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The discovery of a living coelacanth specimen in was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago.

The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land.

Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods.

Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction.

Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution. To connect human biology to fish biomedical models, we sequenced the genome of spotted gar Lepisosteus oculatus , whose lineage diverged from teleosts before teleost genome duplication TGD.

The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development mediated, for example, by Hox, ParaHox and microRNA genes. Numerous conserved noncoding elements CNEs; often cis regulatory undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies.

Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs.

In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms.

We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification. Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide.

The genomes of 12 Drosophila species, ten of which are presented here for the first time sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi , illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.

Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species. The most recent release of the finished human genome contains euchromatic gaps excluding chromosome Y. Recent work has helped explain a large number of these unresolved regions as 'structural' in nature.

Another class of gaps is likely to be refractory to clone-based approaches, and cannot be approached in ways previously described. We present an approach for closing these gaps using sequencing. As a proof of principle, we closed all three remaining non-structural gaps in chromosome The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci.

While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog similar to , expressed loci. Syntenic comparison with the human genome revealed an additional similar to 3, loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set.

In addition to,20, high-confidence protein coding loci, we found,4, antisense transcripts overlapping exons of protein coding genes, similar to 7, intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs lincRNAs and,11, transcripts were reported by two different library construction methods but did not fit any of the above categories.

Of the lincRNAs, about 6, have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts. Although its genome was previously sequenced, here we report a new assembly sequenced by us with substantially higher N50 values for scaffolds and contigs.

Here we report a high-quality draft genome sequence of the domestic dog Canis familiaris , together with a dense map of single nucleotide polymorphisms SNPs across breeds.

The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development.

Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health. The domestic ferret Mustela putorius furo is an important animal model for multiple human respiratory diseases.

It is considered the 'gold standard' for modeling human influenza virus infection and transmission 1- 4. Here we describe the 2. We annotated 19, protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We characterized the ferret host response to two influenza virus infections by RNA-seq analysis of 42 ferret samples from influenza time-course data and showed distinct signatures in ferret trachea and lung tissues specific to or human pandemic influenza virus infections.

Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease. The fission yeast clade-comprising Schizosaccharomyces pombe, S. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres.

Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response.

Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade. DiVA diva-portal. Enkel sökning Avancerad sökning - Forskningspublikationer Avancerad sökning - Studentuppsatser Statistik.

English Svenska Norsk. Avgränsa sökresultatet. Permanent länk. Fler format. Fler språk. Skapa Stäng. Träffar per sida. Rensa markeringar. Maxantalet träffar du kan exportera från sökgränssnittet är Vid större uttag använd dig av utsökningar. The African coelacanth genome provides insights into tetrapod evolution Amemiya, Chris T. Alfoeldi, Jessica. Abstract [en]. Förlagets fulltext. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons Braasch, Ingo.

Gehrke, Andrew R. Ladda ner fulltext pdf fulltext. The genomic substrate for adaptive radiation in African cichlid fish Brawand, David et al.

Wagner, Catherine E. Evolution of genes and genomes on the Drosophila phylogeny. Clark, Andrew G. Eisen, Michael B. Closing gaps in the human genome using sequencing by synthesis Garber, Manuel et al. Zody, Michael C. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.

Lundquist, Andrew. Craig, Thomas. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Lindblad-Toh, Kerstin et al. Wade, Claire M. The draft genome sequence of the ferret Mustela putorius furo facilitates study of human respiratory disease Peng, Xinxia et al. Chen, Zehua. Om DiVA portal. Om DiVA-konsortiet.

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