genomics. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592123.bard.
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Background: Genomics tools for enhancement of melon research, with an emphasis on fruit, were developed through a previous BARD project of the PIs (IS -333-02). These included the first public melon EST collection, a database to relay this information to the research community and a publicly available microarray. The current project (IS-3877- 06) aimed to apply these tools for identification of important genes for improvement of melon (Cucumis melo) fruit quality. Specifically, the research plans included expression analysis using the microarray and functional analyses of selected genes. The original project objectives, as they appeared in the approved project, were: Objective 1: Utilization of a public melon microarray developed under the existing project to characterize melon transcriptome activity during the ripening of normal melon fruit (cv. Galia) in order to provide a basis for both a general view of melon transcriptome activity during ripening and for comparison with existing transcriptome data of developing tomato and pepper fruit. Objective 2: Utilization of the same public melon microarray to characterize melon transcriptome activity in lines available in the collection of the Israeli group, focusing on sugar, organic acids and aroma metabolism, so as to identify potentially useful candidates for functional analysis and possible manipulation, through comparison with the general fruit development profile resulting from (1) above. Objective 3: Expansion of our existing melon EST database to include publicly available gene expression data and query tools, as the US group has done with tomato. Objective 4: Selection of 6-8 candidate genes for functional analysis and development of DNA constructs for repression or over-expression. Objective 5: Creation of transgenic melon lines, or transgenic heterologous systems (e.g. E. coli or tomato), to assess putative functions and potential as tools for molecular enhancement of melon fruit quality, using the candidate gene constructs from (4).
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Lidstrom, Mary E., Ludmila Chistoserdova, Marina G. Kalyuzhnaya, Victoria J. Orphan, and David A. Beck. Systems level insights into alternate methane cycling modes in a freshwater lake via community transcriptomics, metabolomics and nano-SIMS analysis. Office of Scientific and Technical Information (OSTI), August 2014. http://dx.doi.org/10.2172/1149958.
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Libray, Spring. The Booming Field of Epitranscriptomics and its Role in Human Disease. Spring Library, April 2021. http://dx.doi.org/10.47496/sl.blog.26.
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Currently, the detection techniques used for transcriptome-wide identification of chemical modifications mainly depend on chemical and antibody-based detection methods followed by sequencing analysis.
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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.
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The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.
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Westwood, James H., Yaakov Tadmor, and Hanan Eizenberg. Identifying the genes involved in host root perception by root parasitic weeds: Genetic and transcriptomic analysis of Orobanche hybrids differing in signal response specificity. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598145.bard.
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Seeds of the root parasitic plants of the genus Orobanchegerminate specifically in response to host-derived germination signals, which enables parasites to detect and attack preferred hosts. The best characterized class of germination stimulants is the strigolactones (SL), although some species respond to sesquiterpene lactones such as dehydrocostuslactone (DCL). Despite great progress in characterizing the SL signaling system in plants, the mechanism(s) by which parasite species detect specific compounds remains poorly understood. The goal of our project was to identify and characterize the genes responsible for stimulant specificity in O. cernuaand O. cumana. These two species are closely related, but differ in host range, with O. cernuaparasitizingSolanaceous crops such as tomato (and responding to SLs), and O. cumanaspecifically parasitizing sunflower (and responding to DCL). We used a genetic approach based on O. cernuax O. cumanahybrids to associate germination response with genes. We found that these parasite species each have multiple copies of KAI2d genes, which function in SL perception. In O. cernua, the OrceKAI2d2 responds to SL stimulants and is most consistently associated with hybrid lines that respond to SLs. For O. cumana, an apparently linked block of KAI2d genes was associated with response to DCL in hybrid lines, but we found no strong evidence that any of the OrcuKAI2d genes specifically recognize the DCL stimulant. Remarkably, one O. cumanagene, OrcuKAI2d5, responds to certain SLs in a genetic complementation assay, even though hybrid lines containing this gene show fidelity to DCL. In summary, we have identified the SL receptor in O. cernua, but the DCL receptor in O. cumanaremains unknown. Our data point to involvement of additional genes and yet greater levels of complexity regulating germination specificity in Orobanche. BARD Report - Project 4616 Page 2 of 8