Search results for "Genome"
showing 10 items of 1913 documents
Role of Symbiosis in Evolution
2013
The biological relevance of the widespread prokaryote–eukaryote symbioses as a source of evolutionary innovation has been unveiled by the advent of the Genomic era, allowing deep knowledge on single or consortia uncultivable species. The establishment and maintenance of symbiosis are complex issues where partners’ fitness determines the evolutionary outcome. Comparative genomics allows to dissect the evolutionary process that begins with host invasion, takes the path from facultative to obligate symbiosis, and ends up in replacement or coexistence with new bacterial symbionts. Whole genomes of several intracellular bacterial symbionts have been sequenced, allowing the comparison among the d…
&ldquo;Out of the Can&rdquo;: A Draft Genome Assembly, Liver Transcriptome and Nutrigenomics of the European Sardine, <em>Sardina p<…
2018
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25579 bp and BUSCO completeness of 82.1% (Actinopteryg…
A multi-phase multi-objective dynamic genome-scale model shows different redox balancing among yeast species in fermentation
2021
ABSTRACTYeasts constitute over 1500 species with great potential for biotechnology. Still, the yeastSaccharomyces cerevisiaedominates industrial applications and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabolic specificity in batch cultures. Here we propose a multi-phase multi-objective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kin…
Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol
2019
International audience; Guanine-rich DNA and RNA sequences can fold into higher-order structures known as G-quadruplexes (or G4-DNA and G4-RNA, respectively). The prevalence of the G4 landscapes in the human genome, transcriptome and ncRNAome (non-coding RNA), collectively known as G4ome, is strongly suggestive of biological relevance at multiple levels (gene expression , replication). Small-molecules can be used to track G4s in living cells for the functional characterization of G4s in both normal and disease-associated changes in cell biology. Here, we describe biotinylated biomimetic ligands referred to as Bio-TASQ and their use as molecular tools that allow for isolating G4s through aff…
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
2009
Abstract Background ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without suitable software their further analysis and mapping would have to await finalization of the corresponding genome. Results The tool JANE rapidly maps ESTs or variable sequence reads in prokaryotic sequencing and transcriptome efforts to related template genomes. It provides an easy-to-use graphics interface for information retrieval and a toolkit for EST or nucleotide sequence function prediction. Furthermore, we developed for rapid mapping an enhanced sequence align…
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems
2015
This is a post-peer-review, pre-copyedit version of an article published in IEEE - ACM Transactions on Computational Biology and Bioinformatics. The final authenticated version is available online at: http://dx.doi.org/10.1109/TCBB.2015.2389958 [Abstract] High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-SNP interactions) in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. Computational methods to detect epistasis therefore suffer from prohibitively lon…
Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes.
2019
How to make an organelle in eukaryotes A key step in the evolution of complex organisms like eukaryotes was the organization of specific tasks into organelles. Reinkemeier et al. designed an artificial, membraneless organelle into mammalian cells to perform orthogonal translation. In response to a specific codon in a selected messenger RNA, ribosomes confined to this organelle were able to introduce chemical functionalities site-specifically, expanding the canonical set of amino acids. This approach opens possibilities in synthetic cell engineering and biomedical research. Science , this issue p. eaaw2644
Boolean Networks: A Primer
2021
Abstract Autism Spectrum Disorders (ASDs) stand out as a relevant example where omics-data approaches have been extensively and successfully employed. For instance, an outstanding outcome of the Autism Genome Project relies in the identification of biomarkers and the mapping of biological processes potentially implicated in ASDs’ pathogenesis. Several of these mapped processes are related to molecular and cellular events (e.g., synaptogenesis and synapse function, axon growth and guidance, etc.) that are required for the development of a correct neuronal connectivity. Interestingly, these data are consistent with results of brain imaging studies of some patients. Despite these remarkable pr…
The ten grand challenges of synthetic life
2011
The construction of artificial life is one of the main scientific challenges of the Synthetic Biology era. Advances in DNA synthesis and a better understanding of regulatory processes make the goal of constructing the first artificial cell a realistic possibility. This would be both a fundamental scientific milestone and a starting point of a vast range of applications, from biofuel production to drug design. However, several major issues might hamper the objective of achieving an artificial cell. From the bottom-up to the selection-based strategies, this work encompasses the ten grand challenges synthetic biologists will have to be aware of in order to cope with the task of creating life i…
Enforcing Conceptual Modeling to improve the understanding of human genome
2010
It is widely accepted that the use of Conceptual Modeling techniques in modern Software Engineering leads to a more accurate description of the problem domain. The application of these techniques in the context of challenging domains as the human genome is a fascinating task. The relevant biological concepts should be properly addressed through the creation of the corresponding conceptual schema. This schema will improve the description of the global process followed from a DNA sequence to a fully functional protein. Once the conceptual model is established, the corresponding database is created. The database is intended to act as a unified repository of integrated information that will all…