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Sökning: WFRF:(Grabherr Manfred)

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1.
  • Baumann, Martina, et al. (författare)
  • Artificially designed promoters : understanding the role of spatial features and canonical binding sites in transcription
  • 2012
  • Ingår i: Bioengineered Bugs. - 1949-1018 .- 1949-1026. ; 3:2, s. 120-123
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>The promoter is a key element in gene transcription and regulation. We previously reported that artificial sequences rich in the dinucleotide CpG are sufficient to drive expression in vitro in mammalian cell lines, without requiring canonical binding sites for transcription factor proteins. Here, we report that introducing a promoter organization that alternates in CpGs and regions rich in A and T further increases expression strength, as well as how insertion of specific binding sites makes such sequences respond to induced levels of the transcription factor NFκB. Our findings further contribute to the mechanistic understanding of promoters, as well as how these sequences might be shaped by evolutionary pressure in living organisms.</p>
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2.
  • Grabherr, Manfred G., et al. (författare)
  • Exploiting Nucleotide Composition to Engineer Promoters
  • 2011
  • Ingår i: PLoS One. - 1932-6203. ; 6:5, s. e20136
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>The choice of promoter is a critical step in optimizing the efficiency and stability of recombinant protein production in mammalian cell lines. Artificial promoters that provide stable expression across cell lines and can be designed to the desired strength constitute an alternative to the use of viral promoters. Here, we show how the nucleotide characteristics of highly active human promoters can be modelled via the genome-wide frequency distribution of short motifs: by overlapping motifs that occur infrequently in the genome, we constructed contiguous sequence that is rich in GC and CpGs, both features of known promoters, but lacking homology to real promoters. We show that snippets from this sequence, at 100 base pairs or longer, drive gene expression in vitro in a number of mammalian cells, and are thus candidates for use in protein production. We further show that expression is driven by the general transcription factors TFIIB and TFIID, both being ubiquitously present across cell types, which results in less tissue-and species-specific regulation compared to the viral promoter SV40. We lastly found that the strength of a promoter can be tuned up and down by modulating the counts of GC and CpGs in localized regions. These results constitute a "proof-of-concept" for custom-designing promoters that are suitable for biotechnological and medical applications.</p>
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3.
  • Ahmed Osman, Omneya, et al. (författare)
  • Interactions of Freshwater Cyanobacteria with Bacterial Antagonists
  • 2017
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 83:7
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1: 1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. L, D-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.</p>
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4.
  • Al-Jaff, Mohammed, et al. (författare)
  • microTaboo a general and practical solution to the k-disjoint problem
  • 2017
  • Ingår i: BMC Bioinformatics. - BIOMED CENTRAL LTD. - 1471-2105 .- 1471-2105. ; 18
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Background: A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting. However, there are several areas that would benefit from a more stringent definition of "unique", requiring that these sub-sequences of length W differ by more than k mismatches (i.e. a Hamming distance greater than k) from any other sub-sequence, which we term the k-disjoint problem. Examples include finding sequences unique to a pathogen for probe-based infection diagnostics; reducing off-target hits for re-sequencing or genome editing; detecting sequence (e.g. phage or viral) insertions; and multiple substitution mutations. Since both sensitivity and specificity are critical, an exhaustive, yet efficient solution is desirable.</p><p>Results: We present microTaboo, a method that allows for efficient and extensive sequence mining of unique (k-disjoint) sequences of up to 100 nucleotides in length. On a number of simulated and real data sets ranging from microbe-to mammalian-size genomes, we show that microTaboo is able to efficiently find all sub-sequences of a specified length W that do not occur within a threshold of k mismatches in any other sub-sequence. We exemplify that microTaboo has many practical applications, including point substitution detection, sequence insertion detection, padlock probe target search, and candidate CRISPR target mining.</p><p>Conclusions: microTaboo implements a solution to the k-disjoint problem in an alignment-and assembly free manner. microTaboo is available for Windows, Mac OS X, and Linux, running Java 7 and higher, under the GNU GPLv3 license, at:https://MohammedAlJaff.github.io/microTaboo</p>
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5.
  • Alfoeldi, Jessica, et al. (författare)
  • The genome of the green anole lizard and a comparative analysis with birds and mammals
  • 2011
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 477:7366, s. 587-591
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.</p>
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6.
  • Bornelöv, Susanne, 1984-, et al. (författare)
  • Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
  • 2018
  • Ingår i: BMC Genomics. - 1471-2164 .- 1471-2164. ; 19
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Background: The mammalian adipose tissue plays a central role in energy-balance control, whereas the avian visceral fat hardly expresses leptin, the key adipokine in mammals. Therefore, to assess the endocrine role of adipose tissue in birds, we compared the transcriptome and proteome between two metabolically different types of chickens, broilers and layers, bred towards efficient meat and egg production, respectively.</p><p>Results: Broilers and layer hens, grown up to sexual maturation under free-feeding conditions, differed 4.0-fold in weight and 1.6-fold in ovarian-follicle counts, yet the relative accumulation of visceral fat was comparable. RNA-seq and mass-spectrometry (MS) analyses of visceral fat revealed differentially expressed genes between broilers and layers, 1106 at the mRNA level (FDR ≤ 0.05), and 203 at the protein level (<em>P</em> ≤ 0.05). In broilers, Ingenuity Pathway Analysis revealed activation of the PTEN-pathway, and in layers increased response to external signals. The expression pattern of genes encoding fat-secreted proteins in broilers and layers was characterized in the RNA-seq and MS data, as well as by qPCR on visceral fat under free feeding and 24 h-feed deprivation. This characterization was expanded using available RNA-seq data of tissues from red junglefowl, and of visceral fat from broilers of different types. These comparisons revealed expression of new adipokines and secreted proteins (<em>LCAT</em>, <em>LECT2</em>, <em>SERPINE2</em>, <em>SFTP1</em>, <em>ZP1</em>, <em>ZP3</em>, <em>APOV1</em>, <em>VTG1</em> and <em>VTG2</em>) at the mRNA and/or protein levels, with dynamic gene expression patterns in the selected chicken lines (except for <em>ZP1</em>; FDR/<em>P</em> ≤ 0.05) and feed deprivation (<em>NAMPT</em>, <em>SFTPA1</em> and <em>ZP3</em>) (<em>P</em> ≤ 0.05). In contrast, some of the most prominent adipokines in mammals, leptin, <em>TNF</em>, <em>IFNG</em>, and <em>IL6</em> were expressed at a low level (FPKM/RPKM&lt; 1) and did not show differential mRNA expression neither between broiler and layer lines nor between fed vs. feed-deprived chickens.</p><p>Conclusions: Our study revealed that RNA and protein expression in visceral fat changes with selective breeding, suggesting endocrine roles of visceral fat in the selected phenotypes. In comparison to gene expression in visceral fat of mammals, our findings points to a more direct cross talk of the chicken visceral fat with the reproductive system and lower involvement in the regulation of appetite, inflammation and insulin resistance.</p>
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7.
  • Bornelöv, Susanne, 1984-, et al. (författare)
  • Correspondence on Lovell et al. identification of chicken genes previously assumed to be evolutionarily lost
  • 2017
  • Ingår i: Genome Biology. - 1465-6906 .- 1474-760X. ; 18
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases. Hence, the occurrence of syntenic groups of vertebrate genes that have not been observed in Aves does not prove the evolutionary loss of such genes.</p>
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8.
  • Butler, Geraldine, et al. (författare)
  • Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
  • 2009
  • Ingår i: Nature. - 1476-4687. ; 459:7247, s. 657-62
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.</p>
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9.
  • Delhomme, N., et al. (författare)
  • Serendipitous Meta-Transcriptomics The Fungal Community of Norway Spruce (Picea abies)
  • 2015
  • Ingår i: PLoS ONE. - 1932-6203 .- 1932-6203. - 1932-6203 (Electronic) 1932-6203 (Linking) ; 10:9
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>After performing de novo transcript assembly of &gt;1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.</p>
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10.
  • Delhomme, Nicolas, et al. (författare)
  • Serendipitous Meta-Transcriptomics The Fungal Community of Norway Spruce (Picea abies)
  • 2015
  • Ingår i: PLoS ONE. - 1932-6203 .- 1932-6203. ; 10:9
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>After performing de novo transcript assembly of &gt;1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.</p>
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