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Статті в журналах з теми "Transcriptome size":
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Mora-Márquez, Fernando, José Luis Vázquez-Poletti, Víctor Chano, Carmen Collada, Álvaro Soto, and Unai López de Heredia. "Hardware Performance Evaluation of De novo Transcriptome Assembly Software in Amazon Elastic Compute Cloud." Current Bioinformatics 15, no. 5 (October 14, 2020): 420–30. http://dx.doi.org/10.2174/1574893615666191219095817.
Анотація:
Background: Bioinformatics software for RNA-seq analysis has a high computational requirement in terms of the number of CPUs, RAM size, and processor characteristics. Specifically, de novo transcriptome assembly demands large computational infrastructure due to the massive data size, and complexity of the algorithms employed. Comparative studies on the quality of the transcriptome yielded by de novo assemblers have been previously published, lacking, however, a hardware efficiency-oriented approach to help select the assembly hardware platform in a cost-efficient way. Objective: We tested the performance of two popular de novo transcriptome assemblers, Trinity and SOAPdenovo-Trans (SDNT), in terms of cost-efficiency and quality to assess limitations, and provided troubleshooting and guidelines to run transcriptome assemblies efficiently. Methods: We built virtual machines with different hardware characteristics (CPU number, RAM size) in the Amazon Elastic Compute Cloud of the Amazon Web Services. Using simulated and real data sets, we measured the elapsed time, cost, CPU percentage and output size of small and large data set assemblies. Results: For small data sets, SDNT outperformed Trinity by an order the magnitude, significantly reducing the time duration and costs of the assembly. For large data sets, Trinity performed better than SDNT. Both the assemblers provide good quality transcriptomes. Conclusion: The selection of the optimal transcriptome assembler and provision of computational resources depend on the combined effect of size and complexity of RNA-seq experiments.
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Ikeda, Hiroki, Shintaro Miyao, So Nagaoka, Tomoya Takashima, Sze-Ming Law, Takuya Yamamoto, and Kazuki Kurimoto. "High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis." Life Science Alliance 6, no. 11 (September 18, 2023): e202301929. http://dx.doi.org/10.26508/lsa.202301929.
Анотація:
High-quality, straightforward single-cell RNA sequencing (RNA-seq) with spatial resolution remains challenging. Here, we developed DRaqL (direct RNA recovery and quenching for laser capture microdissection), an experimental approach for efficient cell lysis of tissue sections, directly applicable to cDNA amplification. Single-cell RNA-seq combined with DRaqL allowed transcriptomic profiling from alcohol-fixed sections with efficiency comparable with that of profiling from freshly dissociated cells, together with effective exon–exon junction profiling. The combination of DRaqL with protease treatment enabled robust and efficient single-cell transcriptome analysis from formalin-fixed tissue sections. Applying this method to mouse ovarian sections, we were able to predict the transcriptome of oocytes by their size and identified an anomaly in the size–transcriptome relationship relevant to growth retardation of oocytes, in addition to detecting oocyte-specific splice isoforms. Furthermore, we identified differentially expressed genes in granulosa cells in association with their proximity to the oocytes, suggesting distinct epigenetic regulations and cell-cycle activities governing the germ–soma relationship. Thus, DRaqL is a versatile, efficient approach for high-quality single-cell RNA-seq from tissue sections, thereby revealing histological heterogeneity in folliculogenic transcriptome.
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Gonzalez-Ibeas, Daniel, Pedro J. Martinez-Garcia, Randi A. Famula, Annette Delfino-Mix, Kristian A. Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, and Jill L. Wegrzyn. "Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)." G3 Genes|Genomes|Genetics 6, no. 12 (December 1, 2016): 3787–802. http://dx.doi.org/10.1534/g3.116.032805.
Анотація:
Abstract Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.
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Stern, M. D., S. V. Anisimov, and K. R. Boheler. "Can transcriptome size be estimated from SAGE catalogs?" Bioinformatics 19, no. 4 (March 1, 2003): 443–48. http://dx.doi.org/10.1093/bioinformatics/btg018.
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Beisser, Daniela, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, and Jens Boenigk. "Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes." PeerJ 5 (January 10, 2017): e2832. http://dx.doi.org/10.7717/peerj.2832.
Анотація:
BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (December 28, 2017): 16. http://dx.doi.org/10.12688/gatesopenres.12783.1.
Анотація:
Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised the single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 transcripts across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels between 54.1-75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (February 13, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.2.
Анотація:
Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae): a case study of the endosymbiont composition." Gates Open Research 1 (March 8, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.3.
Анотація:
Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
9
Caurcel, Carlos, Dominik R. Laetsch, Richard Challis, Sujai Kumar, Karim Gharbi, and Mark Blaxter. "MolluscDB: a genome and transcriptome database for molluscs." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1825 (April 5, 2021): 20200157. http://dx.doi.org/10.1098/rstb.2020.0157.
Анотація:
As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
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Jensen, Michael Krogh, Josef Korbinian Vogt, Simon Bressendorff, Andaine Seguin-Orlando, Morten Petersen, Thomas Sicheritz-Pontén, and John Mundy. "Transcriptome and Genome Size Analysis of the Venus Flytrap." PLOS ONE 10, no. 4 (April 17, 2015): e0123887. http://dx.doi.org/10.1371/journal.pone.0123887.
Дисертації з теми "Transcriptome size":
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Schivre, Geoffrey. "Transcriptome augmentation, Polycomb-mediated chromatin dynamics and their links to metabolism during Arabidopsis thaliana photomorphogenesis." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASB014.
Анотація:
La lumière permet aux plantes de métaboliser le carbone atmosphérique grâce à la photosynthèse, constituant ainsi leur source d'énergie. Par ailleurs, les différentes propriétés de la lumière constituent une source d'informations essentielles sur leur environnement perçues par de multiples capteurs de lumière, les photorécepteurs, déclenchant des réponses adaptatives spécifiques. Parmi elles, l'une des adaptations développementales les plus spectaculaires des plantes, appelée photomorphogenèse, se produit lorsqu'une jeune plantule en cours de germination est exposée à la lumière pour la première fois. Les plantules germant sous terre, à l'abri de la lumière, suivent un développement étiolé ou skotomorphogénique, au cours duquel l'allongement rapide de l'hypocotyle facilite l'émergence de la plante à la surface, tandis que la maturation des cotylédons et la mise en place de la photosynthèse sont inhibés. La croissance skotomorphogénique repose donc entièrement sur les réserves métaboliques principalement stockées dans les cotylédons. Lorsque la surface du sol est atteinte, la détection de la lumière par les photorécepteurs déclenche l'expansion, sans division cellulaire, des cotylédons et la biogenèse des chloroplastes permettant l'acquisition de la photo-autotrophie. Au niveau moléculaire, le dé-étiolement des cotylédons est associé à une spécialisation du transcriptome et à une intensification de l'activité de l'ARN polymérase II (ARN Pol II). A l'échelle cytologique, de profonds réarrangements de la chromatine conduisent à l'élargissement du noyau et à la condensation des régions péricentromériques au sein de foyers hétérochromatiniens. Considérant qu'une grande partie de ces contrôles métaboliques, cellulaires, moléculaires et cytologiques sont réalisés de manière synchrone au cours de la transition, la photomorphogenèse d'A. thaliana constitue un modèle de choix pour caractériser les interactions entre la signalisation lumière, la régulation des gènes et les dynamiques chromatiniennes avec le statut énergétique de la plante. Au cours de ma thèse, j'ai développé une analyse de données de séquençage ARN normalisées grâce à une référence exogène pour revisiter les connaissances actuelles sur les changements transcriptomiques au vu de l'augmentation globale de l'activité de l'ARN Pol II. Ceci a permis d'identifier un doublement de l'abondance des transcrits pendant la photomorphogenèse des cotylédons qui résulte très probablement de l'augmentation de l'activité de l'ARN Pol II. J'ai ensuite exploré le rôle joué par le senseur métabolique Target Of Rapamycin (TOR) dans la régulation du régime transcriptionnel ainsi que dans la composition et l'organisation de la chromatine lors du dé-étiolement des cotylédons. Cette seconde partie de mon étude apporte un nouvel éclairage sur les liens fonctionnels entre la voie TOR et l'homéostasie d'une marque d'histone, la triméthylation de la lysine 27 de l'histone H3 (H3K27me3), catalysée par le complexe Polycomb Repressive Complexe 2 (PRC2). En particulier, elle révèle que H3K27me3 est moins abondant dans la chromatine des cotylédons étiolés que dans celle des cotylédons photomorphogéniques, un effet général qui s'avère sensible au sucre et à la signalisation TOR. Par conséquent, ces travaux mettent en évidence des rôles inattendus de la signalisation TOR et de la marque H3K27me3 dans la régulation du régime transcriptionnel général et ouvrent de nouvelles perspectives sur la régulation transcriptionnelle régie par TOR. De futures études visant à décrypter le rôle de l'homéostasie de H3K27me3, en particulier sur les gènes de réponse à la lumière, devraient permettre de mieux comprendre comment la signalisation métabolique interagit avec les dynamiques de l'épigénome et la répression transcriptionnelle régies par PRC2 avec des implications au-delà de la photomorphogenèse des plantesLight fuels plant photosynthesis providing the energy source for growth. Light intensity and quality also convey essential information on the plant's immediate surroundings, which are integrated through multiple light sensors, the photoreceptors, enabling developmental and physiological adaptations. The photomorphogenic transition, or de-etiolation, occurs when a young germinating plantlet is exposed to light for the first time, and is one of the most spectacular plant developmental adaptations to light. Seedlings germinating underground, protected from light, undergo an etiolated development, or skotomorphogenesis, during which rapid hypocotyl elongation facilitates plant drilling through the soil, while cotyledon maturation is arrested and the plantlet remains non-photosynthetic. In the absence of photosynthesis, skotomorphogenic growth relies entirely on the plant metabolic reserves, predominantly stored in cotyledons. Upon reaching the soil surface, photoreceptor light sensing triggers the expansion and greening of cotyledons, independently from cell divisions. Inducing chloroplast biogenesis and the acquisition of photosynthesis, this developmental switch marks the transition toward photo-autotrophy. At the molecular scale, cotyledon de-etiolation associates with a specialization of the transcriptome and an intensification of RNA polymerase II (RNA Pol II) activity. At the cytological scale, chromatin rearrangements lead to nucleus enlargement and the condensation of pericentromeric regions in conspicuous heterochromatic foci. Considering that much of these metabolic, cellular, molecular and cytological controls are synchronously achieved during the transition, A. thaliana photomorphogenesis is a model of choice to characterize the interplays between light signaling, gene regulation and chromatin dynamics as well as their link to the plant energetic status. During my thesis, I first contributed to develop an RNA-seq normalization methodology to revisit transcriptome changes in light of the global increase in RNA Pol II activity. This identified a 2-fold increase in transcript abundance during cotyledon photomorphogenesis, which most likely results from the increase in RNA Pol II activity. I further explored the role played by the conserved metabolic sensor Target Of Rapamycin (TOR) in defining the transcriptional regime along with chromatin composition and organization during cotyledon photomorphogenesis. This notably shed a new light on the functional links between the TOR pathway and the homeostasis of a specific histone mark, trimethylation of histone H3 at lysine 27 (H3K27me3), mediated by Polycomb Repressive Complex 2 (PRC2). More precisely, this study revealed that H3K27me3 is less abundant at chromatin in etiolated cotyledons as compared to photomorphogenic ones, a global effect that was further shown here to be sensitive to sugar and TOR signaling. Hence, this work points towards unexpected roles of TOR signaling and the PRC2-regulated mark H3K27me3 in the global regulation of transcription and opens new perspectives on TOR-mediated gene regulation. Future studies aimed at deciphering the role of H3K27me3 homeostasis, especially at specific genes induced by light, should provide new insight on how metabolic signaling interplays with Polycomb-mediated chromatin dynamics and transcription with implications beyond plant photomorphogenesis
2
Díaz, Blanco Noelia 1975. "Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/380903.
Анотація:
In many gonochoristic fish, sex is plastic since it can be altered by the influence of environmental factors. In this thesis, using the European sea bass (Dicentrarchus labrax) model, a teleost fish with a polygenic sex determining system influenced by the environment, we have studied the effects of different environmental factors —including food supply, elevated temperatures and presence of estrogens— on growth, sex differentiation and gonadal development of juveniles. Global analysis of gene expression was carried out by a custom-made microarray. We found that, like in mammals, sex determines growth and that the first sex-related differences in growth are established before the appearance of the first molecular markers indicative of sex. Further, the juvenile testis transcriptome is influenced by poor growth during sex differentiation, while proper food supply during juvenile development is able to rescue the testis transcriptome of previously poor-growing individuals. We found that the previously observed masculinization as a result of elevated temperatures is caused by long-lasting effects at the transcriptomic level, by favoring the expression of male-related genes and decreasing that of female-related genes. In contrast, exposure to estrogen negatively affects both male- and female-related genes and pathways. Interestingly, the expression patterns of a suite of genes related to epigenetic regulatory mechanisms of gene expression showed different degrees of dependency to genetic background, developmental time and external influences according to their functional category.A molts peixos gonocoristes, el sexe és plàstic donat que pot ésser alterat per la influència de factors ambientals. En aquesta tesi, utilitzant el llobarro (Dicentrarchus labrax) com a model, un peix teleosti amb un sistema poligènic de determinació del sexe influït per l'ambient, hem estudiat els efectes de diferents factors ambientals —incloent la disponibilitat d'aliment, temperatures elevades i presència d’estrògens— en el creixement, la diferenciació sexual i el desenvolupament gonadal dels juvenils. L'anàlisi global de l'expressió gènica s'ha realitzat mitjançant un xip d’ADN fet a mida. Hem trobat que, de la mateixa manera que ocorre en els mamífers, el sexe determina el creixement i que les primeres diferències en el creixement vinculades amb el sexe s'estableixen prèviament a l'aparició dels primers marcadors moleculars indicatius del sexe. A més, el transcriptoma de testicles juvenils està influït per un creixement pobre durant la diferenciació sexual, mentre que un subministrament adequat de menjar durant l’etapa juvenil és capaç de rescatar el transcriptoma testicular d’animals amb un pobre creixement previ. Hem trovat que la masculinització observada anteriorment com a resultat de les temperatures elevades està causada per efectes persistents a nivell transcriptòmic, afavorint l'expressió de gens relacionats amb el desenvolupament masculí i disminuint la dels gens relacionats amb el desenvolupament femení. Per contra, l'exposició a estrògens afecta negativament tant als gens relacionats amb el desenvolupament masculí com el femení. És destacable com els patrons d'expressió d'una sèrie de gens relacionats amb la regulació epigenètica de l’expressió gènica mostren graus diferents de dependència a factors genètics, període del desenvolupament i factors ambientals segons la seva categoria funcional.
3
Tang, Shiyuyun. "Improving algorithms of gene prediction in prokaryotic genomes, metagenomes, and eukaryotic transcriptomes." Diss., Georgia Institute of Technology, 2016. http://hdl.handle.net/1853/54998.
Анотація:
Next-generation sequencing has generated enormous amount of DNA and RNA sequences that potentially carry volumes of genetic information, e.g. protein-coding genes. The thesis is divided into three main parts describing i) GeneMarkS-2, ii) GeneMarkS-T, and iii) MetaGeneTack.
In prokaryotic genomes, ab initio gene finders can predict genes with high accuracy. However, the error rate is not negligible and largely species-specific. Most errors in gene prediction are made in genes located in genomic regions with atypical GC composition, e.g. genes in pathogenicity islands. We describe a new algorithm GeneMarkS-2 that uses local GC-specific heuristic models for scoring individual ORFs in the first step of analysis. Predicted atypical genes are retained and serve as ‘external’ evidence in subsequent runs of self-training. GeneMarkS-2 also controls the quality of training process by effectively selecting optimal orders of the Markov chain models as well as duration parameters in the hidden semi-Markov model. GeneMarkS-2 has shown significantly improved accuracy compared with other state-of-the-art gene prediction tools.
Massive parallel sequencing of RNA transcripts by the next generation technology (RNA-Seq) provides large amount of RNA reads that can be assembled to full transcriptome. We have developed a new tool, GeneMarkS-T, for ab initio identification of protein-coding regions in RNA transcripts. Unsupervised estimation of parameters of the algorithm makes unnecessary several steps in the conventional gene prediction protocols, most importantly the manually curated preparation of training sets. We have demonstrated that the GeneMarkS-T self-training is robust with respect to the presence of errors in assembled transcripts and the accuracy of GeneMarkS-T in identifying protein-coding regions and, particularly, in predicting gene starts compares favorably to other existing methods.
Frameshift prediction (FS) is important for analysis and biological interpretation of metagenomic sequences. Reads in metagenomic samples are prone to sequencing errors. Insertion and deletion errors that change the coding frame impair the accurate identification of protein coding genes. Accurate frameshift prediction requires sufficient amount of data to estimate parameters of species-specific statistical models of protein-coding and non-coding regions. However, this data is not available; all we have is metagenomic sequences of unknown origin. The challenge of ab initio FS detection is, therefore, twofold: (i) to find a way to infer necessary model parameters and (ii) to identify positions of frameshifts (if any). We describe a new tool, MetaGeneTack, which uses a heuristic method to estimate parameters of sequence models used in the FS detection algorithm. It was shown on several test sets that the performance of MetaGeneTack FS detection is comparable or better than the one of earlier developed program FragGeneScan.
4
Raborn, R. Taylor. "Genome-wide analysis of transcription initiation and promoter architecture in eukaryotes." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/4728.
Анотація:
The transcriptome represents the entirety of RNA molecules within a cell or tissue at a given time. Recent advances have facilitated the production of large-scale, global interrogations of transcriptomes, finding that genomes are extensively transcribed and contain diverse classes of RNAs (Dinger et al., 2009). Information generated by high-throughput analyses of mRNA transcription start sites (TSSs) such as CAGE (Cap Analysis of Gene Expression) indicate that eukaryotic genomes have complex landscapes of transcription initiation. The TSS is important for the annotation of cis-regulatory sequences, because it provides a link between the mRNA transcript and the promoter. The patterns of TSS distributions observed within mRNA 5' end profiling studies prevent straightforward annotation of putative promoters.
To address this challenge, we developed a method to identify- on a genome-wide basis- the putative promoter, which we define by TSS distributions and designate the transcription start region (TSR). We applied a clustering method to identify and annotate TSRs within the budding yeast Saccharomyces cerevisiae using a full-length cDNA dataset (Miura et al., 2006). To validate these TSR annotations, we performed an integrative genomic analysis using multiple datasets. Our method identified TSRs at positions consistent with bona fide promoters in S. cerevisiae. In addition, using 5'RACE, we find overall agreement between computationally-defined TSRs and TSSs identified experimentally. From this analysis, we find that a significant proportion of genes exhibiting alternative promoter usage within sporulation are associated with respiration, suggesting that this is regulated on a condition-specific basis in budding yeast.
We further developed our TSS clustering method into a bioinformatics tool called TSRchitect, which identifies and annotates TSRs from large-scale TSS profiling information. TSRchitect is capable of handling both tag and sequence-based TSS information and efficiently computes TSRs from global TSS datasets on a desktop computer. We find support for TSRchitect's annotations in human from a CAGE experiment from the ENCODE (Encyclopedia of DNA Elements) project.
Finally, we use TSRchitect to identify TSRs from the transcriptomes of diverse eukaryotes. We investigated the conservation of TSRs among orthologous genes. We frequently identify multiple TSRs for a given gene, suggesting that alternative promoter usage is widespread. Overall, using TSS profiling data derived from separate tissues within mouse and human, we find that the positions of TSRs are relatively stable across tissues surveyed; however, a small fraction of genes exhibit tissue-specific differences in TSR use.
As transcriptome profiling information continues to be generated at an rapid pace, computational approaches are increasingly important. It is anticipated that the method and approach we describe within this dissertation will contribute to an improved of gene regulation and promoter architecture in eukaryotes.
5
Colman, Hélène. "Régulations traductionnelles lors de l'infection par le virus de l'hépatite C (VHC)." Nantes, 2010. https://archive.bu.univ-nantes.fr/pollux/show/show?id=867ac444-7efa-4ea8-a33f-89bd65a8dc7d.
Анотація:
Le virus de l'hépatite C (VHC) est un problème majeur de santé publique, il infecte de façon chronique 3% de la population mondiale et cause cirrhose et cancer du foie. Il n'existe pas de vaccin et son traitement est inactif chez près de la moitié des patients. Le génome du VHC est un ARN positif simple brin, présentant une grande variabilité génétique. Sa traduction est initiée par un IRES (Internal Ribosome Entry Site), permettant de recruter le ribosome sans l'aide de tous les facteurs classiques d'initiation de la traduction. Cette région possède des structures secondaires et sa séquence est conservée parmi les génotypes viraux. Elle est donc une cible thérapeutique potentielle. La traduction virale est modulée par des facteurs viraux et cellulaires, dont les modalités ne pas encore bien connues. A partir de variants naturels de l’IRES présentant des efficacités traductionnelles et des tropismes cellulaires différents, nous avons cherché à comprendre quels sont les déterminants (séquence virale et facteurs cellulaires agissant en trans (les ITAF, IRES Trans Acting Factors)) conditionnant l'efficacité de l'IRES dans l'hépatocyte. Nous avons parallèlement analysé les modifications traductionnelles des ARN cellulaires lors de l'infection virale dans le modèle des cellules Huh-7 infectées par la souche JFH-1 en comparant le transcriptome traduit, liés aux ribosomes (polysome) et le transcriptome libre. Nous avons montré la régulation traductionnelle de gènes régulant le cytosquelette, la traduction, le métabolisme mitochondrial et le cycle cellulaire. Certaines de ces régulations pourraient impliquer des microARN cellulairesThe hepatitis C virus (HCV) infection is a major world health problem, since 3% of the world’s population is chronically infected and it can lead to cirrhosis and hepatocellular carcinoma. There is currently no vaccine against this virus and the treatment is inactive for about half of the patients. HCV is a positive sense single strand RNA virus with highly sequence variability. Its translation initiation occurs through an internal ribosome entry site (IRES) in its 5’untranslated region, allowing the ribosome recruitment without the need of all the canonical translation initiation factors. This region is highly structured and is well conserved amongst the viral genotypes. That makes the IRES an attractive target for future therapies. The IRES function is modulated by viral and cellular factors, but the mecanisms of this regulation are not well understood. With the study of natural IRES variants harboring different translationnal efficiencies and cellular tropisms, we have tried to understand some factors (the viral sequence and the cellular proteins acting in trans (ITAFs, IRES Trans Acting Factors)) conditionning the efficiency of HCV translation in hepatocytes. We have also studied the translational modifications of the cellular genes during HCV infection in Huh7 cells harbouring replication of the JHF-1 strain, by comparing the translated transriptome, bound to the ribosomes (polysome) and the free transcriptome. We have shown that the viral infection modulates the translation of genes belonging to specific functional categories (cytoskeleton, translation, mitochondrial metabolism, cell cycle regulation). Some of this regulations could occur via microRNA modulation
6
Konishi, Atsushi. "Studies on the thermostabilization of reverse transcriptases from Moloney murine leukemia virus and avian myeloblastosis virus." Kyoto University, 2015. http://hdl.handle.net/2433/199340.
Анотація:
Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第19016号
農博第2094号
新制||農||1029(附属図書館)
学位論文||H27||N4898(農学部図書室)
31967
京都大学大学院農学研究科食品生物科学専攻
(主査)教授 保川 清, 教授 河田 照雄, 教授 谷 史人
学位規則第4条第1項該当
7
Dufour, Emmanuelle. "Interaction de la transcriptase inverse de HIV-1 avec son tRNA amorce : études biochimiques et détermination du site de liaison de l'enzyme à l'extrémité 3' du tRNA-Lys3." Bordeaux 2, 1997. http://www.theses.fr/1997BOR28523.
8
Borcier, Elodie. "Vulnérabilité de populations de poissons (Platichthys flesus) face aux multi-stress en estuaires : une approche intégrative Bioenergetic transcriptomic responses of European flounder (Platichthys flesus) populations in contrasted environments: impacts of pollution and global warming, in Journal of Xenobiotics 6(6586), 2016." Thesis, Brest, 2019. http://www.theses.fr/2019BRES0020.
Анотація:
Le niveau de vulnérabilité de populations naturelles de flet a été abordé dans cette étude, par l’intégration des réponses du poisson aux niveaux moléculaire, individuel et populationnel. Une approche multi-estuaire est développée ; les réponses du flet sont ainsi mesurées dans des conditions contrastées (stress thermique : estuaire du Mondego ; stress chimique : estuaire de Seine ; faibles niveaux de stress : Baie de Douarnenez, estuaires de Vilaine et Canche). Par une approche démo-génétique basée sur la variabilité des marqueurs microsatellites, nous avons mis en évidence une faible taille efficace de la population du Mondego située en limite Sud de l’aire de distribution, et donc caractérisée par un risque écologique élevé. La population de Seine présente une faible variabilité interindividuelle dans l’expression de différents gènes impliqués dans le métabolisme énergétique (COII, 12S), qui pourrait expliquer son faible potentiel à résister au réchauffement climatique. Cette population montre des signatures d’adaptation face au stress chimique (métabolisme énergétique élevé, gestion du stress oxydant, modification des phospholipides membranaires), engendrant probablement un coût physiologique fort (réduction des réserves énergétiques au niveau musculaire). La population de Seine présente donc un risque écologique élevé. Enfin, un encagement de flet a été mené sur un mois en estuaire de Seine; les réponses du poisson analysées par protéomique shot-gun ont mis en évidence un gradient de pollution décroissant amont-aval, soit une estimation de l’état écologique du système à micro-échelle. Cette thèse a identifié différents outils pertinents pour estimer le niveau de vulnérabilité de populations de flet, et pour explorer l’état écologique des écosystèmes estuariensThe vulnerability level of natural flounder populations was assessed, integrating responses at the molecular, individual and population levels. A multi-estuary approach was carried out on the fish responses in contrasted environments (thermal stress: Mondego estuary; chemical stress: Seine estuary; moderately stressed systems: Bay of Douarnenez, Vilaine and Canche estuaries).A demo-genetic approach, considering the variability of microsatellites, underlined a reduced effective size for the southern peripheral population of the Mondego estuary, thus characterized by a high ecological risk.In the Seine population, a reduced interindividual variability was observed considering the expression levels of genes involved in bioenergetics (COII, 12S); this pattern could explain the reduced ability of this population to cope with another stress (ie thermal stress).Signatures of adaptation to pollutants (high level of energetic metabolism, management of oxidative stress, modification of membrane phopholipids) were observed in the Seine, but could be very costly (reduced muscle energetic reserve). Thus, we consider that the Seine population is displaying a high ecological risk.A one month fish caging experiment was conducted in the Seine estuary. Fish responses were analyzed by proteomic; they underlined a decreasing pollution gradient from upstream to downstream, and thus allowed to characterize the ecological status of the estuary atmicroscale.This study highlighted pertinent tools for the assessment of flounder population vulnerability and for the exploration of the ecological status of estuarine systems
9
Noiret, Maud. "Étude des protéines de liaison à l'ARN des familles PTB et ARE-BP au cours du développement chez le xénope." Phd thesis, Rennes 1, 2012. https://ecm.univ-rennes1.fr/nuxeo/site/esupversions/a420494c-0828-469e-bd2f-60a70118ef9f.
Анотація:
Mes travaux ont porté sur l'étude de deux familles de protéines de liaison à l'ARN, la famille des ARE-BP (AU-rich elements binding protein) et la famille des PTB (Polypyrimidine tract binding protein) au cours du développement chez le xénope. L'étude de l'expression de cinq membres de la famille ARE-BP a mis en évidence une redondance d'expression tissulaire et temporelle entre quatre de ces ARE-BP (AUF1, KSRP, HuR et TIA1). A l'inverse, l'expression atypique de TTP a permis de suggérer son implication dans l'hématopoïèse. Mes travaux sur la famille PTB (PTBP1, PTBP2, PTBP3) ont montré que chacun des paralogues présente une expression spécifique ce qui suggère qu'elles aient des fonctions différentes lors du développement. Des résultats du laboratoire montraient que l'inactivation de PTBP1 ou de EXOSC9, un composant de l'exosome ARN, entraînait des défauts de morphogenèse de l'épiderme dorsal. Afin d'identifier l'origine moléculaire de ces défauts, j'ai réalisé l'analyse transcriptomique par séquençage à haut débit (RNA-Seq) des morphants PTBP1 et EXOSC9. J'ai produit des banques d'ADNc à partir des morphants ou d'embryons témoins et celles-ci ont été séquencées au Génoscope. L'analyse d'une cible connue de PTBP1 a montré que des modifications minoritaires de l'épissage étaient détectées à partir de ces données. De plus ces défauts d'épissage ne sont pas retrouvés dans les morphants EXOSC9, validant son utilisation comme crible additionnel permettant d'exclure les évènements d'épissage qui ne sont pas impliqués dans le défaut d'épiderme. Une approche gène candidat a été initiée afin de cibler l'analyse de transcrits impliqués dans la morphogenèse de l'épiderme dorsaleMy work has focused on the function of RNA binding-proteins during early development in Xenopus. I first documented the expression pattern of members of the AU-rich element binding protein (ARE-BP) and of the polypyrimidin tract binding protein (PTB) families during development. Study of the expression patterns of five members of the ARE-BP family (AUF1, KSRP, HuR, TIA1 and TTP) has underlined the broad role and the redundancy of expression of four of these proteins. Conversely, the highly specific expression pattern of TTP in macrophages suggests a potential function for this ARE-BP in hematopoietic development. My study of the PTB family (PTBP1, PTBP2 and PTBP3), has showed that each paralog presents a unique pattern of expression emphasizing their diverse functions during development. From previous work in the lab we knew that morpholino mediated knockdown of both PTBP1 and EXOSC9, a component of the RNA exosome, generated similar defects in the dorsal fin morphology. To identify the molecular origin of these defects we realized the transcriptome analysis by high throughput sequencing (RNA-Seq) of both morphants embryos. I produced cDNA libraries of control and morphant embryos and the sequencing was performed at the Genoscope. Analysis of a known PTBP1 target showed that even modest modifications of alternative splicing could be detected in our data sets. In addition, because these defects are not found in the EXOSC9 morphants it validated its use as an additional screen to exclude splicing events not involved in the epidermal defects. Identification of RNA whose deregulation may be involved in the fin phenotype is currently under study for a set of candidate genes
10
Boukharta, Lars. "Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212103.
Анотація:
Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. We report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 G-protein coupled receptor and a series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Site-directed mutagenesis, homology modelling and docking were further used to characterize agonist binding to the human neuropeptide Y2 receptor, which is important in feeding behavior and an obesity drug target. In a separate project, homology modelling was also used for rationalization of mutagenesis data for an integron integrase involved in antibiotic resistance. Blockade of the hERG potassium channel by various drug-like compounds, potentially causing serious cardiac side effects, is a major problem in drug development. We have used a homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations are in good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships with implications for design of new compounds. Docking, scoring, molecular dynamics, and the linear interaction energy method were also used to predict binding modes and affinities for a large set of inhibitors to HIV-1 reverse transcriptase. Good agreement with experiment was found and the work provides a validation of the methodology as a powerful tool in structure-based drug design. It is also easily scalable for higher throughput of compounds.
Книги з теми "Transcriptome size":
1
Renner, Tanya, Tianying Lan, Kimberly M. Farr, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Stephan C. Schuster, Mitsuyasu Hasebe, Kenji Fukushima, and Victor A. Albert. Carnivorous plant genomes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0011.
Анотація:
Carnivorous plant genome research has focused on members of the Lamiales and Oxalidales; the most complete sequences are for Utricularia gibba and Cephalotus follicularis. The size-limited U. gibba genome highlights the importance of small-scale tandem duplications, which likely play roles in this species’ carnivorous adaptation. Sequencing of the C. follicularis genome detected adaptive changes that may explain the evolution of traits associated with attraction, trapping, digestion, and absorption. Functional consequences of genes putatively missing in the U. gibba genome, yet present in other angiosperms, may have influenced the evolution of polyploidy, physiology, and a rootless Bauplan. Additional draft nuclear genomes and transcriptomes are available for carnivorous Caryophyllales, Ericales, Lamiales, and Poales, but are limited in quantity and quality. Chloroplast genomes of carnivorous Lentibulariaceae have revealed interesting patterns of gene loss, alterations in the proportion of repeat DNA, and plastome-wide increases in substitution rates.
2
Grant, Warren, and Martin Scott-Brown. Principles of oncogenesis. Edited by Patrick Davey and David Sprigings. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199568741.003.0322.
Анотація:
It is obvious that the process of developing cancer—oncogenesis—is a multistep process. We know that smoking, obesity, and a family history are strong independent predictors of developing malignancy; yet, in clinics, we often see that some heavy smokers live into their nineties and that some people with close relatives affected by cancer spend many years worrying about a disease that, in the end, they never contract. For many centuries scientists have struggled to understand the process that make cancer cells different from normal cells. There were those in ancient times who believed that tumours were attributable to acts of the gods. Hippocrates suggested that cancer resulted from an imbalance between the black humour that came from the spleen, and the other three humours: blood, phlegm, and bile. It is only in the last 100 years that biologists have been able to characterize some of the pathways that lead to the uncontrolled replication seen in cancer, and subsequently examine exactly how these pathways evolve. The rampant nature by which cancer invades local and distant tissues, as well its apparent ability to spread between related individuals led some, such as Peyton Rous in 1910, to suggest that cancer was an infectious condition. He was awarded a Nobel Prize in 1966 for the 50 years of work into investigating a link between sarcoma in chickens and a retrovirus that became known as Rous sarcoma virus. He had shown how retroviruses are able to integrate sequences of DNA coding for errors in cellular replication control (oncogenes) by introducing into the human cell viral RNA together with a reverse transcriptase. Viruses are now implicated in many cancers, and in countries where viruses such as HIV and EBV are endemic, the high incidence of malignancies such as Kaposi’s sarcoma and Burkitt’s lymphoma is likely to be directly related. There are several families of viruses associated with cancer, broadly classed into DNA viruses, which mutate human genes using their own DNA, and retroviruses, like Rous sarcoma virus, which insert viral RNA into the cell, where it is then transcribed into genes. This link with viruses has not only led to an understanding that cancer originates from genetic mutations, but has also become a key focus in the design of new anticancer therapies. Traditional chemotherapies either alter DNA structure (as with cisplatin) or inhibit production of its component parts (as with 5-fluorouracil.) These broad-spectrum agents have many and varied side effects, largely due to their non-specific activity on replicating DNA throughout the body, not just in tumour cells. New vaccine therapies utilizing gene-coding viruses aim to restore deficient biological pathways or inhibit mutated ones specific to tumour cells. The hope is that these gene therapies will be effective and easily tolerated by patients, but development is currently progressing with caution. In a trial in France of ten children suffering from X-linked severe combined immunodeficiency and who were injected with a vector that coded for the gene product they lacked, two of the children subsequently died from leukaemia. Further analysis confirmed that the DNA from the viral vector had become integrated into an existing, but normally inactive, proto-oncogene, LM02, triggering its conversion into an active oncogene, and the development of life-threatening malignancy. To understand how a tiny change in genetic structure could lead to such tragic consequences, we need to understand the molecular biology of the cell and, in particular, to pay attention to the pathways of growth regulation that are necessary in all mammalian cell populations. Errors in six key regulatory pathways are known as the ‘hallmarks of cancer’ and will be discussed in the rest of this chapter.
Частини книг з теми "Transcriptome size":
1
Feldman, Moshe, and Avraham A. Levy. "Genome Structure of Triticeae Species." In Wheat Evolution and Domestication, 43–70. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-30175-9_3.
Анотація:
AbstractThis chapter describes characteristic features of the chromosomes and genomes of Triticeae species. Centromeres contain typical CENH3 nucleosomes, but these are associated with repeats that are larger than in other plant species. The sub-telomeric ends are rich in transposable elements and contain diverse repeats and recombination hotspots. The nucleolar organizer regions contain hundreds or thousands of ribosomal genes, rDNA repeats, arranged in tandem arrays that form a constriction known as the nucleolar organizer (NOR). We describe their mapping as well as the phenomenon known as Nucleolar dominance. Genome sizes in the Triticeae are large, with 1C values ranging in diploids from 4.0–9.4 pg, compared to related grasses such as rice (1C = 0.5 pg). These size differences are mostly due to a large amount of repetitive DNA, in particular of transposable elements, with retroelements as the most prominent repeats. In hexaploid bread wheat, genome size reaches 1C = 16 pg, with ~ 108,000 high-confidence protein-coding genes, and a high number of pseudogenes and RNA genes. The wheat transcriptome shows complex expression patterns for homoeologous loci. We discuss gene organization in islands as well as the high synteny between the different species and the role of introgression in shaping genomes.
2
Rungrotmongkol, Thanyada, Nadtanet Nunthaboot, Ornjira Aruksakunwong, and Supot Hannongbua. "HIV-1 Reverse Transcriptase – Computational Studies on the Polymerase Active Site." In Encyclopedia of Biophysics, 989–92. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_240.
3
de Souza Moreira, Leonora Rios, Camila Louly Corrêa, Helder Andrey Rocha Gomes, Glaucia Emy Okida Midorikawa, Robert Neil Gerard Miller, and Edivaldo Ximenes Ferreira Filho. "The Role of Fungal Transcriptome Analysis and Side-Chain Hydrolyzing Enzymes in Sugarcane Bagasse Breakdown." In Advances of Basic Science for Second Generation Bioethanol from Sugarcane, 81–106. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-49826-3_6.
4
Swaminathan, Angavai, Paul F. Harrison, Thomas Preiss, and Traude H. Beilharz. "PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distribution in Yeast Transcriptomes." In Methods in Molecular Biology, 141–64. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9736-7_9.
5
R. Sripathi, Venkateswara, Varsha C. Anche, Zachary B. Gossett, and Lloyd T. Walker. "Recent Applications of RNA Sequencing in Food and Agriculture." In Applications of RNA-Seq in Biology and Medicine [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97500.
Анотація:
RNA sequencing (RNA-Seq) is the leading, routine, high-throughput, and cost-effective next-generation sequencing (NGS) approach for mapping and quantifying transcriptomes, and determining the transcriptional structure. The transcriptome is a complete collection of transcripts found in a cell or tissue or organism at a given time point or specific developmental or environmental or physiological condition. The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade. This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA-Seq, metatranscriptomics, and systems biology. A few popular RNA-Seq databases and analysis tools are also presented for each application. We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture.
6
Lata, Suman, Ramesh Kumar Yadav, and B. S. Tomar. "Genomic Tools to Accelerate Improvement in Okra (Abelmoschus esculentus)." In Landraces - Traditional Variety and Natural Breed. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97005.
Анотація:
Okra (Abelmoschus esculentus L. Moench), is an important vegetable crop with limited studies on genomics. It is considered as an essential constituent for balanced food due to its dietary fibers, amino-acid and vitamins. It is most widely cultivated for its pods throughout Asia and Africa. Most of the okra cultivation is done exclusively in the developing countries of Asia and Africa with very poor productivity. India ranks first in the world with a production of 6.3 million MT (72% of the total world production). Cultivated okra is mostly susceptible to a large number of begomoviruses. Yellow vein mosaic disease (YVMD) caused by Yellow vein mosaic virus (YVMV) of genus Begomovirus (family Geminiviridae) results in the serious losses in okra cultivation. Symptoms of YVMD are chlorosis and yellowing of veins and veinlets at various levels, small size leaves, lesser and smaller fruits, and stunting growth. The loss in yield, due to YVMD in okra was found ranging from 30 to 100% depending on the age of the plant at the time of infection. Exploitation of biotechnological tools in okra improvement programmes is often restricted, due to the non availability of abundant polymorphic molecular markers and defined genetic maps. Moreover, okra genome is allopolyploid in nature and possess a large number of chromosomes (2n = 56–196) which makes it more complicated. Genomics tools like RNA- seq. for transcriptome analysis has emerged as a powerful tool to identify novel transcript/gene sequences in non-model plants like okra.
7
"Non-nucleoside reverse transcriptase inhibitors (NNRTIs)." In Meyler's Side Effects of Drugs, 234–35. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-444-53717-1.01164-1.
8
"Nucleoside analogue reverse transcriptase inhibitors (NRTIs)." In Meyler's Side Effects of Drugs, 280–86. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-444-53717-1.01173-2.
9
Pervaiz, Saima, and Shehryar Awan. "Molecular Mechanisms of Human Immunodeficiency Virus Resistance to Antiretroviral." In Fundamentals of Cellular and Molecular Biology, 225–41. BENTHAM SCIENCE PUBLISHERS, 2024. http://dx.doi.org/10.2174/9789815238037124010020.
Анотація:
Antiretroviral therapy (ART) has transformed the treatment of human immunodeficiency virus (HIV) infection, improving life expectancy and quality of life for millions worldwide. However, the emergence of drug-resistant HIV strains poses a significant challenge to the effectiveness of ART. The molecular mechanisms underlying HIV resistance to antiretroviral drugs involve multiple genetic changes in the viral genome that reduce drug susceptibility, often through alterations in the viral enzymes targeted by the drugs. The primary targets of ART are the viral reverse transcriptase (RT), protease (PR), and integrase (IN) enzymes, which are essential for HIV replication. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs) results from mutations in the viral RT enzyme that reduce drug incorporation into the viral DNA chain. Non-nucleoside reverse transcriptase inhibitors (NNRTIs) bind to a hydrophobic pocket near the RT active site, and resistance to these drugs arises from mutations that alter the binding pocket conformation. Protease inhibitors (PIs) bind to the viral PR enzyme, and resistance results from mutations that alter the enzyme's conformation, reducing drug binding affinity. Integrase strand transfer inhibitors (INSTIs) bind to the viral IN enzyme, and resistance arises from mutations that affect drug binding or alter the IN active site. The emergence of drug-resistant HIV strains can also result from poor adherence to ART, leading to the selection of pre-existing resistant viruses or the development of new resistance mutations. In addition, the genetic diversity of HIV and the high viral replication and mutation rate contribute to the rapid evolution and emergence of drug-resistant strains.
10
"Non-nucleoside reverse transcriptase inhibitors (NNRTIs)." In Meyler's Side Effects of Drugs: The International Encyclopedia of Adverse Drug Reactions and Interactions, 2553–55. Elsevier, 2006. http://dx.doi.org/10.1016/b0-44-451005-2/00768-3.
Тези доповідей конференцій з теми "Transcriptome size":
1
BIROL, INANÇ, ANTHONY RAYMOND, READMAN CHIU, KA MING NIP, SHAUN D. JACKMAN, MAAYAN KREITZMAN, T. RODERICK DOCKING, CATHERINE A. ENNIS, A. GORDON ROBERTSON, and ALY KARSAN. "KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2014. http://dx.doi.org/10.1142/9789814644730_0034.
2
Gebim, Anna Beatriz Silva, RENATO MASSAHARU HASSUNUMA, and PATRÍCIA CARVALHO GARCIA. "AÇÃO DA TELOMERASE NA REPLICAÇÃO DO DNA TELOMÉRICO." In III Congresso Brasileiro de Ciências Biologicas. Revista Multidisciplinar de Educação e Meio Ambiente, 2022. http://dx.doi.org/10.51189/iii-conbracib/6602.
Анотація:
Introdução: O telômero representa a extremidade dos cromossomos, sendo formado por repetições da sequência de nucleotídeos TTAGGG. Durante o processo de duplicação do DNA, a enzima DNA polimerase não é capaz de transcrever o final da fita 3´ da molécula de DNA, o que poderia causar o encurtamento dos telômeros. Este encurtamento é evitado pela ação da enzima telomerase, uma transcriptase reversa, capaz de sintetizar a extremidade da fita de DNA, pois, possui uma fita RNA molde em seu interior que é complementar a sequência do telômero. Esta enzima possui duas subunidades; a TER (transcriptase reversa da telomerase) e as RNPs (partículas de ribonucleoproteínas de telomerase ativa). Objetivos: O objetivo principal da pesquisa foi o desenvolvimento de scripts para o software RasMol, 2.7.4.2, no intuído de produzir imagens que representem a enzima telomerase, RNA e DNA teloméricos. Metodologia: Foi realizado o levantamento no site Protein Data Bank para seleção de arquivos PDB sobre a telomerase. A partir do arquivo 6D6V.pdb foi desenvolvido um script para o software RasMol para demonstrar a estrutura da enzima telomerase, RNA e DNA teloméricos. Resultados: A partir de scripts desenvolvidos para o arquivo 6D6V.pdb foram produzidas imagens onde observa-se a telomerase representada no modo Backbone. Pode-se observar também o trecho de RNA usado como molde corresponde à sequência CAACCC e o restante da molécula de RNA. Também é observada a síntese de três sequências de DNA telomérico: GTTGGG. Conclusão: Por meio do script desenvolvido foi possível observar a estrutura da enzima telomerase, do RNA e do DNA teloméricos, bem como a região da molécula de RNA usada com molde para a produção das sequências repetitivas de DNA telomérico.
3
Garcia, Luan Ednelson Soares, Fábio Aparecido Da Silva, Renato Massaharu Hassunuma, and Patrícia Carvalho Garcia. "TELOMERASE: UMA SOLUÇÃO BIOQUÍMICA PARA O ENVELHECIMENTO?" In II Congresso Brasileiro de Bioquímica Humana On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/conbraqui/19.
Анотація:
Introdução: O processo de envelhecimento está intimamente ligado com o encurtamento dos telômeros, que correspondem à extremidade dos cromossomos. O DNA telomérico apresenta cerca de mil repetições da sequência TTAGGG e é protegido por várias proteínas, chamadas coletivamente de “shelterin” (do inglês shelter, que significa proteger). A telomerase é uma transcriptase reversa composta por ribonucleoproteínas, capaz de adicionar DNA telomérico às extremidades de cromossomos de células eucariontes, prevenindo o envelhecimento precoce. Estudos indicam que a baixa atividade da telomerase está associada ao aumento de risco de desenvolvimento de neoplasias. Objetivos: o objetivo principal da presente pesquisa foi o desenvolvimento de scripts para o software RasMol 2.7.4.2, no intuito de produzir imagens que apresentem a estrutura da telomerase. Material e métodos: Foi realizado o levantamento e a seleção de arquivos PDB sobre a telomerase obtidos no site Protein Data Bank. A partir da análise dos arquivos PDB selecionados e da análise de artigos publicados sobre a estrutura bioquímica da telomerase, foram desenvolvidos vários scripts para o programa computacional RasMol, com o objetivo de demonstrar a estrutura molecular da telomerase. Resultados: Nos scripts desenvolvidos para o arquivo 6D6V.pdb foi observado que a telomerase corresponde a complexo formado por RNA-proteína, sendo que a sequência de RNA da telomerase (TER) é utilizada como molde para a síntese de DNA dos telômeros; enquanto que a proteína é uma transcriptase reversa especializada (TERT). A função enzimática da telomerase depende da interação de várias proteínas associadas à telomerase (TAPs). O script desenvolvido apresenta um segmento de DNA, a TER, a TERT e as TAPs: proteínas 50, 82 e p65 associadas à telomerase (TAP50, TAP82 e P65, respectivamente) e proteínas 2 e 3 de ligação a repetições teloméricas (TEB2 e TEB3). As TAPs participam da fixação do complexo junto ao telômero e da movimentação da telomerase durante a síntese de DNA. Conclusão: Os scripts desenvolvidos mostraram a disposição espacial da TER, TERT, TAPs e DNA. Futuras pesquisas sobre este assunto poderão ser importantes na busca de tratamento e prevenção das doenças relacionadas ao processo de envelhecimento.
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Raghunathan, Megha, Elliot Imler, Christy Trejo, Peter Shepard, and Bruce Seligmann. "Abstract LB-097: Whole transcriptome dose response profiling enables characterization of efficacy, metabolism, side effects and cytotoxicity in a single comprehensive assay." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-lb-097.
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Raghunathan, Megha, Elliot Imler, Christy Trejo, Peter Shepard, and Bruce Seligmann. "Abstract LB-097: Whole transcriptome dose response profiling enables characterization of efficacy, metabolism, side effects and cytotoxicity in a single comprehensive assay." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-lb-097.
Звіти організацій з теми "Transcriptome size":
1
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.
Анотація:
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
2
Sherman, A., D. N. Kuhn, Y. Cohen, R. Ophir, and R. Goenaga. Exploring the polyembryonic seed trait in mango as a basis for a biotechnology platform for fruit tree crops. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134176.bard.
Анотація:
Mango is one of the most important fruit crops. However, the biology of this fruit tree is under studied. The lack of genetic and genomic resources has limited progress in mango research and breeding. Several research groups have recently started developing genomic tools for mango by creating transcriptome and genomic data. Sexual reproduction in plants is the main pathway for the creation of new genetic combinations. In modern agriculture, breeders exploit the genetic diversity generated through sexual reproduction to develop elite cultivars; however, these cultivars require genetic stabilization before they are suitable for mass propagation for uniform crop production. In heterozygous plants such as fruit trees, vegetative propagation (cloning) is the primary path for the propagation of genetically uniform plants. Another natural plant mechanism that can create genetically uniform plants (clones) is apomixes. Apomixis is defined as asexual reproduction through seeds that lead to the production of clonal progeny whose genotype is identical to that of the mother plant. In fruit crops like citrus and mango, sporophytic apomixes result in polyembryony, where seeds contain multiple embryos, one of which is sexually originated, and the others are clones of the mother tree. As part of this research, the reference genome of mango was established as a basic platform for mango breeding and research. It was used to map two important mango traits fruit size and polyembryony. The draft genome 'Tommy Atkins' sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins,' supplemented by 10X Genomics long read sequencing to improve the initial assembly. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango. The availability of a genome enables the genetic dissection of important traits. We demonstrated the utility of the genome assembly and the 'Tommy Atkins' x 'Kensington Pride' map by analyzing fruit weight phenotypic data and identifying two QTLs for this trait.
3
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.
Анотація:
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).
4
Crowley, David E., Dror Minz, and Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7594387.bard.
Анотація:
PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.
5
Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597923.bard.
Анотація:
Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explore the response of the duplicate peanut pod transcriptome to drought stress. Study how entire duplicated PF regulatory processes are networked within a polyploid organism. Discover locus-specific SNP markers and map pod quality traits under different environments. The research included genotypes and segregating populations from Israel and US that are varied in PF, SF and their tolerance to water deficit. Initially, an extensive field trial was conducted to investigate the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Significant irrigation and genotypic effect was observed for the two main PF related traits, "seed ratio" and "dead-end ratio", demonstrating that reduction in irrigation directly influences the developing pods as a result of low water potential. Although the Irrigation × Genotype interaction was not statistically significant, one genotype (line 53) was found to be more sensitive to low irrigation treatments. Two RNAseq studies were simultaneously conducted in IL and the USA to characterize expression changes that accompany shell ("source") and seed ("sink") biogenesis in peanut. Both studies showed that SF and PF processes are very dynamic and undergo very rapid change in the accumulation of RNA, nutrients, and oil. Some genotypes differ in transcript accumulation rates, which can explain their difference in SF and PF potential; like cvHanoch that was found to be more enriched than line 53 in processes involving the generation of metabolites and energy at the beginning of seed development. Interestingly, an opposite situation was found in pericarp development, wherein rapid cell wall maturation processes were up-regulated in line 53. Although no significant effect was found for the irrigation level on seed transcriptome in general, and particularly on subgenomic assignment (that was found almost comparable to a 1:1 for A- and B- subgenomes), more specific homoeologous expression changes associated with particular biosynthesis pathways were found. For example, some significant A- and B- biases were observed in particular parts of the oil related gene expression network and several candidate genes with potential influence on oil content and SF were further examined. Substation achievement of the current program was the development and application of new SNP detection and mapping methods for peanut. Two major efforts on this direction were performed. In IL, a GBS approach was developed to map pod quality traits on Hanoch X 53 F2/F3 generations. Although the GBS approach was found to be less effective for our genetic system, it still succeeded to find significant mapping locations for several traits like testa color (linkage A10), number of seeds/pods (A5) and pod wart resistance (B7). In the USA, a SNP array was developed and applied for peanut, which is based on whole genome re-sequencing of 20 genotypes. This chip was used to map pod quality related traits in a Tifrunner x NC3033 RIL population. It was phenotyped for three years, including a new x-ray method to phenotype seed-fill and seed density. The total map size was 1229.7 cM with 1320 markers assigned. Based on this linkage map, 21 QTLs were identified for the traits 16/64 weight, kernel percentage, seed and pod weight, double pod and pod area. Collectively, this research serves as the first fundamental effort in peanut for understanding the PF and SF components, as a whole, and as influenced by the irrigation level. Results of the proposed study will also generate information and materials that will benefit peanut breeding by facilitating selection for reduced linkage drag during introgression of disease resistance traits into elite cultivars. BARD Report - Project4540 Page 2 of 10
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Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.
Анотація:
Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
7
Eshed-Williams, Leor, and Daniel Zilberman. Genetic and cellular networks regulating cell fate at the shoot apical meristem. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699862.bard.
Анотація:
The shoot apical meristem establishes plant architecture by continuously producing new lateral organs such as leaves, axillary meristems and flowers throughout the plant life cycle. This unique capacity is achieved by a group of self-renewing pluripotent stem cells that give rise to founder cells, which can differentiate into multiple cell and tissue types in response to environmental and developmental cues. Cell fate specification at the shoot apical meristem is programmed primarily by transcription factors acting in a complex gene regulatory network. In this project we proposed to provide significant understanding of meristem maintenance and cell fate specification by studying four transcription factors acting at the meristem. Our original aim was to identify the direct target genes of WUS, STM, KNAT6 and CNA transcription factor in a genome wide scale and the manner by which they regulate their targets. Our goal was to integrate this data into a regulatory model of cell fate specification in the SAM and to identify key genes within the model for further study. We have generated transgenic plants carrying the four TF with two different tags and preformed chromatin Immunoprecipitation (ChIP) assay to identify the TF direct target genes. Due to unforeseen obstacles we have been delayed in achieving this aim but hope to accomplish it soon. Using the GR inducible system, genetic approach and transcriptome analysis [mRNA-seq] we provided a new look at meristem activity and its regulation of morphogenesis and phyllotaxy and propose a coherent framework for the role of many factors acting in meristem development and maintenance. We provided evidence for 3 different mechanisms for the regulation of WUS expression, DNA methylation, a second receptor pathway - the ERECTA receptor and the CNA TF that negatively regulates WUS expression in its own domain, the Organizing Center. We found that once the WUS expression level surpasses a certain threshold it alters cell identity at the periphery of the inflorescence meristem from floral meristem to carpel fate [FM]. When WUS expression highly elevated in the FM, the meristem turn into indeterminate. We showed that WUS activate cytokinine, inhibit auxin response and represses the genes required for root identity fate and that gradual increase in WUCHEL activity leads to gradual meristem enlargement that affect phyllotaxis. We also propose a model in which the direction of WUS domain expansion laterally or upward affects meristem structure differently. We preformed mRNA-seq on meristems with different size and structure followed by k-means clustering and identified groups of genes that are expressed in specific domains at the meristem. We will integrate this data with the ChIP-seq of the 4 TF to add another layer to the genetic network regulating meristem activity.
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Bloch, G., and H. S. Woodard. regulation of size related division of labor in a key pollinator and its impact on crop pollination efficacy. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134168.bard.
Анотація:
Despite the rapid increase in reliance on bumble bees for food production and security, there are many critical knowledge gaps in our understanding of bumble bee biology that limit their colony production, commercial management, and pollination services. Our project focuses on the social, endocrine, and molecular processes regulating body size in the two bumble bee species most important to agriculture: Bombus terrestris in Israel, and B. impatiens in the USA. Variation in body size underline both caste (queen/worker) differentiation and division of labor among workers (foragers are typically larger than nest bees), two hallmarks of insect sociality which are also crucial for the commercial rearing and crop pollination services of bumble bees. Our project has generated several fundamental new insights into the biology of bumble bees, which can be integrated into science-based management strategies for commercial pollination. Using transcriptomic and behavioral approaches we show that in spite of high flexibility, task performance (brood care or foraging) in bumble bee colonies is associated with physiological variation and differential brain gene expression and RNA editing patterns. We further showed that interactions between the brood, the queen, and the workers determine the developmental program of the larva. We identified two important periods. The first is a critical period during the first few days after hatching. Larvae fed by queens during this period develop over less days, are not likely to develop into gynes, and commonly reach a smaller ultimate body size compared to workers reared mostly or solely by workers. The facial exocrine (mandibular and hypopharangeal) glands are involved in this queen effect on larva development. The second period is important for determining the ultimate body size which is positively regulated by the number of tending workers. The presence of the queen during this stage has little, if at all, influence. We further show that stressors such as agrochemicals that interfere with foraging or brood care specific processes can compromise bumble bee colony development and their pollination performance. We also developed new technology (an RFID system) for automated collection of foraging trip data, for future deployment in agroecosystems. In spite of many similarities, our findings suggest important differences between the Eurasian model species (B. terrestris) and the North American model species (B. impatiens) that impact how management strategies translate across the two species. For example, there is a similar influence of the queen on offspring body size in both species, but this effect does not appear to be mediated by development time in B. impatiens as it is in B. terrestris. Taken together, our collaboration highlights the power of comparative work, to show that considerable differences that exist between these two key pollinator species, and in the organization of young bumble bee nests (wherein queens provide the majority of care and then transition away from brood care) relative to later stages of nest development.
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Fluhr, Robert, and Maor Bar-Peled. Novel Lectin Controls Wound-responses in Arabidopsis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697123.bard.
Анотація:
Innate immune responses in animals and plants involve receptors that recognize microbe-associated molecules. In plants, one set of this defense system is characterized by large families of TIR–nucleotide binding site–leucine-rich repeat (TIR-NBS-LRR) resistance genes. The direct interaction between plant proteins harboring the TIR domain with proteins that transmit and facilitate a signaling pathway has yet to be shown. The Arabidopsis genome encodes TIR-domain containing genes that lack NBS and LRR whose functions are unknown. Here we investigated the functional role of such protein, TLW1 (TIR LECTIN WOUNDRESPONSIVE1). The TLW1 gene encodes a protein with two domains: a TIR domain linked to a lectin-containing domain. Our specific aim in this proposal was to examine the ramifications of the TL1-glycan interaction by; A) The functional characterization of TL1 activity in the context of plant wound response and B) Examine the hypothesis that wounding induced specific polysaccharides and examine them as candidates for TL-1 interactive glycan compounds. The Weizmann group showed TLW1 transcripts are rapidly induced by wounding in a JA-independent pathway and T-DNA-tagged tlw1 mutants that lack TLW1 transcripts, fail to initiate the full systemic wound response. Transcriptome methodology analysis was set up and transcriptome analyses indicates a two-fold reduced level of JA-responsive but not JA-independent transcripts. The TIR domain of TLW1 was found to interact directly with the KAT2/PED1 gene product responsible for the final b-oxidation steps in peroxisomal-basedJA biosynthesis. To identify potential binding target(s) of TL1 in plant wound response, the CCRC group first expressed recombinant TL1 in bacterial cells and optimized conditions for the protein expression. TL1 was most highly expressed in ArcticExpress cell line. Different types of extraction buffers and extraction methods were used to prepare plant extracts for TL1 binding assay. Optimized condition for glycan labeling was determined, and 2-aminobenzamide was used to label plant extracts. Sensitivity of MALDI and LC-MS using standard glycans. THAP (2,4,6- Trihydroxyacetophenone) showed minimal background peaks at positive mode of MALDI, however, it was insensitive with a minimum detection level of 100 ng. Using LC-MS, sensitivity was highly increased enough to detect 30 pmol concentration. However, patterns of total glycans displayed no significant difference between different extraction conditions when samples were separated with Dionex ICS-2000 ion chromatography system. Transgenic plants over-expressing lectin domains were generated to obtain active lectin domain in plant cells. Insertion of the overexpression construct into the plant genome was confirmed by antibiotic selection and genomic DNA PCR. However, RT-PCR analysis was not able to detect increased level of the transcripts. Binding ability of azelaic acid to recombinant TL1. Azelaic acid was detected in GST-TL1 elution fraction, however, DHB matrix has the same mass in background signals, which needs to be further tested on other matrices. The major findings showed the importance of TLW1 in regulating wound response. The findings demonstrate completely novel and unexpected TIR domain interactions and reveal a control nexus and mechanism that contributes to the propagation of wound responses in Arabidopsis. The implications are to our understanding of the function of TIR domains and to the notion that early molecular events occur systemically within minutes of a plant sustaining a wound. A WEB site (http://genome.weizmann.ac.il/hormonometer/) was set up that enables scientists to interact with a collated plant hormone database.
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Iudicone, Daniele, and Marina Montresor. Omics community protocols. EuroSea, 2023. http://dx.doi.org/10.3289/eurosea_d3.19.
Анотація:
The aim of the WP3 “Network Integration and Improvements” is to coordinate and enhance key aspects of integration of European observing technology (and related data flows) for its use in the context of international ocean monitoring activities. One of the dimensions of the integrations is the constitution of thematic networks, that is, networks whose aim is to address specific observational challenges and thus to favor innovation, innovation that will ultimately support the Blue economy. In this context, the specific aim of Task 3.8 is to accelerate the adoption of molecular methods such as genomic, transcriptomic (and related “omics”) approaches, currently used as monitoring tools in human health, to the assessment of the state and change of marine ecosystems. It was designed to favor the increase the capacity to evaluate biological diversity and the organismal metabolic states in different environmental conditions by the development of “augmented observatories”, utilizing state-of-art methodologies in genomic-enabled research at multidisciplinary observatories at well-established marine LTERs, with main focus on a mature oceanographic observatory in Naples, NEREA. In addition, an effort is dedicated to connecting existing observatories that intend to augment their observations with molecular tools. Molecular approaches come with many different options for the protocols (size fractioning, sample collection and storage, sequencing etc). One main challenge in systematically implementing those approaches is thus their standardization across observatories. Based on a survey of existing methods and on a 3-year experience in collecting, sequencing and analyzing molecular data, this deliverable is thus dedicated to present the SOPs implemented and tested at NEREA. The SOPs consider a size fractioning of the biological material to avoid biases toward more abundant, smaller organisms such as bacteria. They cover both the highly stable DNA and the less stable RNA and they are essentially an evolution of the ones developed for the highly successful Tara Oceans Expedition and recently updated for the Expedition Mission Microbiomes, an All-Atlantic expedition organised and executed by the EU AtlantECO project. Importantly, they have only slight variations with respect the ones adopted by the network of genomic observatories EMOBON. Discussions are ongoing with EMOBON to perfectly align the protocols. The SOPs are being disseminated via the main national and international networks. (EuroSea Deliverable, D3.19)