Distribution and evolution of repeated sequences in genomes of Triatominae (Hemiptera-Reduviidae inferred from genomic in situ hybridization.

Directory of Open Access Journals (Sweden)

Sebastian Pita

Full Text Available The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily.

Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: lessons from endogenous pararetrovirus.

Science.gov (United States)

Liu, Ruifang; Koyanagi, Kanako O; Chen, Sunlu; Kishima, Yuji

2012-12-01

In plant genomes, the incorporation of DNA segments is not a common method of artificial gene transfer. Nevertheless, various segments of pararetroviruses have been found in plant genomes in recent decades. The rice genome contains a number of segments of endogenous rice tungro bacilliform virus-like sequences (ERTBVs), many of which are present between AT dinucleotide repeats (ATrs). Comparison of genomic sequences between two closely related rice subspecies, japonica and indica, allowed us to verify the preferential insertion of ERTBVs into ATrs. In addition to ERTBVs, the comparative analyses showed that ATrs occasionally incorporate repeat sequences including transposable elements, and a wide range of other sequences. Besides the known genomic sequences, the insertion sequences also represented DNAs of unclear origins together with ERTBVs, suggesting that ATrs have integrated episomal DNAs that would have been suspended in the nucleus. Such insertion DNAs might be trapped by ATrs in the genome in a host-dependent manner. Conversely, other simple mono- and dinucleotide sequence repeats (SSR) were less frequently involved in insertion events relative to ATrs. Therefore, ATrs could be regarded as hot spots of double-strand breaks that induce non-homologous end joining. The insertions within ATrs occasionally generated new gene-related sequences or involved structural modifications of existing genes. Likewise, in a comparison between Arabidopsis thaliana and Arabidopsis lyrata, the insertions preferred ATrs to other SSRs. Therefore ATrs in plant genomes could be considered as genomic dumping sites that have trapped various DNA molecules and may have exerted a powerful evolutionary force. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

Science.gov (United States)

Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

2011-01-01

PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

Directory of Open Access Journals (Sweden)

Harvey Steven P

2007-03-01

Full Text Available Abstract Background The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. Results B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were

Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells

DEFF Research Database (Denmark)

Rodriguez, Jairo; Vives, Laura; Jordà, Mireia

2008-01-01

Methylation of the cytosine is the most frequent epigenetic modification of DNA in mammalian cells. In humans, most of the methylated cytosines are found in CpG-rich sequences within tandem and interspersed repeats that make up to 45% of the human genome, being Alu repeats the most common family....

Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

Czech Academy of Sciences Publication Activity Database

Torres, A.T.; Gong, Z.; Iovene, M.; Hirsch, C.D.; Buell, C.R.; Bryan, G.J.; Novák, Petr; Macas, Jiří; Jiang, J.

2011-01-01

Roč. 1, July 2011 (2011), s. 85-92 ISSN 2160-1836 R&D Projects: GA MŠk(CZ) LH11058 Institutional research plan: CEZ:AV0Z50510513 Keywords : Satellite sequences * Potato genome * Repeats Subject RIV: EB - Genetics ; Molecular Biology

The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats.

Directory of Open Access Journals (Sweden)

Andrew J Alverson

2011-01-01

Full Text Available The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean, and show that despite its unexceptional size (401,262 nt, the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38-297 nt repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes.

RECG maintains plastid and mitochondrial genome stability by suppressing extensive recombination between short dispersed repeats.

Directory of Open Access Journals (Sweden)

Masaki Odahara

2015-03-01

Full Text Available Maintenance of plastid and mitochondrial genome stability is crucial for photosynthesis and respiration, respectively. Recently, we have reported that RECA1 maintains mitochondrial genome stability by suppressing gross rearrangements induced by aberrant recombination between short dispersed repeats in the moss Physcomitrella patens. In this study, we studied a newly identified P. patens homolog of bacterial RecG helicase, RECG, some of which is localized in both plastid and mitochondrial nucleoids. RECG partially complements recG deficiency in Escherichia coli cells. A knockout (KO mutation of RECG caused characteristic phenotypes including growth delay and developmental and mitochondrial defects, which are similar to those of the RECA1 KO mutant. The RECG KO cells showed heterogeneity in these phenotypes. Analyses of RECG KO plants showed that mitochondrial genome was destabilized due to a recombination between 8-79 bp repeats and the pattern of the recombination partly differed from that observed in the RECA1 KO mutants. The mitochondrial DNA (mtDNA instability was greater in severe phenotypic RECG KO cells than that in mild phenotypic ones. This result suggests that mitochondrial genomic instability is responsible for the defective phenotypes of RECG KO plants. Some of the induced recombination caused efficient genomic rearrangements in RECG KO mitochondria. Such loci were sometimes associated with a decrease in the levels of normal mtDNA and significant decrease in the number of transcripts derived from the loci. In addition, the RECG KO mutation caused remarkable plastid abnormalities and induced recombination between short repeats (12-63 bp in the plastid DNA. These results suggest that RECG plays a role in the maintenance of both plastid and mitochondrial genome stability by suppressing aberrant recombination between dispersed short repeats; this role is crucial for plastid and mitochondrial functions.

[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

Science.gov (United States)

Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

2009-11-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

Directory of Open Access Journals (Sweden)

Varala Kranthi

2007-05-01

Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

Isolation and characterization of repeat elements of the oak genome and their application in population analysis

International Nuclear Information System (INIS)

Fluch, S.; Burg, K.

1998-01-01

Four minisatellite sequence elements have been identified and isolated from the genome of the oak species Quercus petraea and Quercus robur. Minisatellites 1 and 2 are putative members of repeat families, while minisatellites 3 and 4 show repeat length variation among individuals of test populations. A 590 base pair (bp) long element has also been identified which reveals individual-specific autoradiographic patterns when used as probe in Southern hybridisations of genomic oak DNA. (author)

Two new miniature inverted-repeat transposable elements in the genome of the clam Donax trunculus.

Science.gov (United States)

Šatović, Eva; Plohl, Miroslav

2017-10-01

Repetitive sequences are important components of eukaryotic genomes that drive their evolution. Among them are different types of mobile elements that share the ability to spread throughout the genome and form interspersed repeats. To broaden the generally scarce knowledge on bivalves at the genome level, in the clam Donax trunculus we described two new non-autonomous DNA transposons, miniature inverted-repeat transposable elements (MITEs), named DTC M1 and DTC M2. Like other MITEs, they are characterized by their small size, their A + T richness, and the presence of terminal inverted repeats (TIRs). DTC M1 and DTC M2 are 261 and 286 bp long, respectively, and in addition to TIRs, both of them contain a long imperfect palindrome sequence in their central parts. These elements are present in complete and truncated versions within the genome of the clam D. trunculus. The two new MITEs share only structural similarity, but lack any nucleotide sequence similarity to each other. In a search for related elements in databases, blast search revealed within the Crassostrea gigas genome a larger element sharing sequence similarity only to DTC M1 in its TIR sequences. The lack of sequence similarity with any previously published mobile elements indicates that DTC M1 and DTC M2 elements may be unique to D. trunculus.

The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features.

Directory of Open Access Journals (Sweden)

Janine Kamke

Full Text Available The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake.

Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

Energy Technology Data Exchange (ETDEWEB)

Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)

2007-01-01

Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

Energy Technology Data Exchange (ETDEWEB)

Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

2011-01-01

It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

Large scale analysis of small repeats via mining of the human genome

NARCIS (Netherlands)

van den Berg, I.; Bosnacki, D.; Hilbers, P.A.J.

2009-01-01

Small repetitive sequences, called tandem repeats, are abundant throughout the human genome, both in coding and in non-coding regions. Their role is still mostly unknown, but at least 20 of those repetitive sequences have been related to neurodegenerative disorders. The mutational process that is

Mutations in Cytosine-5 tRNA Methyltransferases Impact Mobile Element Expression and Genome Stability at Specific DNA Repeats

Directory of Open Access Journals (Sweden)

Bianca Genenncher

2018-02-01

Full Text Available The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5 RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects. In contrast, NSun2 function affected mobile element expression and genome integrity in a heat shock-independent fashion. Reduced tRNA stability in both RCMT mutants indicated that tRNA-dependent processes affected mobile element expression and DNA repeat stability. Importantly, further experiments indicated that complex formation with RNA could also contribute to the impact of RCMT function on gene expression control. These results thus uncover a link between tRNA modification enzymes, the expression of repeat DNA, and genomic integrity.

Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

Science.gov (United States)

Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

2015-01-01

Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data.

Science.gov (United States)

Liu, San-Xu; Hou, Wei; Zhang, Xue-Yan; Peng, Chang-Jun; Yue, Bi-Song; Fan, Zhen-Xin; Li, Jing

2018-07-18

The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (Pgenome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

Directory of Open Access Journals (Sweden)

Graner Andreas

2008-10-01

Full Text Available Abstract Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences regions in uncharacterised genomic sequences. The restriction that a particular

A novel rat genomic simple repeat DNA with RNA-homology shows triplex (H-DNA)-like structure and tissue-specific RNA expression

International Nuclear Information System (INIS)

Dey, Indranil; Rath, Pramod C.

2005-01-01

Mammalian genome contains a wide variety of repetitive DNA sequences of relatively unknown function. We report a novel 227 bp simple repeat DNA (3.3 DNA) with a d {(GA) 7 A (AG) 7 } dinucleotide mirror repeat from the rat (Rattus norvegicus) genome. 3.3 DNA showed 75-85% homology with several eukaryotic mRNAs due to (GA/CU) n dinucleotide repeats by nBlast search and a dispersed distribution in the rat genome by Southern blot hybridization with [ 32 P]3.3 DNA. The d {(GA) 7 A (AG) 7 } mirror repeat formed a triplex (H-DNA)-like structure in vitro. Two large RNAs of 9.1 and 7.5 kb were detected by [ 32 P]3.3 DNA in rat brain by Northern blot hybridization indicating expression of such simple sequence repeats at RNA level in vivo. Further, several cDNAs were isolated from a rat cDNA library by [ 32 P]3.3 DNA probe. Three such cDNAs showed tissue-specific RNA expression in rat. pRT 4.1 cDNA showed strong expression of a 2.39 kb RNA in brain and spleen, pRT 5.5 cDNA showed strong expression of a 2.8 kb RNA in brain and a 3.9 kb RNA in lungs, and pRT 11.4 cDNA showed weak expression of a 2.4 kb RNA in lungs. Thus, genomic simple sequence repeats containing d (GA/CT) n dinucleotides are transcriptionally expressed and regulated in rat tissues. Such d (GA/CT) n dinucleotide repeats may form structural elements (e.g., triplex) which may be sites for functional regulation of genomic coding sequences as well as RNAs. This may be a general function of such transcriptionally active simple sequence repeats widely dispersed in mammalian genome

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRi) plasmids | Office of Cancer Genomics

Science.gov (United States)

CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes.

Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

Science.gov (United States)

2012-01-01

Background Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation. Conclusions This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding

DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases.

Directory of Open Access Journals (Sweden)

Boian S Alexandrov

Full Text Available Trinucleotide repeats sequences (TRS represent a common type of genomic DNA motif whose expansion is associated with a large number of human diseases. The driving molecular mechanisms of the TRS ongoing dynamic expansion across generations and within tissues and its influence on genomic DNA functions are not well understood. Here we report results for a novel and notable collective breathing behavior of genomic DNA of tandem TRS, leading to propensity for large local DNA transient openings at physiological temperature. Our Langevin molecular dynamics (LMD and Markov Chain Monte Carlo (MCMC simulations demonstrate that the patterns of openings of various TRSs depend specifically on their length. The collective propensity for DNA strand separation of repeated sequences serves as a precursor for outsized intermediate bubble states independently of the G/C-content. We report that repeats have the potential to interfere with the binding of transcription factors to their consensus sequence by altered DNA breathing dynamics in proximity of the binding sites. These observations might influence ongoing attempts to use LMD and MCMC simulations for TRS-related modeling of genomic DNA functionality in elucidating the common denominators of the dynamic TRS expansion mutation with potential therapeutic applications.

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

Science.gov (United States)

Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

2015-05-01

Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution

Directory of Open Access Journals (Sweden)

Rodolphe François

2006-08-01

Full Text Available Abstract Background Comparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species such as Drosophila or maize, transposable elements (TEs have been shown to be involved in chromosomal rearrangements. In this work, we have explored the presence of interspersed repeats in regions of chromosomal rearrangements, using an updated high-resolution integrated comparative map among cattle, man and mouse. Results The bovine, human and mouse comparative autosomal map has been constructed using data from bovine genetic and physical maps and from FISH-mapping studies. We confirm most previous results but also reveal some discrepancies. A total of 211 conserved segments have been identified between cattle and man, of which 33 are new segments and 72 correspond to extended, previously known segments. The resulting map covers 91% and 90% of the human and bovine genomes, respectively. Analysis of breakpoint regions revealed a high density of species-specific interspersed repeats in the human and mouse genomes. Conclusion Analysis of the breakpoint regions has revealed specific repeat density patterns, suggesting that TEs may have played a significant role in chromosome evolution and genome plasticity. However, we cannot rule out that repeats and breakpoints accumulate independently in the few same regions where modifications are better tolerated. Likewise, we cannot ascertain whether increased TE density is the cause or the consequence of chromosome rearrangements. Nevertheless, the identification of high density repeat clusters combined with a well-documented repeat phylogeny should highlight probable breakpoints, and permit their precise dating. Combining new statistical models taking the present information into account should help reconstruct ancestral karyotypes.

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.

Science.gov (United States)

Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A

2016-07-01

Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.

Genome-wide identification and validation of simple sequence repeats (SSRs) from Asparagus officinalis.

Science.gov (United States)

Li, Shufen; Zhang, Guojun; Li, Xu; Wang, Lianjun; Yuan, Jinhong; Deng, Chuanliang; Gao, Wujun

2016-06-01

Garden asparagus (Asparagus officinalis), an important vegetable cultivated worldwide, can also serve as a model dioecious plant species in the study of sex determination and sex chromosome evolution. However, limited DNA marker resources have been developed and used for this species. To expand these resources, we examined the DNA sequences for simple sequence repeats (SSRs) in 163,406 scaffolds representing approximately 400 Mbp of the A. officinalis genome. A total of 87,576 SSRs were identified in 59,565 scaffolds. The most abundant SSR repeats were trinucleotide and tetranucleotide, accounting for 29.2 and 29.1% of the total SSRs, respectively, followed by di-, penta-, hexa-, hepta-, and octanucleotides. The AG motif was most common among dinucleotides and was also the most frequent motif in the entire A. officinalis genome, representing 14.7% of all SSRs. A total of 41,917 SSR primers pairs were designed to amplify SSRs. Twenty-two genomic SSR markers were tested in 39 asparagus accessions belonging to ten cultivars and one accession of Asparagus setaceus for determination of genetic diversity. The intra-species polymorphism information content (PIC) values of the 22 genomic SSR markers were intermediate, with an average of 0.41. The genetic diversity between the ten A. officinalis cultivars was low, and the UPGMA dendrogram was largely unrelated to cultivars. It is here suggested that the sex of individuals is an important factor influencing the clustering results. The information reported here provides new information about the organization of the microsatellites in A. officinalis genome and lays a foundation for further genetic studies and breeding applications of A. officinalis and related species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Anvendelse af MIP ved kildekarakterisering og vurdering af nedbrydning af chlorerede opløsningsmidler

DEFF Research Database (Denmark)

Broholm, Mette Martina; Janniche, Gry Sander; Damgaard, Ida

2014-01-01

Membrane Interface Probing (MIP) er et 'direct push' screeningsværktøj, som kan anvendes ved karakterisering af forurenede grunde. Karakterisering af kildeområder med chlorerede opløsningsmidler (som DNAPL) udgør et vigtigt led i udviklingen af den konceptuelle forståelse, som er essentiel...... for risikovurdering og valg af afværgestrategi. Integreret karakterisering med en række metoder for direkte såvel som indirekte dokumentation af DNAPL i moræneler, herunder MIP, er beskrevet i Kerrn-Jespersen et al. (2013). Det samlede DNAPL-karakteriseringsprojekt er beskrevet i detaljer i Janniche et al. (2013). En...... vurdering af anvendte detektorer for MIP er foretaget af Olsson (2013). Ved karakterisering af forurening med bl.a. chlorerede opløsningsmidler er der behov for en vurdering af forureningssammensætning og nedbrydning. Tilsvarende vurdering er nødvendig, når udviklingen af stimuleret reduktiv dechlorering...

Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction.

Science.gov (United States)

Wu, Chen; Twort, Victoria G; Crowhurst, Ross N; Newcomb, Richard D; Buckley, Thomas R

2017-11-16

Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

Science.gov (United States)

Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

2015-12-01

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes.

Science.gov (United States)

Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

2017-04-01

For species with minor inverted repeat (IR) boundary changes in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in the IR than the single copy regions (SC). However, the impact of large-scale IR expansion/contraction on plastid nucleotide substitution rates among closely related species remains unclear. We included plastomes from 22 Pelargonium species, including eight newly sequenced genomes, and used both pairwise and model-based comparisons to investigate the impact of the IR on sequence evolution in plastids. Ten types of plastome organization with different inversions or IR boundary changes were identified in Pelargonium. Inclusion in the IR was not sufficient to explain the variation of nucleotide substitution rates. Instead, the rate heterogeneity in Pelargonium plastomes was a mixture of locus-specific, lineage-specific and IR-dependent effects. Our study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Science.gov (United States)

Thybert, David; Roller, Maša; Navarro, Fábio C.P.; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C.; Laukaitis, Christina M.; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A.; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J.; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M.; Odom, Duncan T.; Flicek, Paul

2018-01-01

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. PMID:29563166

Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats

Directory of Open Access Journals (Sweden)

Adler Joël

2007-12-01

Full Text Available Abstract Background Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms. Results We have developed Reptile http://reptile.unibe.ch, a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites. Conclusion Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at http://genomics.unibe.ch/dora.

Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia

Directory of Open Access Journals (Sweden)

Junjie Cui

2017-06-01

Full Text Available Bitter gourd (Momordica charantia is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus, watermelon (Citrullus lanatus, and melon (Cucumis melo genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.

The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

Directory of Open Access Journals (Sweden)

Turmel Monique

2007-07-01

Full Text Available Abstract Background In the Chlorophyta – the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae – the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs deviate considerably from the ancestral pattern described for the prasinophyte Nephroselmis olivacea, the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs. Chlorella vulgaris (Chlorellales is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga Leptosira terrestris (Ctenocladales. Results The 195,081-bp Leptosira chloroplast genome resembles the 150,613-bp Chlorella genome in lacking a large inverted repeat (IR but differs greatly in gene order. Six of the conserved genes present in Chlorella cpDNA are missing from the Leptosira gene repertoire. The 106 conserved genes, four introns and 11 free standing open reading frames (ORFs account for 48.3% of the genome sequence. This is the lowest gene density yet observed among chlorophyte cpDNAs. Contrary to the situation in Chlorella but similar to that in the chlorophycean Scenedesmus obliquus, the gene distribution is highly biased over the two DNA strands in Leptosira. Nine genes, compared to only three in Chlorella, have significantly expanded coding regions relative to their homologues in ancestral-type green algal cpDNAs. As observed in chlorophycean genomes, the rpoB gene is fragmented into two ORFs. Short repeats account for 5.1% of the Leptosira genome sequence and are present mainly in intergenic regions. Conclusion Our results highlight the great plasticity of the chloroplast genome in the Trebouxiophyceae and indicate

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Science.gov (United States)

Thybert, David; Roller, Maša; Navarro, Fábio C P; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C; Laukaitis, Christina M; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M; Odom, Duncan T; Flicek, Paul

2018-04-01

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli , which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. © 2018 Thybert et al.; Published by Cold Spring Harbor Laboratory Press.

[Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].

Science.gov (United States)

Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin

2015-04-01

This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

Genomic tools for behavioural ecologists to understand repeatable individual differences in behaviour.

Science.gov (United States)

Bengston, Sarah E; Dahan, Romain A; Donaldson, Zoe; Phelps, Steven M; van Oers, Kees; Sih, Andrew; Bell, Alison M

2018-06-01

Behaviour is a key interface between an animal's genome and its environment. Repeatable individual differences in behaviour have been extensively documented in animals, but the molecular underpinnings of behavioural variation among individuals within natural populations remain largely unknown. Here, we offer a critical review of when molecular techniques may yield new insights, and we provide specific guidance on how and whether the latest tools available are appropriate given different resources, system and organismal constraints, and experimental designs. Integrating molecular genetic techniques with other strategies to study the proximal causes of behaviour provides opportunities to expand rapidly into new avenues of exploration. Such endeavours will enable us to better understand how repeatable individual differences in behaviour have evolved, how they are expressed and how they can be maintained within natural populations of animals.

Lyden af musik - er lyden af idealisme

DEFF Research Database (Denmark)

Eigtved, Michael

2015-01-01

Programartiklen til Det Ny Teaters opsætning af Rodgers & Hammersteins The Sound of Music, undersøger musicalgenrens - og især de konkrete ophavsmænds- affinitet til fremstillingen af såvel idealistiske som ideologiske universer.......Programartiklen til Det Ny Teaters opsætning af Rodgers & Hammersteins The Sound of Music, undersøger musicalgenrens - og især de konkrete ophavsmænds- affinitet til fremstillingen af såvel idealistiske som ideologiske universer....

Discovery and analysis of an active long terminal repeat-retrotransposable element in Aspergillus oryzae.

Science.gov (United States)

Jie Jin, Feng; Hara, Seiichi; Sato, Atsushi; Koyama, Yasuji

2014-01-01

Wild-type Aspergillus oryzae RIB40 contains two copies of the AO090005001597 gene. We previously constructed A. oryzae RIB40 strain, RKuAF8B, with multiple chromosomal deletions, in which the AO090005001597 copy number was found to be increased significantly. Sequence analysis indicated that AO090005001597 is part of a putative 6,000-bp retrotransposable element, flanked by two long terminal repeats (LTRs) of 669 bp, with characteristics of retroviruses and retrotransposons, and thus designated AoLTR (A. oryzae LTR-retrotransposable element). AoLTR comprised putative reverse transcriptase, RNase H, and integrase domains. The deduced amino acid sequence alignment of AoLTR showed 94% overall identity with AFLAV, an A. flavus Tf1/sushi retrotransposon. Quantitative real-time RT-PCR showed that AoLTR gene expression was significantly increased in the RKuAF8B, in accordance with the increased copy number. Inverse PCR indicated that the full-length retrotransposable element was randomly integrated into multiple genomic locations. However, no obvious phenotypic changes were associated with the increased AoLTR gene copy number.

Identification of genes containing expanded purine repeats in the human genome and their apparent protective role against cancer.

Science.gov (United States)

Singh, Himanshu Narayan; Rajeswari, Moganty R

2016-01-01

Purine repeat sequences present in a gene are unique as they have high propensity to form unusual DNA-triple helix structures. Friedreich's ataxia is the only human disease that is well known to be associated with DNA-triplexes formed by purine repeats. The purpose of this study was to recognize the expanded purine repeats (EPRs) in human genome and find their correlation with cancer pathogenesis. We developed "PuRepeatFinder.pl" algorithm to identify non-overlapping EPRs without pyrimidine interruptions in the human genome and customized for searching repeat lengths, n ≥ 200. A total of 1158 EPRs were identified in the genome which followed Wakeby distribution. Two hundred and ninety-six EPRs were found in geneic regions of 282 genes (EPR-genes). Gene clustering of EPR-genes was done based on their cellular function and a large number of EPR-genes were found to be enzymes/enzyme modulators. Meta-analysis of 282 EPR-genes identified only 63 EPR-genes in association with cancer, mostly in breast, lung, and blood cancers. Protein-protein interaction network analysis of all 282 EPR-genes identified proteins including those in cadherins and VEGF. The two observations, that EPRs can induce mutations under malignant conditions and that identification of some EPR-gene products in vital cell signaling-mediated pathways, together suggest the crucial role of EPRs in carcinogenesis. The new link between EPR-genes and their functionally interacting proteins throws a new dimension in the present understanding of cancer pathogenesis and can help in planning therapeutic strategies. Validation of present results using techniques like NGS is required to establish the role of the EPR genes in cancer pathology.

A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.

Science.gov (United States)

Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F; Li, Shuaicheng; Hu, Kailin

2016-01-07

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

En genlæsning af John Rawls i lyset af hans diskussion af forholdet til fremtidige generationer

DEFF Research Database (Denmark)

Lübcke, Poul

2009-01-01

På grundlag af en konsekventialistisk rekonstruktion af Rawls' politiske position gøres der rede for Rawls eksplicitte og implicitte vurdering af vores ansvar over for fremtidige generationer......På grundlag af en konsekventialistisk rekonstruktion af Rawls' politiske position gøres der rede for Rawls eksplicitte og implicitte vurdering af vores ansvar over for fremtidige generationer...

[Progress of genome engineering technology via clustered regularly interspaced short palindromic repeats--a review].

Science.gov (United States)

Li, Hao; Qiu, Shaofu; Song, Hongbin

2013-10-04

In survival competition with phage, bacteria and archaea gradually evolved the acquired immune system--Clustered regularly interspaced short palindromic repeats (CRISPR), presenting the trait of transcribing the crRNA and the CRISPR-associated protein (Cas) to silence or cleaving the foreign double-stranded DNA specifically. In recent years, strong interest arises in prokaryotes primitive immune system and many in-depth researches are going on. Recently, researchers successfully repurposed CRISPR as an RNA-guided platform for sequence-specific gene expression, which provides a simple approach for selectively perturbing gene expression on a genome-wide scale. It will undoubtedly bring genome engineering into a more convenient and accurate new era.

Energirenovering af parcelhuse

DEFF Research Database (Denmark)

Aggerholm, Søren

af de tre huse består i efterisolering af lofter op til 300 mm, udskiftning af almindelige termoruder til energiruder, og installation af solvarmeanlæg til produktion af varmt brugsvand. I de tre huse er der ved energirenoveringen opnået en reduktion af energiforbruget på 16-22 procent. Rapporten...

The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.

Science.gov (United States)

Zhang, Yanzhen; Ma, Ji; Yang, Bingxian; Li, Ruyi; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Zhang, Lin

2014-05-01

Taxus chinensis var. mairei (Taxaceae) is a domestic variety of yew species in local China. This plant is one of the sources for paclitaxel, which is a promising antineoplastic chemotherapy drugs during the last decade. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of T. chinensis var. mairei. The T. chinensis var. mairei cp genome is 129,513 bp in length, with 113 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). Among the 113 single copy genes, 9 are intron-containing. Compared to other land plant cp genomes, the T. chinensis var. mairei cp genome has lost one of the large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperm such as Cycas revoluta and Ginkgo biloba L. Compared to related species, the gene order of T. chinensis var. mairei has a large inversion of ~110kb including 91 genes (from rps18 to accD) with gene contents unarranged. Repeat analysis identified 48 direct and 2 inverted repeats 30 bp long or longer with a sequence identity greater than 90%. Repeated short segments were found in genes rps18, rps19 and clpP. Analysis also revealed 22 simple sequence repeat (SSR) loci and almost all are composed of A or T. Copyright © 2014 Elsevier B.V. All rights reserved.

Kortlægning af evalueringer og undersøgelser af vejledning knyttet til vejledning af unge i UU-regi

DEFF Research Database (Denmark)

Skovhus, Randi Boelskifte; thomsen, rie

2013-01-01

Kortlægning af evalueringer og undersøgelser af vejledning knyttet til vejledning af unge i UU-regi 2004-2013. Et arbejdspapir......Kortlægning af evalueringer og undersøgelser af vejledning knyttet til vejledning af unge i UU-regi 2004-2013. Et arbejdspapir...

Fremtidssikring af kloaknet

DEFF Research Database (Denmark)

Hansen, Ernst Jan de Place

2008-01-01

Beskrivelse af hvordan man ved udbygning af eksisterende kloaknet og ved nytænkning af planlægning af nye bydele kan sikre sig langsigtet mod konsekvenserne af klimaændinger og kraftigere nedbør...

Microbial species delineation using whole genome sequences.

Science.gov (United States)

Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

2015-08-18

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3

Directory of Open Access Journals (Sweden)

Katarzyna Pachulska-Wieczorek

2016-07-01

Full Text Available Long-terminal repeat (LTR retrotransposons are transposable genetic elements that replicate intracellularly, and can be considered progenitors of retroviruses. Ty1 and Ty3 are the most extensively characterized LTR retrotransposons whose RNA genomes provide the template for both protein translation and genomic RNA that is packaged into virus-like particles (VLPs and reverse transcribed. Genomic RNAs are not divided into separate pools of translated and packaged RNAs, therefore their trafficking and packaging into VLPs requires an equilibrium between competing events. In this review, we focus on Ty1 and Ty3 genomic RNA trafficking and packaging as essential steps of retrotransposon propagation. We summarize the existing knowledge on genomic RNA sequences and structures essential to these processes, the role of Gag proteins in repression of genomic RNA translation, delivery to VLP assembly sites, and encapsidation.

Fermentering af korn øger fordøjeligheden af næringsstoffer

DEFF Research Database (Denmark)

Pedersen, Anni Øyan; Jørgensen, Henry Johs. Høgh; Knudsen, Knud Erik Bach

2010-01-01

Et fordøjelighedsforsøg har vist, at energiværdien af byg og hvede steg ved fermentering. Effekten var størst ved fermentering af byg, hvor fordøjeligheden af organisk stof for enden af tyndtarmen steg statistisk sikkert med 9 %. Ved fermentering af hvede steg fordøjeligheden af organisk stof...... af vand og dels CO2-produktion og dermed tørstoftab. Anbefaling om beregning af energiværdi i fermenteret korn vil blive foretaget ud fra resultaterne af et produktionsforsøg med slagtesvin, som er under publicering. Fosforudnyttelse i fermenteret korn undersøges yderligere i et produktionsforsøg med...

Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers.

Science.gov (United States)

Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu

2014-11-01

Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

The APPLE Score - A Novel Score for the Prediction of Rhythm Outcomes after Repeat Catheter Ablation of Atrial Fibrillation.

Directory of Open Access Journals (Sweden)

Jelena Kornej

Full Text Available Arrhythmia recurrences after catheter ablation occur in up to 50% within one year but their prediction remains challenging. Recently, we developed a novel score for the prediction of rhythm outcomes after single AF ablation demonstrating superiority to other scores. The current study was performed to 1 prove the predictive value of the APPLE score in patients undergoing repeat AF ablation and 2 compare it with the CHADS2 and CHA2DS2-VASc scores.Rhythm outcome between 3-12 months after AF ablation were documented. The APPLE score (one point for Age >65 years, Persistent AF, imPaired eGFR (<60 ml/min/1.73m2, LA diameter ≥43 mm, EF <50% was calculated in every patient before procedure.379 consecutive patients from The Leipzig Heart Center AF Ablation Registry (60±10 years, 65% male, 70% paroxysmal AF undergoing repeat AF catheter ablation were included. Arrhythmia recurrences were observed in 133 patients (35%. While the CHADS2 (AUC 0.577, p = 0.037 and CHA2DS2-VASc scores (AUC 0.590, p = 0.015 demonstrated low predictive value, the APPLE score showed better prediction of arrhythmia recurrences (AUC 0.617, p = 0.002 than other scores (both p<0.001. Compared to patients with an APPLE score of 0, the risk (OR for arrhythmia recurrences was 2.9, 3.0 and 6.0 (all p<0.01 for APPLE scores 1, 2, or ≥3, respectively.The novel APPLE score is superior to the CHADS2 and CHA2DS2-VASc scores for prediction of rhythm outcomes after repeat AF catheter ablation. It may be helpful to identify patients with low, intermediate or high risk for recurrences after repeat procedure.

In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

Directory of Open Access Journals (Sweden)

Evandro Vagner Tambarussi

2009-01-01

Full Text Available The availability of chloroplast genome (cpDNA sequences of Atropa belladonna, Nicotiana sylvestris, N.tabacum, N. tomentosiformis, Solanum bulbocastanum, S. lycopersicum and S. tuberosum, which are Solanaceae species,allowed us to analyze the organization of cpSSRs in their genic and intergenic regions. In general, the number of cpSSRs incpDNA ranged from 161 in S. tuberosum to 226 in N. tabacum, and the number of intergenic cpSSRs was higher than geniccpSSRs. The mononucleotide repeats were the most frequent in studied species, but we also identified di-, tri-, tetra-, pentaandhexanucleotide repeats. Multiple alignments of all cpSSRs sequences from Solanaceae species made the identification ofnucleotide variability possible and the phylogeny was estimated by maximum parsimony. Our study showed that the plastomedatabase can be exploited for phylogenetic analysis and biotechnological approaches.

Genome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation

Science.gov (United States)

Tsai, Chia-Ti; Hsieh, Chia-Shan; Chang, Sheng-Nan; Chuang, Eric Y.; Ueng, Kwo-Chang; Tsai, Chin-Feng; Lin, Tsung-Hsien; Wu, Cho-Kai; Lee, Jen-Kuang; Lin, Lian-Yu; Wang, Yi-Chih; Yu, Chih-Chieh; Lai, Ling-Ping; Tseng, Chuen-Den; Hwang, Juey-Jen; Chiang, Fu-Tien; Lin, Jiunn-Lee

2016-01-01

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. Previous genome-wide association studies had identified single-nucleotide polymorphisms in several genomic regions to be associated with AF. In human genome, copy number variations (CNVs) are known to contribute to disease susceptibility. Using a genome-wide multistage approach to identify AF susceptibility CNVs, we here show a common 4,470-bp diallelic CNV in the first intron of potassium interacting channel 1 gene (KCNIP1) is strongly associated with AF in Taiwanese populations (odds ratio=2.27 for insertion allele; P=6.23 × 10−24). KCNIP1 insertion is associated with higher KCNIP1 mRNA expression. KCNIP1-encoded protein potassium interacting channel 1 (KCHIP1) is physically associated with potassium Kv channels and modulates atrial transient outward current in cardiac myocytes. Overexpression of KCNIP1 results in inducible AF in zebrafish. In conclusions, a common CNV in KCNIP1 gene is a genetic predictor of AF risk possibly pointing to a functional pathway. PMID:26831368

Lyden-af-Leg

DEFF Research Database (Denmark)

Toft, Herdis

Præsentation af seniorforsker-projekt Lyden-af-Leg i et traderingsperspektiv og med indledende fokus på YouTube som traderings-platform.......Præsentation af seniorforsker-projekt Lyden-af-Leg i et traderingsperspektiv og med indledende fokus på YouTube som traderings-platform....

Sundhedseffekter af luftforurening-beregningspriser

DEFF Research Database (Denmark)

Andersen, M. S.; Frohn, L. M.; Jensen, S. S.

Denne rapport afrapporterer det fortsatte arbejde med udvikling af miljøøkonomiske beregningspriser. På grundlag af EcoSense 4.0 fra ExternE-projektet, er der foretaget nye beregninger af eksternaliteter ved luftforurening med sundhedseffekter. Samtidig giver rapporten en vurdering af luftspredni......Denne rapport afrapporterer det fortsatte arbejde med udvikling af miljøøkonomiske beregningspriser. På grundlag af EcoSense 4.0 fra ExternE-projektet, er der foretaget nye beregninger af eksternaliteter ved luftforurening med sundhedseffekter. Samtidig giver rapporten en vurdering af...

Anvendelse af alternative isoleringsmaterialer

DEFF Research Database (Denmark)

Hansen, Ernst Jan de Place

2003-01-01

Resume af By og Byg Anvisning 207 om anvendelse af alternative isoleringsmaterialer, udarbejdet af Statens Byggeforskningsinstitut under udviklingsprogrammet "Miljø- og arbejdsmiljøvenlig isolering"......Resume af By og Byg Anvisning 207 om anvendelse af alternative isoleringsmaterialer, udarbejdet af Statens Byggeforskningsinstitut under udviklingsprogrammet "Miljø- og arbejdsmiljøvenlig isolering"...

Repeat-aware modeling and correction of short read errors.

Science.gov (United States)

Yang, Xiao; Aluru, Srinivas; Dorman, Karin S

2011-02-15

High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at "http://aluru-sun.ece.iastate.edu/doku.php?id = redeem". We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Science.gov (United States)

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Beregning af nitratudvaskning

DEFF Research Database (Denmark)

Petersen, Jens; Petersen, Bjørn Molt; Blicher-Mathiesen, Gitte

2006-01-01

I forbindelse med kommunalreformen ønskes en ensartet forvaltning af reglerne for vurdering af virkninger på miljøet (VVM) ved ansøgninger om udvidelse af husdyrbrug, herunder beregning af nitratudvaskningen. Rapporten foreslår et beregningskoncept, der bygger på den ansøgende bedrifts samlede kv...

Genome-scale portrait and evolutionary significance of human-specific core promoter tri- and tetranucleotide short tandem repeats.

Science.gov (United States)

Nazaripanah, N; Adelirad, F; Delbari, A; Sahaf, R; Abbasi-Asl, T; Ohadi, M

2018-04-05

While there is an ongoing trend to identify single nucleotide substitutions (SNSs) that are linked to inter/intra-species differences and disease phenotypes, short tandem repeats (STRs)/microsatellites may be of equal (if not more) importance in the above processes. Genes that contain STRs in their promoters have higher expression divergence compared to genes with fixed or no STRs in the gene promoters. In line with the above, recent reports indicate a role of repetitive sequences in the rise of young transcription start sites (TSSs) in human evolution. Following a comparative genomics study of all human protein-coding genes annotated in the GeneCards database, here we provide a genome-scale portrait of human-specific short- and medium-size (≥ 3-repeats) tri- and tetranucleotide STRs and STR motifs in the critical core promoter region between - 120 and + 1 to the TSS and evidence of skewing of this compartment in reference to the STRs that are not human-specific (Levene's test p human-specific transcripts was detected in the tri and tetra human-specific compartments (mid-p genome-scale skewing of STRs at a specific region of the human genome and a link between a number of these STRs and TSS selection/transcript specificity. The STRs and genes listed here may have a role in the evolution and development of characteristics and phenotypes that are unique to the human species.

Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes.

Science.gov (United States)

Sabir, Jamal; Schwarz, Erika; Ellison, Nicholas; Zhang, Jin; Baeshen, Nabih A; Mutwakil, Muhammed; Jansen, Robert; Ruhlman, Tracey

2014-08-01

Land plant plastid genomes (plastomes) provide a tractable model for evolutionary study in that they are relatively compact and gene dense. Among the groups that display an appropriate level of variation for structural features, the inverted-repeat-lacking clade (IRLC) of papilionoid legumes presents the potential to advance general understanding of the mechanisms of genomic evolution. Here, are presented six complete plastome sequences from economically important species of the IRLC, a lineage previously represented by only five completed plastomes. A number of characters are compared across the IRLC including gene retention and divergence, synteny, repeat structure and functional gene transfer to the nucleus. The loss of clpP intron 2 was identified in one newly sequenced member of IRLC, Glycyrrhiza glabra. Using deeply sequenced nuclear transcriptomes from two species helped clarify the nature of the functional transfer of accD to the nucleus in Trifolium, which likely occurred in the lineage leading to subgenus Trifolium. Legumes are second only to cereal crops in agricultural importance based on area harvested and total production. Genetic improvement via plastid transformation of IRLC crop species is an appealing proposition. Comparative analyses of intergenic spacer regions emphasize the need for complete genome sequences for developing transformation vectors for plastid genetic engineering of legume crops. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Identifikation af referencevandløb til implementering af vandrammedirektivet i Danmark

DEFF Research Database (Denmark)

Kristensen, Esben Astrup; Baattrup-Pedersen, Annette; Skriver, Jens

Definition og beskrivelse af referencetilstanden er centralt for implementering af vandrammedirektivet, da bedømmelse af den økologiske tilstand sker som afvigelsen fra den upåvirkede referencetilstand. I denne rapport præsenteres analyser af danske, udenlandske og historiske data med det formål...

Inter-simple sequence repeat (ISSR) loci mapping in the genome of perennial ryegrass

DEFF Research Database (Denmark)

Pivorienė, O; Pašakinskienė, I; Brazauskas, G

2008-01-01

The aim of this study was to identify and characterize new ISSR markers and their loci in the genome of perennial ryegrass. A subsample of the VrnA F2 mapping family of perennial ryegrass comprising 92 individuals was used to develop a linkage map including inter-simple sequence repeat markers...... demonstrated a 70% similarity to the Hordeum vulgare germin gene GerA. Inter-SSR mapping will provide useful information for gene targeting, quantitative trait loci mapping and marker-assisted selection in perennial ryegrass....

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming.

Science.gov (United States)

Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der

2017-11-06

Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

Restaurering af Skjern Å

DEFF Research Database (Denmark)

Jessen, K.; Boysen Larsen, B.; Bundgaard, P.

Denne rapport indeholder resultaterne af den natur- og miljøovervågning, der blev iværksat som en del af naturgenopretningen af Skjern Å 1999-2002. Ved projektet ophørte den kunstige afvanding af den vestlige del af Skjern Å dalen. Størstedelen af de dyrkede arealer ændredes til ekstensive græsni...

Relevansen af Aristoteles' etik for konceptionen af eksistentiel terapi

DEFF Research Database (Denmark)

Dræby, Anders

Siden sin undfangelse i begyndelsen af det 20. århundrede har den eksistentielle terapi repræsenteret et filosofisk funderet alternativ til de former for terapeutisk praksis, der er funderet i den funktionalistiske medicinske metafysik. Anvendelse af elementer fra Aristoteles' etik muliggør en...... fremhævelse af den eksistentielle terapi som en praktisk eksistensfænomenologisk livskunst, hvis anliggende er en frembringelse af det enkelte menneskes muligheder fra det skjulte og ind i det uskjulte, så mennesket viser sig som det er ved sig selv...

Om distributionen af hvidhed

DEFF Research Database (Denmark)

Frello, Birgitta

2007-01-01

Med udgangspunkt i John Fords Western, Forfølgeren fra 1956, præsenteres en analyse af repræsentationer af race og overskridelse af raceskel, særligt i relation til konstitueringen af subjektpositioner, hvorfra spørgsmål om hvidhed og ikke-hvidhed kan afgøres.......Med udgangspunkt i John Fords Western, Forfølgeren fra 1956, præsenteres en analyse af repræsentationer af race og overskridelse af raceskel, særligt i relation til konstitueringen af subjektpositioner, hvorfra spørgsmål om hvidhed og ikke-hvidhed kan afgøres....

In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

Science.gov (United States)

Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

2015-10-01

Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

Energirenovering af Traneparken

DEFF Research Database (Denmark)

Rose, Jørgen; Thomsen, Kirsten Engelund; Mørck, Ove

Nærværende rapport udgør en del af afrapporteringen af PSO ELFORSK projektet Vejledning for energirenovering af boligblokke til lavenergiklasse 2015 og 2020. Arbejdet har været finansieret af PSO midler via ELFORSK, projekt: 347-023. Formålet med projektet er at udvikle en vejledning for dybtgående...

Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: Evidence for differences and commonalities in size distributions and size restrictions

NARCIS (Netherlands)

M. Schaap (Michiel); R.J.L.F. Lemmers (Richard); R. Maassen (Roel); P.J. van der Vliet (Patrick); L.F. Hoogerheide (Lennart); H.K. van Dijk (Herman); N. Basturk (Nalan); P. de Knijff (Peter); S.M. van der Maarel (Silvère)

2013-01-01

textabstractBackground: Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extreme example of copy number variation, but their structure and

Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions

NARCIS (Netherlands)

Schaap, M.; Lemmers, R.J.L.F.; Maassen, R.; van der Vliet, P.J.; Hoogerheide, L.F.; van Dijk, H.K.; Basturk, N.; de Knijff, P.; van der Maarel, S.M.

2013-01-01

Background: Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extreme example of copy number variation, but their structure and function is largely

Om Hegels opfattelse af Gorgias, set på baggrund af tidligere filosofihistorikeres fremstilling

DEFF Research Database (Denmark)

Huggler, Jørgen

2010-01-01

En undersøgelse af Hegels tolkning af sofisten Gorgias giver anledning til at se på receptionen af sofisterne hos notable filosofihistorikere i det 18. århundrede. En sådan undersøgelse viser, at Hegel har en original og velvillig tolkning af sofisterne koncentreret omkring begrebet Bildung og det...... at give grunde for noget. Hegels udlægning af Gorgias bygger på hans tolkning af eleaterne, især af Zenon. Når Hegel har en særlig tolkning af eleaterne, skyldes det hans egne mangeårige filosofiske bestræbelser, og en identificering af en særlig, immanent objektiv dialektik hos Zenon, som han finder......, at Gorgias fører videre. Hegels filosofiske forståelse er tilstrækkelig udviklet til at kunne knytte positive kommentarer til alle dele af diskussionen i Gorgias' ræsonnement Om det ikkeværende, eller Om naturen. Det lykkes dog bedst i forhold til de to første af Gorgias' tre underteser. I hegelsk perspektiv...

Simple sequence repeats in mycobacterial genomes

Indian Academy of Sciences (India)

2006-12-18

Dec 18, 2006 ... Although prokaryotic genomes derive some plasticity due to microsatellite mutations they have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these ...

Ensretning af historieundervisningen

DEFF Research Database (Denmark)

Rønhede, Søren

2008-01-01

"Det er ikke kun i Putins Rusland, at statsmagten vil dirigere historieundervisningen." (Politiken havde fokuseret på "ensretning af historieundervisningen" i Rusland) "Kanonen fra 2006 er undfanget af Udvalget til Styrkelse af Historie i Folkeskolen. Dette udvalg havde regeringen nedsat; men bid...... bidrager kanonen til faglig styrkelse?" spørges der. Det vises, at flere kanonpunkter ikke er fagligt funderede, men af mytologisk art....

Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

Directory of Open Access Journals (Sweden)

Marwa H Saied

Full Text Available Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. Two genes (SPHKAP and DPP6 with significantly methylated promoters were of interest and further analysis of their expression showed them to be repressed in AML. We also demonstrated considerable cytogenetic subtype specificity in the methylomes affecting different genomic features. Significantly distinct patterns of hypomethylation of certain interspersed repeat elements were associated with cytogenetic subtypes. The methylation patterns of members of the SINE family tightly clustered all leukemic patients with an enrichment of Alu repeats with a high CpG density (P<0.0001. We were able to demonstrate significant inverse correlation between intragenic interspersed repeat sequence methylation and gene expression with SINEs showing the strongest inverse correlation (R(2 = 0.7. We conclude that the alterations in DNA methylation that accompany the development of AML affect not only the promoters, but also the non-promoter genomic features, with significant demethylation of certain interspersed repeat DNA elements being associated with AML cytogenetic subtypes. MeDIP-seq data were validated using bisulfite pyrosequencing and the Infinium array.

Optimering af byggeprocessen via bedre/forøget brug af digitale modeller

DEFF Research Database (Denmark)

Carlsen, Mads; Grøn, Dorte Marie Frilund; Alon, Nevo

2013-01-01

Projektet klarlægger nødvendigheden for, og muligheder i, en struktureret og konsekvent planlægning ved anvendelsen af BIM i relation til projektering, udførelse og drift af byggeri. Der er udarbejdet et planlægningsværktøj, der muliggør en sådan planlægning. Samtidig kortlægges de nødvendige data......, der kan udtrækkes af en BIM model ved gennemførelsen af en LCA simulering. Projektet afsluttes med en præsentation af en udviklet demonstratorapplikation til gennemførelse af LCA simuleringer koblet med BIM modellen....

Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.

Science.gov (United States)

Cechová, Jana; Lýsek, Jirí; Bartas, Martin; Brázda, Václav

2018-04-01

The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. vaclav@ibp.cz. Supplementary data are available at Bioinformatics online.

Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

Science.gov (United States)

Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

2016-08-05

Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis

Styring af kommunal digitalisering

DEFF Research Database (Denmark)

Jæger, Birgit

2017-01-01

Digitalisering af både interne arbejdsprocesser og kommunikation med borgere og virksomheder har længe været en vigtig faktor i moderniseringen af den offentlige sektor. Derfor er der stort fokus på styring af digitaliseringen. Denne artikel undersøger, dels hvordan digitaliseringen i den kommunale...... sektor styres, og dels hvilke styringsparadigmer der kan identificeres. Med udgangspunkt i en konkret kommune analyseres styringen af digitalisering gennem et hierarki af offentlige digitaliseringsstrategier. Gennem udvikling af en helt ny form for organisering, en såkaldt Digitaliseringsforening...

GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species.

Directory of Open Access Journals (Sweden)

Darshan Shimoga Chandrashekar

Full Text Available Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to short-list before exploring their potential functional significance via experimental studies and/or detailed in silico analyses.We developed the 'Genomic Repeat Element Analyzer for Mammals' (GREAM for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a enrichment within chromosomal region(s of interest, and b comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20 known to contain functional motifs. In other case studies, we could use GREAM to short-list repetitive elements in the azoospermia factor a (AZFa region of the human Y chromosome and those around the genes associated with rat liver injury. GREAM could also identify five over-represented repeats around some of the human and mouse transcription factor coding genes that had conserved expression patterns across the two species.GREAM has been developed to provide an impetus to research on the role of repetitive sequences in mammalian genomes by offering easy selection of more interesting repeats in various

Livscyklusvurdering af basiskemikalier

DEFF Research Database (Denmark)

Olsen, Stig Irving

1998-01-01

Dette resumé af metoder og væsentlige erfaringer fra erhvervsforskerprojektet Livscyklusvurdering af basiskemikalier er skrevet i erkendelse af, at hovedrapporten er for omfattende til en hurtig introduktion i problemstillingerne. Formålet med denne rapport er derfor at give et kort overblik over...

Globalisering af uddannelse

DEFF Research Database (Denmark)

Jensen, Henning Høgh

2005-01-01

Det globale marked for uddannelse er i voldsom vækst og er ved at blive et af Danmarks vigtigste vareområder. Hvorledes kan KVL agere i globaliseringen af uddannelse for at sikre en høj kvalitet af egne kandidater med gode jobmuligheder?...

Undervisning af tosprogede elever

DEFF Research Database (Denmark)

Horst, Christian

2003-01-01

Artiklen fremdrager hovedresultaterne fra Virginia P. Collier's og Wayne P. Thomas's længdeundersøgelser af tosprogede elever i USA, som formentlig er de mest omfattende undersøgelser af undervisningen af tosprogede elever overhovedet. Resultaterne diskuteres i relation til udviklingen af en...

The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses

Science.gov (United States)

Shukla, Avi; Chatterjee, Anirvan

2018-01-01

Abstract Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption. PMID:29308275

6 belysninger af vejledning

DEFF Research Database (Denmark)

Toft, Helle Mary; Jessing, Carla Tønder; Nymann, Anette

Artiklerne belyser vejledning af unge og vejledning af voksne. I relation til unge drejer det sig om: 1. vejledning af unge med vanskeligheder i forhold til uddannelse - her unge med særlige vejledningsbehov, og mentorordninger for unge, og 2. vejledning af unge i ungdomsuddannelser og i erhvervs...

Brug af alternativ isolering i forbindelse med renovering af ældre etageejendomme

DEFF Research Database (Denmark)

Hansen, Ernst Jan de Place

2003-01-01

Resume af rapport om praktiske erfaringer med brug af alternative isoleringsmaterialer i en renoveringsopgave, udarbejdet af Byfornyelse København m.fl. under Energistyrelsens udviklingsprogram "Miljø- og arbejdsmiljøvenlig isolering"...

Leucine-Rich repeat receptor kinases are sporadically distributed in eukaryotic genomes

Directory of Open Access Journals (Sweden)

Diévart Anne

2011-12-01

Full Text Available Abstract Background Plant leucine-rich repeat receptor-like kinases (LRR-RLKs are receptor kinases that contain LRRs in their extracellular domain. In the last 15 years, many research groups have demonstrated major roles played by LRR-RLKs in plants during almost all developmental processes throughout the life of the plant and in defense/resistance against a large range of pathogens. Recently, a breakthrough has been made in this field that challenges the dogma of the specificity of plant LRR-RLKs. Results We analyzed ~1000 complete genomes and show that LRR-RK genes have now been identified in 8 non-plant genomes. We performed an exhaustive phylogenetic analysis of all of these receptors, revealing that all of the LRR-containing receptor subfamilies form lineage-specific clades. Our results suggest that the association of LRRs with RKs appeared independently at least four times in eukaryotic evolutionary history. Moreover, the molecular evolutionary history of the LRR-RKs found in oomycetes is reminiscent of the pattern observed in plants: expansion with amplification/deletion and evolution of the domain organization leading to the functional diversification of members of the gene family. Finally, the expression data suggest that oomycete LRR-RKs may play a role in several stages of the oomycete life cycle. Conclusions In view of the key roles that LRR-RLKs play throughout the entire lifetime of plants and plant-environment interactions, the emergence and expansion of this type of receptor in several phyla along the evolution of eukaryotes, and particularly in oomycete genomes, questions their intrinsic functions in mimicry and/or in the coevolution of receptors between hosts and pathogens.

Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.

Science.gov (United States)

Cavallini, Andrea; Natali, Lucia; Zuccolo, Andrea; Giordani, Tommaso; Jurman, Irena; Ferrillo, Veronica; Vitacolonna, Nicola; Sarri, Vania; Cattonaro, Federica; Ceccarelli, Marilena; Cionini, Pier Giorgio; Morgante, Michele

2010-02-01

A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

Behandling af elmesyge

DEFF Research Database (Denmark)

Thomsen, Iben Margrete; Kristoffersen, Palle

2004-01-01

Ingen midler er p.t. godkendt og dermed lovlige til bekæmpelse af elmesyge i Danmark. Lovprisning af nye behandlinger ses f.eks. på internettet, men dokumentation mangler. Økonomien og nytten ved en kemisk bekæmpelse frem for sanering af syge træer skal afvejes nøje....

Energirenovering af Sems Have

DEFF Research Database (Denmark)

Jensen, Søren Østergaard; Rose, Jørgen; Mørck, Ove

Nærværende rapport udgør en del af afrapporteringen af PSO ELFORSK projektet Vejledning for energirenovering af boligblokke til lavenergiklasse 2015 og 2020. Arbejdet har været finansieret af PSO midler via ELFORSK, projekt: 347-023. Formålet med projektet er at udvikle en vejledning for dybtgående...

Midler til lindring af mundtørhed og stimulation af spytsekretion

DEFF Research Database (Denmark)

Dynesen, Anja Weirsøe; Pedersen, Anne Marie Lynge; Jensen, Allan Bardow

2013-01-01

effekt. I relation til risikoen for at udvikle caries, der er forhøjet hos den mundtørre patient, er det dog væsentligt at anbefale produkter uden sukker. Ligesom produktets indhold af syre og dermed det erosive potentiale er af betydning i forhold til udviklingen af dentale erosioner. Systemisk...

Af Upraktiske Grunde

DEFF Research Database (Denmark)

Vaaben, Nana Katrine

2001-01-01

som både Claude Levi-Strauss lægger op til i sine klassiske studier af "den vilde tanke", og som Jean Baudrillard siden har lagt op til i sine analyser af samlere som en slags ekstreme forbrugere, der er i færd med at komplettere deres identitet gennem besiddelser af genstande. Imidlertid tillægger...

Ledelse af projektmyldret

DEFF Research Database (Denmark)

større arbejdsgrupper, og det kan være selvorganiserede store udviklingsprogrammer. Et projekt kører sjældent alene, og derfor er der ikke kun tale om projektledelse, men i lige så høj grad om ledelse af projekter. Ledelse af virksomhedens mylder af projekter er ikke let, og forfatterne gennemgår derfor...

Evaluering af ordning med psykologbehandling af personer med let til moderat depression

DEFF Research Database (Denmark)

Fjeldsted, Rita; Christensen, Kaj Sparle

Herværende rapport evaluerer den pr. 1.4.2008 indførte ordning med mulighed for henvisning til psykologbehandling med 60 % tilskud for patienter med let til moderat depression. Evalueringen har betjent sig af flere gensidigt supplerende metoder: spørgeskemaundersøgelser overfor patienter, psykolo......Herværende rapport evaluerer den pr. 1.4.2008 indførte ordning med mulighed for henvisning til psykologbehandling med 60 % tilskud for patienter med let til moderat depression. Evalueringen har betjent sig af flere gensidigt supplerende metoder: spørgeskemaundersøgelser overfor patienter...... tidligere evaluering af forsøgsordning af psykologbehandling af depression i perioden 2005-06. 18.419 personer i alderen 18-37 år blev henvist til psykolog i den undersøgte ordning i perioden 1.2.2009 – 31.1.2010, svarende til en henvisningshyppighed på 1,6 % af baggrundsbefolkningen i samme aldersgruppe....... Ordningen giver mulighed for én rehenvisning, og 9 % blev rehenvist i perioden. Spørgeskemaresultater viser, at kun 33 % af de henviste falder ind under henvisningskriteriet ” let til moderat depression” på tidspunktet for opstart af psykologbehandling, 39 % har ingen tegn på depression, og 28 % har svær...

Evaluering af metoder til risikovurdering af kombinationseffekter og etablering af PBTK/TD modeller for pesticider - et ph.d.-projekt

DEFF Research Database (Denmark)

Reffstrup, Trine Klein

2012-01-01

I dette ph.d.-projekt ved DTU Fødevareinstituttet er den nuværende viden om metoder til risikovurdering af kombinationseffekter af kemiske stoffer med fokus på pesticider gennemgået. Endvidere undersøgtes, hvordan man kan implementere matematiske computermodeller som et værktøj i vurderingen af...

Snit af målinger: VK afhængig af DF og NA

DEFF Research Database (Denmark)

Thomsen, Søren Risbjerg

2007-01-01

ANALYSE: Ekstra Risbjerg-snit af meningsmålinger grundet fortsat valgrummel - VK-regeringen vil blive afhængig af både DF og NA. Udgivelsesdato: 21. august 2007......ANALYSE: Ekstra Risbjerg-snit af meningsmålinger grundet fortsat valgrummel - VK-regeringen vil blive afhængig af både DF og NA. Udgivelsesdato: 21. august 2007...

Optimering af model for spredning af luftforurening

DEFF Research Database (Denmark)

Pedersen, Jens Christian

2008-01-01

De nuværende luftforureningsmodeller har problemer med at bevare massen af diverse kemiske stoffer og med at der ind i mellem optræder negative værdier. Derfor arbejder specialestuderende Ayoe Buus Hansen på om at forbedre den model DMU bruger til at beskrive transport og spredning af luftforuren...... luftforurening på alle skalaer på den nordlige halvkugle ved at sammenligne tre alternative beregningsmodeller. ...

En verden af medier

DEFF Research Database (Denmark)

Tække, Jesper

2009-01-01

Bogen: 'En verden af medier – Medialiseringen af politik, sprog, religion og leg' anmeldes. Anmeldelsen kan læses på: http://ojs.statsbiblioteket.dk/index.php/mediekultur/article/view/1370/1499 Udgivelsesdato: 2009......Bogen: 'En verden af medier – Medialiseringen af politik, sprog, religion og leg' anmeldes. Anmeldelsen kan læses på: http://ojs.statsbiblioteket.dk/index.php/mediekultur/article/view/1370/1499 Udgivelsesdato: 2009...

Udforskning af journalistiske moralnormer

DEFF Research Database (Denmark)

Mogensen, Kirsten

2010-01-01

Kirsten Mogensen beskriver professionelle journalistiske normer. Med udgangspunkt i amerikansk tv's dækning af begivenhederne 11. september kombinerer Kirsten Mogensen kvalitative interviews og tekstanalyse for på den måde at beskrive professionelle journalistiske normer. Metoden er en kombinatio...... af halvstrukturerede, udforskende interviews med både kvantitative og kvalitative analyser af den faktiske dækning, og er primært udledt af Alf Ross' essay om normer og direktiver....

Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats.

Science.gov (United States)

Wang, Jianye; Huang, Yu; Zhou, Mingxu; Zhu, Guoqiang

2016-09-01

Genomic information about Muscovy duck parvovirus is still limited. In this study, the genome of the pathogenic MDPV strain YY was sequenced. The full-length genome of YY is 5075 nucleotides (nt) long, 57 nt shorter than that of strain FM. Sequence alignment indicates that the 5' and 3' inverted terminal repeats (ITR) of strain YY contain a 14-nucleotide-pair deletion in the stem of the palindromic hairpin structure in comparison to strain FM and FZ91-30. The deleted region contains one "E-box" site and one repeated motif with the sequence "TTCCGGT" or "ACCGGAA". Phylogenetic trees constructed based the protein coding genes concordantly showed that YY, together with nine other MDPV isolates from various places, clustered in a separate branch, distinct from the branch formed by goose parvovirus (GPV) strains. These results demonstrate that, despite the distinctive deletion, the YY strain still belongs to the classical MDPV group. Moreover, the deletion of ITR may contribute to the genome evolution of MDPV under immunization pressure.

Pilotprojekt - In situ test af stimuleret aerob nedbrydning til oprensning af pesticidpunktkilder

DEFF Research Database (Denmark)

Tsitonaki, Katerina; Roost, Sandra; Larsen, Lars

Denne rapport omhandler et pilotforsøg i felten, hvor det er undersøgt, hvorvidt aerob nedbrydning af phenoxysyre-pesticider kan stimuleres ved tilsætning af ilt suppleret med tilsætning af specifikke pesticidnedbrydende bakterier. Forsøget er udført på en forurenet lokalitet, Skelstofte, hvor der...

Intelligent styring af dynamisk LED belysning

DEFF Research Database (Denmark)

Thorseth, Anders; Corell, Dennis Dan; Hansen, Søren Stentoft

Denne slutrapport giver en kort beskrivelse af arbejdet, der er udført af DTU Fotonik i projektet ”Intelligent styring af dynamisk LED belysning” støttet af EUDP. Arbejdet er udført i perioden 2011‐2012 i samarbejde med Lighten.......Denne slutrapport giver en kort beskrivelse af arbejdet, der er udført af DTU Fotonik i projektet ”Intelligent styring af dynamisk LED belysning” støttet af EUDP. Arbejdet er udført i perioden 2011‐2012 i samarbejde med Lighten....

Identification, variation and transcription of pneumococcal repeat sequences

Science.gov (United States)

2011-01-01

Background Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen of humans. However, little is known about the role they play in pneumococcal genetics. Results Analysis of the genome of S. pneumoniae ATCC 700669 revealed the presence of a third repeat family, which we have named SPRITE. All three repeats are present at a reduced density in the genome of the closely related species S. mitis. However, they are almost entirely absent from all other streptococci, although a set of elements related to the pneumococcal BOX repeat was identified in the zoonotic pathogen S. suis. In conjunction with information regarding their distribution within the pneumococcal chromosome, this suggests that it is unlikely that these repeats are specialised sequences performing a particular role for the host, but rather that they constitute parasitic elements. However, comparing insertion sites between pneumococcal sequences indicates that they appear to transpose at a much lower rate than IS elements. Some large BOX elements in S. pneumoniae were found to encode open reading frames on both strands of the genome, whilst another was found to form a composite RNA structure with two T box riboswitches. In multiple cases, such BOX elements were demonstrated as being expressed using directional RNA-seq and RT-PCR. Conclusions BOX, RUP and SPRITE repeats appear to have proliferated extensively throughout the pneumococcal chromosome during the species' past, but novel insertions are currently occurring at a relatively slow rate. Through their extensive secondary structures, they seem likely to affect the expression of genes with which they are co-transcribed. Software for annotation of these repeats is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/strep_repeats/. PMID:21333003

Evaluering af afdeling H

DEFF Research Database (Denmark)

Kjær Minke, Linda; Birkmose, Sofie Meldal

2016-01-01

Som led i Kriminalforsorgens flerårsaftale 2013-2016 blev det åbne statsfængsel Søbysøgård i januar 2015 udvidet med 42 lukkede pladser i den nybyggede afdeling H. Nærværende evaluering kortlægger de erfaringer personalet og indsatte har gjort sig i løbet af det første år. Etableringen af den...... lukkede fængselsafdeling H giver en unik mulighed for at følge henholdsvis hvilke faktorer, der bidrager til udvikling af fængselskultur, og hvordan de respektive faktorer influerer på udvikling af fængselskulturen. Evalueringens metoder består af kvalitative og kvantitative metoder såsom dokumentanalyse...

Overførsel af viden ved flytning af produktion

DEFF Research Database (Denmark)

Madsen, Erik Skov; Riis, Jens Ove; Wæhrens, Brian Vejrum

2010-01-01

Empiriske studier i tre industrielle virksomheder har afsløret, at selv virksomheder med mange års erfaring i at overføre produktion til andre lande hovedsagelig fokuserer på planlægning af den fysiske overflytning af produktionsudstyr og fokuserer på den eksplicitte viden, der er tilknyttet prod...

In silico reversal of repeat-induced point mutation (RIP identifies the origins of repeat families and uncovers obscured duplicated genes

Directory of Open Access Journals (Sweden)

Hane James K

2010-11-01

Full Text Available Abstract Background Repeat-induced point mutation (RIP is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable by similarity search tools such as BLAST. Results DeRIP is a new software tool developed to predict the original sequence of a RIP-mutated region prior to the occurrence of RIP. In this study, we apply deRIP to the genome of the wheat pathogen Stagonospora nodorum SN15 and predict the origin of several previously uncharacterised classes of repetitive DNA. Conclusions Five new classes of transposon repeats and four classes of endogenous gene repeats were identified after deRIP. The deRIP process is a new tool for fungal genomics that facilitates the identification and understanding of the role and origin of fungal repetitive DNA. DeRIP is open-source and is available as part of the RIPCAL suite at http://www.sourceforge.net/projects/ripcal.

AF-6 Protects Against Dopaminergic Dysfunction and Mitochondrial Abnormalities in Drosophila Models of Parkinson’s Disease

Directory of Open Access Journals (Sweden)

Adeline H. Basil

2017-08-01

Full Text Available Afadin 6 (AF-6 is an F-actin binding multidomain-containing scaffolding protein that is known for its function in cell-cell adhesion. Interestingly, besides this well documented role, we recently found that AF-6 is a Parkin-interacting protein that augments Parkin/PINK1-mediated mitophagy. Notably, mutations in Parkin and PINK1 are causative of recessively inherited forms of Parkinson’s disease (PD and aberrant mitochondrial homeostasis is thought to underlie PD pathogenesis. Given the novel role of AF-6 in mitochondrial quality control (QC, we hypothesized that AF-6 overexpression may be beneficial to PD. Using the Drosophila melanogaster as a model system, we demonstrate in this study that transgenic overexpression of human AF-6 in parkin and also pink1 null flies rescues their mitochondrial pathology and associated locomotion deficit, which results in their improved survival over time. Similarly, AF-6 overexpression also ameliorates the pathological phenotypes in flies expressing the Leucine Rich Repeat Kinase 2 (LRRK2 G2019S mutant, a mutation that is associated with dominantly-inherited PD cases in humans. Conversely, when endogenous AF-6 expression is silenced, it aggravates the disease phenotypes of LRRK2 mutant flies. Aside from these genetic models, we also found that AF-6 overexpression is protective against the loss of dopaminergic neurons in flies treated with rotenone, a mitochondrial complex I inhibitor commonly used to generate animal models of PD. Taken together, our results demonstrate that AF-6 protects against dopaminergic dysfunction and mitochondrial abnormalities in multiple Drosophila models of PD, and suggest the therapeutic value of AF-6-related pathways in mitigating PD pathogenesis.

Test af Software

DEFF Research Database (Denmark)

Dette dokument udgør slutrapporten for netværkssamarbejdet ”Testnet”, som er udført i perioden 1.4.2006 til 31.12.2008. Netværket beskæftiger sig navnlig med emner inden for test af indlejret og teknisk software, men et antal eksempler på problemstillinger og løsninger forbundet med test af...... administrativ software indgår også. Rapporten er opdelt i følgende 3 dele: Overblik. Her giver vi et resumé af netværkets formål, aktiviteter og resultater. State of the art af software test ridses op. Vi omtaler, at CISS og netværket tager nye tiltag. Netværket. Formål, deltagere og behandlede emner på ti...

From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.

Science.gov (United States)

Misas, Elizabeth; Muñoz, José Fernando; Gallo, Juan Esteban; McEwen, Juan Guillermo; Clay, Oliver Keatinge

2016-04-01

The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention. Copyright © 2016 Elsevier Ltd. All rights reserved.

Implementering af MultifunC

DEFF Research Database (Denmark)

Henze-Pedersen, Sofie; Kohl, Katrine Syppli; Oldrup, Helene

(MultifunC), som allerede havde vist lovende resultater i Norge og Sverige. I 2011 og 2012 åbnede to danske MultifunC-institutioner derfor i henholdsvis København og Aarhus. Denne rapport undersøger, hvordan implementeringen af MultifunC-programmet er forløbet i Danmark. Undersøgelsen viser, at ingen af de...... to danske institutioner lykkedes med at implementere MultifunC tilfredsstillende i løbet af implementeringsperioden. Det har fx været vanskeligt at implementere det tætte tværfaglige samarbejde mellem medarbejdere med forskellige fagprofessionelle baggrunde, som behandlingsprogrammet indebærer. Det har...... desuden været særdeles vanskeligt for de danske MultifunC-institutioner at få etableret det eksterne samarbejde med de sociale myndigheder i kommunerne, politiet, skoler og praktiksteder samt fritidstilbud i nærområdet, som også er en væsentlig del af behandlingsprogrammet. Undersøgelsen af finansieret af...

Test af spørgeskema

DEFF Research Database (Denmark)

Hermansen, Jonathan

2017-01-01

Denne bog gennemgår alle surveyarbejdets faser og giver en praktisk indføring i •design af undersøgelsen og udvælgelse af stikprøver, •formulering af spørgeskemaer samt indsamling og kodning af data, •metoder til at analysere resultaterne....

Test af to versioner af Modflow-LGR til simulering af grundvandsstrømninger i områder med begravede dale – syntetisk studie

DEFF Research Database (Denmark)

Vilhelmsen, Troels Norvin; Christensen, Steen

.eks. findes i begravede dale. Manglende opløsning af geologiske aflejringer på lokal skala kan potentielt resultere i fejlagtige prædiktioner af konsekvensen af grundvandsindvinding på kildeplads niveau. For i højere grad at kunne forvalte disse grundvandsressourcerne skal nye metoder undersøges. Dette er...... specielt gældende for komplekse begravede dalsystemer, som interagerer med omkringliggende regionale grundvandsystemer. I dette syntetiske studie er to versioner af MODFLOW - Local Grid Refinment (LGR) testet til simulering af grundvandsstrømninger i områder med begravede dale. Forsøgene er gennemført som...

Professor: Lær af Canada

DEFF Research Database (Denmark)

Greve, Carsten

2013-01-01

Transportdebatten: En mulig finansiering af fremtidige infrastrukturprojekter kunne være OPP. Danmark bør tage ved lære af erfaringer fra Canada.......Transportdebatten: En mulig finansiering af fremtidige infrastrukturprojekter kunne være OPP. Danmark bør tage ved lære af erfaringer fra Canada....

Algorithms and Complexity Results for Genome Mapping Problems.

Science.gov (United States)

Rajaraman, Ashok; Zanetti, Joao Paulo Pereira; Manuch, Jan; Chauve, Cedric

2017-01-01

Genome mapping algorithms aim at computing an ordering of a set of genomic markers based on local ordering information such as adjacencies and intervals of markers. In most genome mapping models, markers are assumed to occur uniquely in the resulting map. We introduce algorithmic questions that consider repeats, i.e., markers that can have several occurrences in the resulting map. We show that, provided with an upper bound on the copy number of repeated markers and with intervals that span full repeat copies, called repeat spanning intervals, the problem of deciding if a set of adjacencies and repeat spanning intervals admits a genome representation is tractable if the target genome can contain linear and/or circular chromosomal fragments. We also show that extracting a maximum cardinality or weight subset of repeat spanning intervals given a set of adjacencies that admits a genome realization is NP-hard but fixed-parameter tractable in the maximum copy number and the number of adjacent repeats, and tractable if intervals contain a single repeated marker.

Anmeldelse af World Drug Report 2005

DEFF Research Database (Denmark)

Møller, Kim

2005-01-01

Internationale udfordringer i spændingsfeltet mellem organiseret kriminalitet og narkotika. Værdien af det illegale narkotikamarked. Skabelsen af et Illicit Drug Index. Ny organisationsstruktur bag udgivelsen af denne WDR. Udgivelsesdato: December......Internationale udfordringer i spændingsfeltet mellem organiseret kriminalitet og narkotika. Værdien af det illegale narkotikamarked. Skabelsen af et Illicit Drug Index. Ny organisationsstruktur bag udgivelsen af denne WDR. Udgivelsesdato: December...

A Mitochondrial Genome of Rhyparochromidae (Hemiptera: Heteroptera) and a Comparative Analysis of Related Mitochondrial Genomes.

Science.gov (United States)

Li, Teng; Yang, Jie; Li, Yinwan; Cui, Ying; Xie, Qiang; Bu, Wenjun; Hillis, David M

2016-10-19

The Rhyparochromidae, the largest family of Lygaeoidea, encompasses more than 1,850 described species, but no mitochondrial genome has been sequenced to date. Here we describe the first mitochondrial genome for Rhyparochromidae: a complete mitochondrial genome of Panaorus albomaculatus (Scott, 1874). This mitochondrial genome is comprised of 16,345 bp, and contains the expected 37 genes and control region. The majority of the control region is made up of a large tandem-repeat region, which has a novel pattern not previously observed in other insects. The tandem-repeats region of P. albomaculatus consists of 53 tandem duplications (including one partial repeat), which is the largest number of tandem repeats among all the known insect mitochondrial genomes. Slipped-strand mispairing during replication is likely to have generated this novel pattern of tandem repeats. Comparative analysis of tRNA gene families in sequenced Pentatomomorpha and Lygaeoidea species shows that the pattern of nucleotide conservation is markedly higher on the J-strand. Phylogenetic reconstruction based on mitochondrial genomes suggests that Rhyparochromidae is not the sister group to all the remaining Lygaeoidea, and supports the monophyly of Lygaeoidea.

Ledelse af Organisationens Kreativitet

DEFF Research Database (Denmark)

Hedemann, Lars

2008-01-01

forskel, så er man som leder nødt til at arbejde mere målrettet med de medarbejdere som forventes at præstere et kreativt udbytte. Inspireret af analyseværktøjet "KEYS, Assessing the Work Environment for Creativity" udviklet af den amerikanske psykolog og ledelsesforsker ved Harvard University, Teresa...... Amabile, blev en undersøgelse derfor gennemført i udviklingsafdelingerne, Idéland og Idélab hos Bang og Olufsen, for at få et indblik i anvendeligheden af KEYS som inspirationskilde for succesfuld ledelse af organisationens kreativitet....

Genomic organization and developmental fate of adjacent repeated sequences in a foldback DNA clone of Tetrahymena thermophila

International Nuclear Information System (INIS)

Tschunko, A.H.; Loechel, R.H.; McLaren, N.C.; Allen, S.L.

1987-01-01

DNA sequence elimination and rearrangement occurs during the development of somatic cell lineages of eukaryotes and was first discovered over a century ago. However, the significance and mechanism of chromatin elimination are not understood. DNA elimination also occurs during the development of the somatic macronucleus from the germinal micronucleus in unicellular ciliated protozoa such as Tetrahymena thermophila. In this study foldback DNA from the micronucleus was used as a probe to isolate ten clones. All of those tested (4/4) contained sequences that were repetitive in the micronucleus and rearranged in the macronucleus. Inverted repeated sequences were present in one clone. This clone, pTtFBl, was subjected to a detailed analysis of its developmental fate. Subregions were subcloned and used as probes against Southern blots of micronuclear and macronuclear DNA. DNA was labeled with [ 33 P]-labeled dATP. The authors found that all subregions defined repeated sequence families in the micronuclear genome. A minimum of four different families was defined, two of which are retained in the macronucleus and two of which are completely eliminated. The inverted repeat family is retained with little rearrangement. Two of the families, defined by subregions that do not contain parts of the inverted repeat are totally eliminated during macronuclear development-and contain open reading frames. The significance of retained inverted repeats to the process of elimination is discussed

Digital formidling af kulturarv

DEFF Research Database (Denmark)

En af tidens store kulturelle dagsordner drejer sig om digital tilgængeliggørelse af kulturarv. Fortidens spor dukker op i nye former på nettet - næsten alle kulturinstitutioner arbejder med, og befolkningen har fået helt nye muligheder for at se med og deltage. Digital formidling af kulturarv...

Epichlorhydrin og bisphenol A i mat-kontaktmaterialer af epoxylakeret metal og/eller af plast

DEFF Research Database (Denmark)

Petersen, Jens Højslev; Pedersen, Gitte Alsing; Foverskov, Annie

Det er ikke længere tilladt af bruge bisphenol A baseret polycarbonatplast til fremstilling af tåteflasker. Mattilsynet udtog i vinteren 2012/2013 7 typer af sutteflasker som blev kontrolleret for om de indeholdt polycarbonatbaserede plastdele. I alt 28 enkeltdele blev kontrolleret ved infrarød...... spektrometri. Herudover blev 6 tutekopper, bestående af 38 enkeltdele, analyseret med samme teknik. Der blev ikke påvist bisphenol A baseret plast ved analyserne. Dåser, bægre, tuber og skruelåg kan være lakeret på matkontaktsiden med epoxylakker fremstillet af monomererne epichlorhydrin og bisphenol A. Alle...... 50 enkeltdele fra disse prøver blev undersøgt ved infrarød spektrometri og 9 af prøverne viste tegn på at indeholde epoxylak. Disse prøver blev undersøgt ved en ”worst case” ekstraktionstest hvor der kunne påvises små indhold af bisphenol A i ekstrakterne mens der ikke kunne påvises epichlorhydrin...

ARCgame - gamification af undervisning

DEFF Research Database (Denmark)

Jensen, Camilla Gyldendahl

2014-01-01

Gamification er et begreb, der anvendes til at beskrive brugen af spilelementer i andre miljøer for at forbedre brugernes oplevelse. Følgende tekst har til formål at behandle emnet i forhold til af opnå en forståelse for de elementer der indvirker på en ”gamification af et undervisningsforløb”, her...

Hvad griner du af?

DEFF Research Database (Denmark)

Lorenzen, Tobias Hiort

2012-01-01

latterliggørelse indenfor en sådan teori. Sociologiens begreb om ”un-laughter” angives som en mulig udvej af dette problem. I forlængelse af dette kritiseres den moderne humor-psykologis lære om populationers humor-patologi og til slut argumenteres der for at en moderne dannelse af humor må have en moralsk...

Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes.

Science.gov (United States)

Gibbons, John G; Rokas, Antonis

2009-03-01

Intragenic tandem repeats (ITRs) are consecutive repeats of three or more nucleotides found in coding regions. ITRs are the underlying cause of several human genetic diseases and have been associated with phenotypic variation, including pathogenesis, in several clades of the tree of life. We have examined the evolution and functional role of ITRs in 10 genomes spanning the fungal genus Aspergillus, a clade of relevance to medicine, agriculture, and industry. We identified several hundred ITRs in each of the species examined. ITR content varied extensively between species, with an average 79% of ITRs unique to a given species. For the fraction of conserved ITR regions, sequence comparisons within species and between close relatives revealed that they were highly variable. ITR-containing proteins were evolutionarily less conserved, compositionally distinct, and overrepresented for domains associated with cell-surface localization and function relative to the rest of the proteome. Furthermore, ITRs were preferentially found in proteins involved in transcription, cellular communication, and cell-type differentiation but were underrepresented in proteins involved in metabolism and energy. Importantly, although ITRs were evolutionarily labile, their functional associations appeared. To be remarkably conserved across eukaryotes. Fungal ITRs likely participate in a variety of developmental processes and cell-surface-associated functions, suggesting that their contribution to fungal lifestyle and evolution may be more general than previously assumed.

Skoling af lyst

DEFF Research Database (Denmark)

Bjerg, Helle

2011-01-01

På baggrund af interview med tre elevgenerationer fremanalyseres skolens virkningsfuldhed i skoling af lyst i et historisk perspektiv. I afhandlingen udvikles to teoretisk-analytiske optikker: Skolen som ideologisk rum - med inspiration fra Slavoj Zizeks ideologikritik, samt Skolen som affektivt...

Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

Directory of Open Access Journals (Sweden)

Eunyoung Seo

2016-08-01

Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

Udviklingen af rumopfattelsen 1600-2000

DEFF Research Database (Denmark)

Brock, Steen

2010-01-01

Hovedtræk af rumopfattelsens idehistorie fra Descartes til Wittgenstein med speciel vægt på Kant, værkbegrebet, modelbegrebet og den fænomenologiske opfattelse af rummet som handlingens sted......Hovedtræk af rumopfattelsens idehistorie fra Descartes til Wittgenstein med speciel vægt på Kant, værkbegrebet, modelbegrebet og den fænomenologiske opfattelse af rummet som handlingens sted...

Undersøgelsen af brugernes evaluering af kontorpakker på Århus Sygehus og i Psykiatrien i Århus

DEFF Research Database (Denmark)

Hørlück, Jens

En analyse af brugernes opfattelse af kvaliteten af tre office pakker: MS Office 2003 / 2007 og OpenOffice.  ......En analyse af brugernes opfattelse af kvaliteten af tre office pakker: MS Office 2003 / 2007 og OpenOffice.  ...

Supervision af psykoterapi

DEFF Research Database (Denmark)

SUPERVISION AF PSYKOTERAPI indtager en central position i uddannelsen og udviklingen af psykoterapeuter. Trods flere lighedspunkter med psykoterapi, undervisning og konsultation er psykoterapisupervision et selvstændigt virksomhedsområde. Supervisor må foruden at være en trænet psykoterapeut kende...... supervisionens rammer og indplacering i forhold til organisation og samfund. En række kapitler drejer sig om supervisors opgaver, roller og kontrolfunktion, supervision set fra supervisandens perspektiv samt betragtninger over relationer og processer i supervision. Der drøftes fordele og ulemper ved de...... forskellige måder, hvorpå en sag kan fremlægges. Bogens første del afsluttes med refleksioner over de etiske aspekter ved psykoterapisupervision. Bogens anden del handler om de særlige forhold, der gør sig gældende ved supervision af en række specialiserede behandlingsformer eller af psykoterapi med bestemte...

Anmeldelse af Evolution, Literature and Film

DEFF Research Database (Denmark)

Grodal, Torben Kragh

2011-01-01

Diskussion af basisproblemer i evolutionær fiktionsteori med udgangspunkt i en anmeldelse af Evolution, Literature and Film......Diskussion af basisproblemer i evolutionær fiktionsteori med udgangspunkt i en anmeldelse af Evolution, Literature and Film...

Strategisk ledelse af evalueringskulturen

Directory of Open Access Journals (Sweden)

Gitte Orlowitz

2016-02-01

Full Text Available Hvis evaluering skal anvendes til at udvikle uddannelser, er en af ledelsen vigtigste opgaver at udvikle en strategi for udvikling af evalueringskulturen – herunder strategier for udvikling af kommunikation og evalueringskapacitet. Den strategiske ledelse kan i den sammenhæng anvendes til at håndtere de ofte modsatte krav, som eksterne og interne interessenter stiller til evaluering.

Evaluering af FIU`s akademiuddannelser

DEFF Research Database (Denmark)

Hansen, Agnete Meldgaard; Nielsen, Kurt Aagaard

I rapporten præsenteres en empirisk evaluerinf af to nye uddannelser i FIUs regi. I forlængelse af evalueringen præsenteres en forskningsmæssig analyse a uddannelsernes rolle i fagbevægelsens modernisering......I rapporten præsenteres en empirisk evaluerinf af to nye uddannelser i FIUs regi. I forlængelse af evalueringen præsenteres en forskningsmæssig analyse a uddannelsernes rolle i fagbevægelsens modernisering...

Udvikling af systemleverancer, parametri og BIM

DEFF Research Database (Denmark)

Kortegaard, Per

2016-01-01

Seminaret rummede indlæg fra både nogle af projektets tidligere ph.d.-studerende og forskellige kompetente professionelle personer fra forskellige grene af praksis. Seminaret gav samlet et fint billede af status indenfor udviklingen af systemleverancer og deres anvendelse i relation til BIM...

Administration af informationsmodeller

DEFF Research Database (Denmark)

Hundebøl, Jesper

2013-01-01

En informationsmodel er i denne sammenhæng en digital repræsentation af et givent byggeri. Både offentlige og private bygherrer anvender informationsmodeller, når der 'bygges digitalt'. I denne artikel undersøges det, hvilke konkrete udfordringer der følger af digitaliseringen, hvor gennemgribend...

Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome

Directory of Open Access Journals (Sweden)

Vandamme Peter

2003-03-01

Full Text Available Abstract Background Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired via recent horizontal gene transfer or is part of an ancestral single chromosome, we compared the abundance, distribution and compositon of simple sequence repeats (SSRs between both replicons and also compared the respective compositional biases. Results Our data show that both replicons are very similar in respect to distribution and composition of SSRs and presence of compositional biases. Minor variations in SSR and compositional biases observed may be attributable to minor differences in gene expression and regulation of gene expression or can be attributed to the small sample numbers observed. Conclusions The observed similarities indicate that both replicons have shared a similar evolutionary history and thus suggest that the megaplasmid was not recently acquired from other organisms by lateral gene transfer but is a part of an ancestral R. solanacearum chromosome.

Dansk oversættelse af MiDAS, et redskab til assessment af musikterapi for personer med demens

DEFF Research Database (Denmark)

Ridder, Hanne Mette Ochsner; Lykkegaard, Chris; McDermott, Orii

2018-01-01

Music in Dementia Assessment Scales, MiDAS, er udviklet til at vurdere ændringer i trivsel hos borgere med demens som har deltaget i musikterapi. Målingen udføres af 1) personale før og efter musikterapien for at vurdere om der er en indflydelse i hverdagssituationer efterfølgende, eller af 2......) musikterapeuten umiddelbart efter sessionen for at vurdere forandringer i selve sessionen. Der har været stor interesse for at anvende MiDAS i flere Europæiske lande, herunder Danmark. Derfor undersøgte udviklerne af MiDAS hvilke procedurer der anvendes til oversættelse og kulturel tilpasning af...... assessmentredskaber, og anbefalede på den baggrund en ti-trins procedure. Vi anvendte denne procedure til oversættelsen af MiDAS og således udviklingen af den danske MiDAS-DK. Den danske version af MiDAS er afprøvet af mere end 20 fagpersoner på baggrund af 296 udfyldte MiDAS-skemaer. Målet med artiklen er...

The Whole Genome Assembly and Comparative Genomic Research of Thellungiella parvula (Extremophile Crucifer Mitochondrion

Directory of Open Access Journals (Sweden)

Xuelin Wang

2016-01-01

Full Text Available The complete nucleotide sequences of the mitochondrial (mt genome of an extremophile species Thellungiella parvula (T. parvula have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs, and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1% through simple sequence repeat (SSR analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

Fremtidens biblioteksbetjening af børn

DEFF Research Database (Denmark)

Høyrup, Helene

2008-01-01

Rapporten er resultatet af et tværministerielt udvalgsarbejde nedsat af Kulturministeriet.  Kommissoriet har været at nytænke biblioteksbetjeningen af børn, så den passer til vidensamfundet.  Udvalgsarbejdet munder ud i ti bud for fremtidens biblioteksbetjening af børn....

Beregning af luftlydisolation mellem to rum

DEFF Research Database (Denmark)

Donovan, A.

Meddelelsen bringer resultaterne af en forundersøgelse af to beregningsmetoder. Den ene metode belyses nærmere gennem nogle forenklede eksempler, der viser omfanget af regnearbejdet og peger på nogle af de vanskeligheder det vil indebære at opstille en praktisk anvendelig beregningsmetode....

Regulering af det psykiske arbejdsmiljø

DEFF Research Database (Denmark)

Nielsen, Klaus T.

nationale informationer om reguleringen af det psykiske arbejdsmiljø. Rapport er bygget op med ◊ et internationalt overblik over regulering af psykisk arbejdsmiljø ◊ en bredere diskussion af reguleringens dilemmaer ◊ en gennemgang af den aktuelle danske udvikling ◊ udfordringerne på området...

Anvendeligheden af GIS

DEFF Research Database (Denmark)

Winstrup, Mie; Levin, Gregor

2011-01-01

Fragmentering af naturen er en trussel mod biodiversiteten, og etablering af økologiske forbindelser/korridorer mellem naturområderne er én måde hvorved nedgangen i biodiversitet kan stoppes. Med Næstved Kommune som case-område har jeg undersøgt, hvordan analyser i GIS kan bruges til at udvælge...... omdannet til reelle korridorer, hvor bredden afhænger af arealdækket som forbindelserne krydser. I implementerings øjemed er det anvendeligt at vide om nogle forbindelser er særlig vigtige for at skabe mere sammenhængende natur. GIS er anvendeligt hertil, idet GIS kan bruges til at bestemme den enkelte...

Kants Kritik af dømmekraften

DEFF Research Database (Denmark)

Introduktion til Kants Kritik af dømmekraften bestående af otte artikler, der følger værkets egen tematiske opbygning......Introduktion til Kants Kritik af dømmekraften bestående af otte artikler, der følger værkets egen tematiske opbygning...

Energioptimering af bæredygtighedscertificeringsprocesserne

DEFF Research Database (Denmark)

Christensen, Dorthe Holmberg; Carlsen, Mads; Alon, Shlomo Nevo

2014-01-01

Større fokus på bæredygtighedscertificeringer som DGNB har yderligere øget kompleksiteten af designet af bygninger. Introduktionen af teknologier som building information modelling (BIM) og proces metoder som integreret design proces (IDP) kan hjælpe med at reducere kompleksiteten og bedre...

Pædagogisk brug af test

DEFF Research Database (Denmark)

Nordenbo, Sven Erik; Allerup, Peter; Andersen, Hanne Leth

Publikationen er resultatet af et systematisk review foretaget i regi af Dansk Clearinghouse for Uddannelsesforskning. Reviewets grundspørgsmål er: Hvordan kan grundskolelæreres individ- og klassecentrerede brug af data fra test forbedre læreres didaktiske og/eller fagdidaktiske tiltag i klasser...... med almindelige elever? Spørgsmålet vedrører alene testtyper, som indgår i nationale test i de nordiske lande. Og hvordan indvirker indførelsen af testning på læreres didaktiske beslutninger og elevers læringsadfærd? Vi fandt frem til at grundskolelæreres individ- og klassecentrerede brug af testdata...... i klasser med almindelige elever forbedres, når de didaktiske og/eller fagdidaktiske tiltag bygger på test, som lærerne oplever et medejerskab for. Vi fandt fremtil, at introduktion af test fra instanser over klasseniveau med det formål at indvirke på undervisning og elevers læringsadfærd har...

Anvendelse af koldpresset rapsolie på varebiler

DEFF Research Database (Denmark)

Nielsen, Claus Suldrup; Ivarsson, Anders; Schramm, Jesper

Denne rapport sammenfatter resultaterne af undersøgelserne omkring anvendelse af koldpresset rapsolie på varebiler. Undersøgelsen, som er udført af Danmarks Tekniske Universitet, Institut for Mekanisk Teknologi, er en del af et større projekt, som er finansieret af Trafikstyrelsens (tidligere Fær...... Færdselsstyrelsen) tilskudsordning til forsøg med biodiesel. Projektet har været administreret af Odense Kommune....

Studerende og underviseres brug af digitale medier - En kvantitativ undersøgelse af Aarhus Universitets studerende og underviseres brug af digitale medier og internettet anno 2008

Directory of Open Access Journals (Sweden)

Maria Hvid Stenalt

2009-06-01

• Hvilke medier anvender universitetsstuderende generelt? • Ligner undervisernes medievalg/forbrug de studerendes? • Hvilke medier inddrager underviserne i undervisningen? Nærværende artikel vil forsøge at besvare disse spørgsmål på baggrund af en kvantitativ spørgeskemaundersøgelse af Aarhus Universitets studerende og underviseres brug af digitale medier og internettet. Undersøgelsen blev gennemført i efteråret 2008 af E-læringsenheden ved Aarhus Universitet som led i en almen kvalitetssikring på media- og e-læringsområdet, samt som led i en behovsafklaring vedrørende etablering af et medie- og podcastarkiv. E-læringsenheden er en administrativ enhed, der teknisk og pædagogisk understøtter underviseres inddragelse af digitale medier i undervisningen.

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events.

Directory of Open Access Journals (Sweden)

Angela N Brooks

Full Text Available Although recurrent somatic mutations in the splicing factor U2AF1 (also known as U2AF35 have been identified in multiple cancer types, the effects of these mutations on the cancer transcriptome have yet to be fully elucidated. Here, we identified splicing alterations associated with U2AF1 mutations across distinct cancers using DNA and RNA sequencing data from The Cancer Genome Atlas (TCGA. Using RNA-Seq data from 182 lung adenocarcinomas and 167 acute myeloid leukemias (AML, in which U2AF1 is somatically mutated in 3-4% of cases, we identified 131 and 369 splicing alterations, respectively, that were significantly associated with U2AF1 mutation. Of these, 30 splicing alterations were statistically significant in both lung adenocarcinoma and AML, including three genes in the Cancer Gene Census, CTNNB1, CHCHD7, and PICALM. Cell line experiments expressing U2AF1 S34F in HeLa cells and in 293T cells provide further support that these altered splicing events are caused by U2AF1 mutation. Consistent with the function of U2AF1 in 3' splice site recognition, we found that S34F/Y mutations cause preferences for CAG over UAG 3' splice site sequences. This report demonstrates consistent effects of U2AF1 mutation on splicing in distinct cancer cell types.

Estimating the Prevalence of Atrial Fibrillation from A Three-Class Mixture Model for Repeated Diagnoses

Science.gov (United States)

Li, Liang; Mao, Huzhang; Ishwaran, Hemant; Rajeswaran, Jeevanantham; Ehrlinger, John; Blackstone, Eugene H.

2016-01-01

Atrial fibrillation (AF) is an abnormal heart rhythm characterized by rapid and irregular heart beat, with or without perceivable symptoms. In clinical practice, the electrocardiogram (ECG) is often used for diagnosis of AF. Since the AF often arrives as recurrent episodes of varying frequency and duration and only the episodes that occur at the time of ECG can be detected, the AF is often underdiagnosed when a limited number of repeated ECGs are used. In studies evaluating the efficacy of AF ablation surgery, each patient undergo multiple ECGs and the AF status at the time of ECG is recorded. The objective of this paper is to estimate the marginal proportions of patients with or without AF in a population, which are important measures of the efficacy of the treatment. The underdiagnosis problem is addressed by a three-class mixture regression model in which a patient’s probability of having no AF, paroxysmal AF, and permanent AF is modeled by auxiliary baseline covariates in a nested logistic regression. A binomial regression model is specified conditional on a subject being in the paroxysmal AF group. The model parameters are estimated by the EM algorithm. These parameters are themselves nuisance parameters for the purpose of this research, but the estimators of the marginal proportions of interest can be expressed as functions of the data and these nuisance parameters and their variances can be estimated by the sandwich method. We examine the performance of the proposed methodology in simulations and two real data applications. PMID:27983754

Prøvetagning af grundvand

DEFF Research Database (Denmark)

Sørensen, Inga

Bogen fokuserer på prøveatgning af grundvand og drikkevand til forskellige formål såsom undersøgelse af forurenede grunde, grundvandsmonitering samt produktion af drikkevand. Da grundvand i sagens natur findes under jordoverfladen, beskriver bogen også væsentlige forhold om hydrogeologi og...

Isolation of human simple repeat loci by hybridization selection.

Science.gov (United States)

Armour, J A; Neumann, R; Gobert, S; Jeffreys, A J

1994-04-01

We have isolated short tandem repeat arrays from the human genome, using a rapid method involving filter hybridization to enrich for tri- or tetranucleotide tandem repeats. About 30% of clones from the enriched library cross-hybridize with probes containing trimeric or tetrameric tandem arrays, facilitating the rapid isolation of large numbers of clones. In an initial analysis of 54 clones, 46 different tandem arrays were identified. Analysis of these tandem repeat loci by PCR showed that 24 were polymorphic in length; substantially higher levels of polymorphism were displayed by the tetrameric repeat loci isolated than by the trimeric repeats. Primary mapping of these loci by linkage analysis showed that they derive from 17 chromosomes, including the X chromosome. We anticipate the use of this strategy for the efficient isolation of tandem repeats from other sources of genomic DNA, including DNA from flow-sorted chromosomes, and from other species.

Global opvarmning neutraliserer effekten af parasitisme på strandsnegles konsumption af makroalger

DEFF Research Database (Denmark)

Larsen, Martin H.; Mouritsen, Kim Nørgaard

Det er veldokumenteret, at parasitter kan påvirke værternes adfærd, overlevelse, reproduktion, fysiologi og evolution. Disse parasit-vært interaktioner kan føre til radikale ændringer af naturlige samfunds struktur og diversitet. Eksperimenter har eksempelvis vist, at trematoder indirekte kan ændre...... strukturen af makroalgesamfund ved at reducere konsumptionsraten hos den herbivore strandsnegl Littorina littorea. Det er endvidere vist, at produktionen af trematode-larver (cercarier) i sneglens fordøjelseskanal og gonade kompleks øges kraftigt når vandtemperaturen stiger. Man kan derfor forvente...

Characterization of Genomic Deletion Efficiency Mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 Nuclease System in Mammalian Cells*♦

Science.gov (United States)

Canver, Matthew C.; Bauer, Daniel E.; Dass, Abhishek; Yien, Yvette Y.; Chung, Jacky; Masuda, Takeshi; Maeda, Takahiro; Paw, Barry H.; Orkin, Stuart H.

2014-01-01

The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 nuclease system has provided a powerful tool for genome engineering. Double strand breaks may trigger nonhomologous end joining repair, leading to frameshift mutations, or homology-directed repair using an extrachromosomal template. Alternatively, genomic deletions may be produced by a pair of double strand breaks. The efficiency of CRISPR/Cas9-mediated genomic deletions has not been systematically explored. Here, we present a methodology for the production of deletions in mammalian cells, ranging from 1.3 kb to greater than 1 Mb. We observed a high frequency of intended genomic deletions. Nondeleted alleles are nonetheless often edited with inversions or small insertion/deletions produced at CRISPR recognition sites. Deleted alleles also typically include small insertion/deletions at predicted deletion junctions. We retrieved cells with biallelic deletion at a frequency exceeding that of probabilistic expectation. We demonstrate an inverse relationship between deletion frequency and deletion size. This work suggests that CRISPR/Cas9 is a robust system to produce a spectrum of genomic deletions to allow investigation of genes and genetic elements. PMID:24907273

Måling af stress hos mink

DEFF Research Database (Denmark)

Malmkvist, Jens

2010-01-01

Sammendrag Stress indgår som et element ved vurdering af dyrevelfærd. Endvidere kan stress mål anvendes i undersøgelser, hvor forskellige typer af avl, burmiljø og pasning af mink sammenlignes. Men hvad er stress egentlig og hvordan måles det? Er unormal adfærd koblet til stress hos mink? På...... temadagen præsenteres nye resultater og metoder til at vurdere stress hos mink. I en metode måles koncentrationen af nedbrydningsprodukter af hormonet cortisol i gødning fra mink. Der er en række fordele ved denne metode, frem for blodprøvetagning. Forsøg viste, at hovedparten af cortisol udskilles i fæces...... (83 %) frem for i urin (17 %), samt at omsætningen af radioaktivt mærket cortisol ikke er forskellig mellem mink med hhv. lav og høj forekomst af stereotypi. Denne viden kan bruges til bedre at forstå koblingen f.eks. unormal adfærd og stress hos mink....

På sporet af de gyldne opskrifter?

DEFF Research Database (Denmark)

Poulfelt, Flemming

2015-01-01

Børsen Ledelse. Markedet for kogebøger er stort. For der produceres hvert år et hav nye af slagsen. Nogle udgives af kendte kokke, nogle af særlige eksperter inden for kost og motion, og andre af personer, der har en ægte interesse inden for gastronomi og mad. På ledelsesområdet findes en...

Påvisning af PCV2

DEFF Research Database (Denmark)

Neumann, Katrine; Buse, Katja Strøm; Hjulsager, Charlotte Kristiane

2018-01-01

Mængden af PCV2-virus i poolede serumprøver kan anvendes til at finde grise med meget PCV2-virus, hvorimod mængden af PCV2-virus i spyt og fæces er velegnede til at vurdere tilstedeværelsen af eller tidspunktet for en begyndende PCV2-infektion...

Påvisning af PCV2

DEFF Research Database (Denmark)

Neumann, Katrine; Buse, Katja Strøm; Hjulsager, Charlotte Kristiane

Mængden af PCV2-virus i poolede serumprøver kan anvendes til at finde grise med meget PCV2-virus, hvorimod mængden af PCV2-virus i spyt og fæces er velegnede til at vurdere tilstedeværelsen af eller tidspunktet for en begyndende PCV2-infektion...

Topological ferrimagnetic behaviours of coordination polymers containing manganese(II) chains with mixed azide and carboxylate bridges and alternating F/AF/AF'/AF'/AF interactions.

Science.gov (United States)

Wang, Yan-Qin; Liu, Hou-Ting; Qi, Yan; Gao, En-Qing

2014-08-21

Two Mn(ii) complexes with azide and a new zwitterionic tetracarboxylate ligand 1,2,4,5-tetrakis(4-carboxylatopyridinium-1-methylene)benzene (L(1)), {[Mn5(L(1))2(N3)8(OH)2]·12H2O}n () and {[Mn5(L(1))2(N3)8(H2O)2](ClO4)2·6H2O}n (), have been synthesized and characterized crystallographically and magnetically. and contain similar alternating chains constructed by azide and carboxylate bridges. The independent sets of bridges alternate in an ABCCB sequence between adjacent Mn(ii) ions: (EO-N3)2 double bridges (EO = end-on) (denoted as A), [(EO-N3)(OCO)2] triple bridges (denoted as B) and [(EO-N3)(OCO)] double bridges (denoted as C). The alternating chains are interlinked into 2D coordination networks by the tetrapyridinium spacers. Magnetic studies demonstrate that the magnetic coupling through the double EO azide bridges is ferromagnetic and that through mixed azide/carboxylate bridges is antiferromagnetic. The unprecedented F/AF/AF'/AF'/AF coupling sequence along the chain dictates an uncompensated ground spin state (S = 5/2 per Mn5 unit) and leads to one-dimensional topological ferrimagnetism, which features a minimum in the χT versus T plot.

Health Information in Somali (Af-Soomaali )

Science.gov (United States)

... and Wound Healing - Af-Soomaali (Somali) Bilingual PDF Health Information Translations Fasting Blood Sugar Test - Af-Soomaali (Somali) Bilingual PDF Health Information Translations GTT (Glucose Tolerance Test) - Af-Soomaali ( ...

Barrierer for ibrugtagning af videooptaget universitetsundervisning

DEFF Research Database (Denmark)

Rattleff, Pernille

2009-01-01

tilgængelige for studerende og andre interesserede. Der kan således iagttages nogle barrierer i forhold til ibrugtagning af videooptaget undervisning på universitetsniveau, idet underviserne for en umiddelbar betragtning tilsyneladende for det første har nogle forbehold af psykologisk, for det andet af...... begrebsafklaring, præsenterer forfatterne i denne artikel erfaringerne med tilbud af videostreamet og podcastet universitetsundervisning til studerende på Danmarks Pædagogiske Universitetsskole med henblik på en diskussion af de potentialer og især de barrierer, der kan iagttages i forhold til en mere systematisk...

Dialektisk billede af Benjamin

DEFF Research Database (Denmark)

Bøggild, Jacob

2004-01-01

Anmeldelse af Lars Brückner: "Løse blade. Læseren, kritikeren og fortælleren Walter Benjamin"......Anmeldelse af Lars Brückner: "Løse blade. Læseren, kritikeren og fortælleren Walter Benjamin"...

Genomic repeat abundances contain phylogenetic signal

Czech Academy of Sciences Publication Activity Database

Dodsworth, S.; Chase, M.W.; Kelly, L.J.; Leitch, I.J.; Macas, Jiří; Novák, Petr; Piednoël, M.; Weiß-Schneeweiss, H.; Leitch, A.R.

2015-01-01

Roč. 64, č. 1 (2015), s. 112-126 ISSN 1063-5157 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Repetitive DNA * continuous characters * genomics * next-generation sequencing * phylogenetics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.225, year: 2015

Strategi til udbredelse og udvikling af aquaponik

OpenAIRE

Bartholin, Aline; Nielsen, Per

2014-01-01

Denne rapport omhandler, hvorledes aquaponik i fremtiden skal udbredes med henblik på at produktionsmetoden bliver en del af den etablerede fødevaresektor. Ud fra et interview med PlanteLaboratoriet som er en del af foreningen Akvaponisk Selskab, samt observationer af en workshop afholdt af PlanteLaboratoriet forsøger vi at kortlægge den førte strategi til udbredelse og udvikling af aquaponik, samt undersøge hvorledes aquaponik som innovation bliver taget imod af mulige adoptere. Empirien sam...

Bekæmpelse af elmesyge

DEFF Research Database (Denmark)

Thomsen, Iben Margrete; Kristoffersen, Palle; Ravn, Hans Peter

2004-01-01

Elmesygen kom til Danmark i 1970’erne. Efter 1985 er udbredelsen gået stærkt, og elmesygen har været katastrofal for bestanden af bytræer og træer i landskabet. Bekæmpelse består fortrinsvis af sanering, dvs. fjernelse af syge og billeangrebne træer inden 1. maj....

Energiforbrug til opvarmning af bygninger

DEFF Research Database (Denmark)

Budde, J.; Pedersen, D.O.

Rapporten giver oplysninger om enhedsforbrug til varme og varmt brugsvand i forskellige typer af bygninger baseret på en analyse af et omfattende datamateriale. Formålet med undersøgelsen har været at ajourføre denne del af grundlaget for både landsdækkende og lokal varmeplanlægning i Danmark....

Udlejers godkendelse af ny erhvervslejer

DEFF Research Database (Denmark)

Munk-Hansen, Carsten

2009-01-01

I artiklen er taget udgangspunkt i den »klassiske« afståelsessituation, hvor en lejer vil afhænde den i de lejede lokaler drevne virksomhed, og lejeren har afståelsesret til en af udlejer godkendt lejer, uden at kravene til den ny lejer er specificeret. På baggrund af Vestre Landsrets dom af 9/2 ...

Dannelsen af den ansvarlige elev

DEFF Research Database (Denmark)

Larsen, Jesper

2010-01-01

Denne artikel handler om den del af lærergerningen, der har at gøre med udarbejdelse af elevplaner. Der tages udgangspunkt i en foucaultsk forståelse, hvor beskrivelsen af den enkelte elev udtrykker et særligt normativt ideal om, hvilke former for elevhed der er de ønskværdige i den danske...

Didaktisk design af et pervasive learning game

DEFF Research Database (Denmark)

Oldenskov, Joakim; Westergren, Jens; Frank, Anders Bredahl

2010-01-01

Projektet er et studie i det teoretiske grundlag for, og en empirisk undersøgelse, af en prototype for et didaktisk design af et pervasive learning game. Der arbejdes overordnet med udviklingen af et didaktisk design af et læringsspil som kombinerer mobile teknologier, det fysiske rum og eleverne...... game med en analyse af legen og motivationen iboende spillet. I det læringsteoretiske felt inddrages og diskuteres forskellige tilgange til læring og pervasive games, som alle repræsenterer et socialkonstruktivistisk syn på læring. Det didaktiske design danner grundlag for et prototypedesign af et...... funktionalitet som en del af undervisningen. Det er afgørende at teknologien er pålidelig og er let at gå til, da det er kernefunktionen i denne type af spil. Legens rolle er vigtig for motivationen, men må ikke overtage de formelle krav til den undervisning, som spillet er del af. Det var entydigt omkring...

Vurdering af omfang og konsekvenser af sprøjtning og gødskning af § 3-beskyttede naturarealer

DEFF Research Database (Denmark)

Strandberg, Morten Tune; Bak, Jesper Leth; Bladt, Jesper Stentoft

2012-01-01

Det er overvejende de ferske enge, der gødskes og sprøjtes, hvorimod dette kun undtagelsesvist er konstateret på andre naturtyper som overdrev og heder m.m. De ferske enge er samtidig den mest udbredte § 3-naturtype. Behandling i form af gødskning og sprøjtning foregår anslået på op til 20 % af a...

På sporet af innovation

DEFF Research Database (Denmark)

Strandgaard, Lone Bak

organisationen blandt ledere og medarbejdere samt eksternt, uden for organisationen, hos dens kunder. Ph.d.-afhandlingen På sporet af innovation har som formål at bidrage til forståelse af, hvordan organisationers arbejde med digital selvbetjening kan fremmes, set i et innovationsteoretisk perspektiv. Foruden en...... indføring i innovationsteorien og dens udvikling belyser afhandlingens resultater hvordan at innovationspotentialet kan styrkes gennem organisatorisk åbenhed og samarbejde i alle dele af den innovative proces. Dette gælder ved både idéudvikling, realisering og spredning af nye digitale løsninger.......Flere og flere private og offentlige servicer digitaliseres, så kunder, borgere og virksomheder, i øget grad betjener sig selv. Digital selvbetjening kan potentielt effektivisere driften og skabe bedre kundeservice. Men processen har udfordringer, da den kan kræve omfattende omstilling internt i...

Dansk oversættelse af MiDAS, et redskab til assessment af musikterapi for personer med demens

DEFF Research Database (Denmark)

Ridder, Hanne Mette Ochsner; Lykkegaard, Chris; McDermott, Orii

2018-01-01

DAS explored which procedures is used for outcome measure translation and cultural adaptation, and based on this recommended a ten-step procedure. We applied this procedure in order to translate MiDAS and hereby develop the Danish MiDAS-DK. The Danish MiDAS version has been tested by more than 20 professionals......) musikterapeuten umiddelbart efter sessionen for at vurdere forandringer i selve sessionen. Der har været stor interesse for at anvende MiDAS i flere Europæiske lande, herunder Danmark. Derfor undersøgte udviklerne af MiDAS hvilke procedurer der anvendes til oversættelse og kulturel tilpasning af...... assessmentredskaber, og anbefalede på den baggrund en ti-trins procedure. Vi anvendte denne procedure til oversættelsen af MiDAS og således udviklingen af den danske MiDAS-DK. Den danske version af MiDAS er afprøvet af mere end 20 fagpersoner på baggrund af 296 udfyldte MiDAS-skemaer. Målet med artiklen er...

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

Science.gov (United States)

Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J; Leitch, Ilia J

2015-01-01

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

Directory of Open Access Journals (Sweden)

Jiří Macas

Full Text Available The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57% of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%. Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

MR-AFS: a global hierarchical file-system

International Nuclear Information System (INIS)

Reuter, H.

2000-01-01

The next generation of fusion experiments will use object-oriented technology creating the need for world wide sharing of an underlying hierarchical file-system. The Andrew file system (AFS) is a well known and widely spread global distributed file-system. Multiple-resident-AFS (MR-AFS) combines the features of AFS with hierarchical storage management systems. Files in MR-AFS therefore may be migrated on secondary storage, such as roboted tape libraries. MR-AFS is in use at IPP for the current experiments and data originating from super-computer applications. Experiences and scalability issues are discussed

Blended Learning Analytics Model for Evaluation (BLAME). Et case-studie af universitetsunderviseres brug af Blackboard

DEFF Research Database (Denmark)

Musaeus, Peter; Bennedsen, Andreas Brændstrup; Hansen, Janne Saltoft

2015-01-01

I denne artikel vil vi præsentere en strategi til inddragelse af læringsanalytik (learning analytics) ved evaluering af universitetsunderviseres brug af et nyt LMS på Aarhus Universitet: Blackboard. Vi diskuterer en model (BLAME: Blended Learning Analytics Model of Evaluation) for, hvordan...... kategorisering af kurser og data om læringsanalytik indsamlet på Blackboard kan integreres. Endvidere belyser vi, hvilke implikationer en sådan læringsanalytik kan have for blended learning ved at analysere to forskellige uddannelses-cases/illustrationer. Dernæst diskuterer vi pædagogisk udvikling i forbindelse...

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

Science.gov (United States)

Kelly, Laura J; Renny-Byfield, Simon; Pellicer, Jaume; Macas, Jiří; Novák, Petr; Neumann, Pavel; Lysak, Martin A; Day, Peter D; Berger, Madeleine; Fay, Michael F; Nichols, Richard A; Leitch, Andrew R; Leitch, Ilia J

2015-10-01

Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Raman af hvide pigmenter

DEFF Research Database (Denmark)

Reeler, Nini Elisabeth Abildgaard; Nielsen, Ole Faurskov; Sauer, Stephan P. A.

2013-01-01

Et samspil mellem kunst og kemi. I et samarbejde mellem Statens Museum for Kunst og Kemisk Institut på KU er Ramanspek-troskopi brugt til at definere sammensætningen af blandinger af blyhvidt og calcit i maleriers hvide pigmenter....

Midtvejsevaluering af EGA handlingsplanen

DEFF Research Database (Denmark)

Møller, Niels; Hasle, Peter; Christiansen, Jørgen Møller

Center for Alternativ Samfundsanalyse (CASA) og Institut for Teknologi og Samfund ved Danmarks Tekniske Universitet har gennemført denne midtvejsevaluering af arbejdsmarkedets parters handlingsplan mod reduktion af ensidigt gentaget arbejde. Undersøgelsen viser, at der er sket en betydelig...

Differential modulation of plant immune responses by diverse members of the Pseudomonas savastanoi pv. savastanoi HopAF type III effector family.

Science.gov (United States)

Castañeda-Ojeda, M Pilar; López-Solanilla, Emilia; Ramos, Cayo

2017-06-01

The Pseudomonas savastanoi pv. savastanoi NCPPB 3335 type III secretion system (T3SS) effector repertoire includes 33 candidates, seven of which translocate into host cells and interfere with plant defences. The present study was performed to investigate the co-existence of both plasmid- and chromosomal-encoded members of the HopAF effector family, HopAF1-1 and HopAF1-2, respectively, in the genome of NCPPB 3335. Here, we show that the HopAF1 paralogues are widely distributed in the Pseudomonas syringae complex, where HopAF1-1 is most similar to the homologues encoded by other P. syringae pathovars infecting woody hosts that belong to phylogroups 1 and 3. We show that the expression of both HopAF1-1 and HopAF-2 is transcriptionally dependent on HrpL and demonstrate their delivery into Nicotiana tabacum leaves. Although the heterologous delivery of either HopAF1-1 or HopAF1-2 significantly suppressed the production of defence-associated reactive oxygen species levels, only HopAF1-2 reduced the levels of callose deposition. Moreover, the expression of HopAF1-2 by functionally effectorless P. syringae pv. tomato DC3000D28E completely inhibited the hypersensitive response in tobacco and significantly increased the competitiveness of the strain in Nicotiana benthamiana. Despite their functional differences, subcellular localization studies reveal that green fluorescent protein (GFP) fusions to either HopAF1-1 or HopAF1-2 are targeted to the plasma membrane when they are expressed in plant cells, a process that is completely dependent on the integrity of their N-myristoylation motif. Our results further support the notion that highly similar T3SS effectors might differentially interact with diverse plant targets, even when they co-localize in the same cell compartment. © 2016 BSPP AND JOHN WILEY & SONS LTD.

Does an interdisciplinary outpatient atrial fibrillation (AF) clinic affect the number of acute AF admissions?

DEFF Research Database (Denmark)

Frydensberg, Vivi Skibdal; Brandes, Axel

2018-01-01

AIMS AND OBJECTIVES: To investigate the impact of a multidisciplinary outpatient clinic for patients with atrial fibrillation (AF-clinic) on the number of acute hospitalizations for atrial fibrillation compared with usual outpatient care for this condition before the establishment of the AF-clinic....... BACKGROUND: Guidelines recommend a structured outpatient clinic follow-up in multidisciplinary teams for patients with atrial fibrillation due to fewer hospitalizations and death. However the evidence base is weak. DESIGN: The study is a retrospective cohort study including a total of 129 patients from...... the cardiac outpatient clinic at a large Danish University Hospital. The study population consisted of two groups: a usual care group before a dedicated AF-clinic was established (n=73) and the AF-clinic group (n=56). The primary endpoint was acute hospitalization for AF. METHODS: Cox regression was used...

Lejere der bliver sat ud af deres bolig

DEFF Research Database (Denmark)

Christensen, Gunvor; Nielsen, Torben Heien

Antallet af lejere, der bliver sat ud af deres bolig, er steget i perioden 2002-06. I 2006 blev 2600 husstande, svarende til 0,1 pct. af samtlige husstande i Danmark, sat ud af deres bolig. Stigningen er især sket i de fem største byer: København, Århus, Odense, Ålborg og Esbjerg. I dette...... skal give viden om, hvilke årsager der er til, at nogle lejere bliver sat ud af deres bolig, og hvorfor der er sket en stigning i antallet af udsættelser. Den endelige afrapportering af undersøgelsen af udsættelser i Danmark vil ske i foråret 2008. Undersøgelsen er finansieret af Socialministeriet....

The first genetic map of a synthesized allohexaploid Brassica with A, B and C genomes based on simple sequence repeat markers.

Science.gov (United States)

Yang, S; Chen, S; Geng, X X; Yan, G; Li, Z Y; Meng, J L; Cowling, W A; Zhou, W J

2016-04-01

We present the first genetic map of an allohexaploid Brassica species, based on segregating microsatellite markers in a doubled haploid mapping population generated from a hybrid between two hexaploid parents. This study reports the first genetic map of trigenomic Brassica. A doubled haploid mapping population consisting of 189 lines was obtained via microspore culture from a hybrid H16-1 derived from a cross between two allohexaploid Brassica lines (7H170-1 and Y54-2). Simple sequence repeat primer pairs specific to the A genome (107), B genome (44) and C genome (109) were used to construct a genetic linkage map of the population. Twenty-seven linkage groups were resolved from 274 polymorphic loci on the A genome (109), B genome (49) and C genome (116) covering a total genetic distance of 3178.8 cM with an average distance between markers of 11.60 cM. This is the first genetic framework map for the artificially synthesized Brassica allohexaploids. The linkage groups represent the expected complement of chromosomes in the A, B and C genomes from the original diploid and tetraploid parents. This framework linkage map will be valuable for QTL analysis and future genetic improvement of a new allohexaploid Brassica species, and in improving our understanding of the genetic control of meiosis in new polyploids.

Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells.

Science.gov (United States)

Canver, Matthew C; Bauer, Daniel E; Dass, Abhishek; Yien, Yvette Y; Chung, Jacky; Masuda, Takeshi; Maeda, Takahiro; Paw, Barry H; Orkin, Stuart H

2014-08-01

The clustered regularly interspaced short [corrected] palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 nuclease system has provided a powerful tool for genome engineering. Double strand breaks may trigger nonhomologous end joining repair, leading to frameshift mutations, or homology-directed repair using an extrachromosomal template. Alternatively, genomic deletions may be produced by a pair of double strand breaks. The efficiency of CRISPR/Cas9-mediated genomic deletions has not been systematically explored. Here, we present a methodology for the production of deletions in mammalian cells, ranging from 1.3 kb to greater than 1 Mb. We observed a high frequency of intended genomic deletions. Nondeleted alleles are nonetheless often edited with inversions or small insertion/deletions produced at CRISPR recognition sites. Deleted alleles also typically include small insertion/deletions at predicted deletion junctions. We retrieved cells with biallelic deletion at a frequency exceeding that of probabilistic expectation. We demonstrate an inverse relationship between deletion frequency and deletion size. This work suggests that CRISPR/Cas9 is a robust system to produce a spectrum of genomic deletions to allow investigation of genes and genetic elements. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Repeated extragenic sequences in prokaryotic genomes: a proposal for the origin and dynamics of the RUP element in Streptococcus pneumoniae.

Science.gov (United States)

Oggioni, M R; Claverys, J P

1999-10-01

A survey of all Streptococcus pneumoniae GenBank/EMBL DNA sequence entries and of the public domain sequence (representing more than 90% of the genome) of an S. pneumoniae type 4 strain allowed identification of 108 copies of a 107-bp-long highly repeated intergenic element called RUP (for repeat unit of pneumococcus). Several features of the element, revealed in this study, led to the proposal that RUP is an insertion sequence (IS)-derivative that could still be mobile. Among these features are: (1) a highly significant homology between the terminal inverted repeats (IRs) of RUPs and of IS630-Spn1, a new putative IS of S. pneumoniae; and (2) insertion at a TA dinucleotide, a characteristic target of several members of the IS630 family. Trans-mobilization of RUP is therefore proposed to be mediated by the transposase of IS630-Spn1. To account for the observation that RUPs are distributed among four subtypes which exhibit different degrees of sequence homogeneity, a scenario is invoked based on successive stages of RUP mobility and non-mobility, depending on whether an active transposase is present or absent. In the latter situation, an active transposase could be reintroduced into the species through natural transformation. Examination of sequences flanking RUP revealed a preferential association with ISs. It also provided evidence that RUPs promote sequence rearrangements, thereby contributing to genome flexibility. The possibility that RUP preferentially targets transforming DNA of foreign origin and subsequently favours disruption/rearrangement of exogenous sequences is discussed.

Registrering af biometriske og biologiske personoplysninger

DEFF Research Database (Denmark)

Blume, Peter Erik; Herrmann, Janne Rothmar

2009-01-01

Med udgangspunkt i menneskeretsdomstolens Marper dom drøftes i artiklen indretningen af dansk rets regler om registrering af fingeraftryk og dna-profil med tilhørende biologisk materiale, og om dommen nødvendiggør ændringer af disse regler....

Hærdeteknologi og Holdbarhed af Betonkonstruktioner

DEFF Research Database (Denmark)

Sørensen, Eigil V.

Kurset Hærdeteknologi og Holdbarhed af Betonkonstruktioner afholdes i 1. og 2. periode af forårssemesteret 2006. Kurset sigter på at give de studerende en grundlæggende forståelse af, hvorledes man designer og udfører holdbare betonkonstruktioner....

International fragmentation af produktionen og vertikal disintegration af styringsformer i produktionskæderne

DEFF Research Database (Denmark)

Refslund, Bjarke

Stigende international økonomisk integration har betydet en stigende fragmentering af produktionen, hvor store dele udføres i forskellige lande. Dertil kommer en stigende disintegration af vertikale styringsformer i produktions-værdikæder (Global Value Chains). Dette konferencepaper diskutere...

Identifikation af forkullet lig ved hjælp af ganeaftryk og koralnyresten

DEFF Research Database (Denmark)

Leth, Peter Mygind; Bindslev, Dorthe Arenholt; Kristensen, Ingrid Bayer

1997-01-01

En retstodontologisk undersøgelse af en dødfunden, uidentificeret person, bygger almindeligvis på en undersøgelse af tandsættet. Hvis personen er tandløs må andre identifikationsmetoder tages i anvendelse. Fingeraftryk er et almindelig kendt eksempel på en alternativ metode, som bygger på, at cri...

An Interface Transformation Strategy for AF-IPPS

Science.gov (United States)

2012-12-01

Oracle, or SAP . Like other AF and Department of Defense (DoD) ERP programs, AF-IPPS is expected to have 100+ interfaces with 90+ external trading partners...platform such as PeopleSoft, Oracle, or SAP . Like other AF and Department of Defense (DoD) ERP programs, AF-IPPS is expected to have 100...currently perform these functions. The core of AF-IPPS will be implemented using an Enterprise Resource Planning ( ERP ) platform such as PeopleSoft

Coaching af dit studieliv

DEFF Research Database (Denmark)

Hansen, Rasmus Thorning

2008-01-01

En generel beskrivelse af de problemer specialestuderende sidder med og hvorledes coaching kan hjælpe med at (gen)skabe motivation og fokus......En generel beskrivelse af de problemer specialestuderende sidder med og hvorledes coaching kan hjælpe med at (gen)skabe motivation og fokus...

Kvalitetsvurdering af sundhedsoplysende materiale

DEFF Research Database (Denmark)

Osler, Merete; Bech, Lars; Sybille, Bojlén

1990-01-01

Lægeforeningens Hygiejnekomités arbejdsgruppe vedrørende sundhedsoplysning har udarbejdet en "huskeliste" til brug for en kvalitetsvurdering af skriftligt sundhedsoplysende materiale......Lægeforeningens Hygiejnekomités arbejdsgruppe vedrørende sundhedsoplysning har udarbejdet en "huskeliste" til brug for en kvalitetsvurdering af skriftligt sundhedsoplysende materiale...

Implementering af evidensbaseret praksis

DEFF Research Database (Denmark)

Scheel, Linda Schumann; Tewes, Marianne; Petersen, Preben Ulrich

2015-01-01

Projektet omhandler implementering af den kliniske retningslinje om identifikation, forebyggelse og behandling af delirium – i denne sammenhæng relateret til hjertepatienter. Projektet foregår på to hospitaler i Hjertecentret på Rigshospitalet, et intensivt afsnit og et sengeafsnit, i tæt...

Implementering af evidensbaseret praksis

DEFF Research Database (Denmark)

Scheel, Linda Schumann; Hansen, Ida Rode

2014-01-01

Projektet omhandler implementering af den kliniske retningslinje om identifikation, forebyggelse og behandling af delirium – i denne sammenhæng relateret til hjertepatienter. Projektet foregår på to hospitaler i Hjertecentret på Rigshospitalet, et intensivt afsnit og et sengeafsnit, i tæt...

Magtens repræsentation af danskhed

DEFF Research Database (Denmark)

Madsen, Carsten

2016-01-01

Med udgangspunkt i Maurice Charlands begreb om konstitutiv retorik og Jacques Derridas dekonstruktion af repræsentationslogik foretager artiklen en kritisk analyse og fortolkning af repræsentationen af dansk nationalidentitet, sådan som den kommer til udtryk i Dronning Margrethes nytårstaler...

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.

Directory of Open Access Journals (Sweden)

Margaret Staton

Full Text Available Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

På kanten af ungdomslivet

DEFF Research Database (Denmark)

Sørensen, Niels Ulrik; Pless, Mette

2015-01-01

). Parallelt hermed fortælles moderne ungdomsliv (i ungdomssociologien) frem gennem ”…theoretical frameworks based on urban experiences which capture neither the lives of rural young people nor the spatial dimensions of the structures and cultures that make up contemporary youth.” (Farrugia 2013......, at yderområder er hårdt ramt af ungdomsarbejdsløshed (Bjørnsted & Andersen 2013), at områderne er præget af høj koncentration af unge med arbejderklassebaggrund (Ottosen et a 2010), mens de uddannelsesorienterede og ressourcestærke unge er tilbøjelige til at flytte væk og ind til byerne (Helve 2003). Og ser man...... stedstilknytning og stedbundne ressourcer. Teoretiske perspektiver, der peger på vigtigheden af en mere ”..spatialised youth sociology that is sensitive to macro-level processes producing different spaces, as well as the local, emplaced ways in which young people are responding to social changest hat shape...

GRAbB : Selective Assembly of Genomic Regions, a New Niche for Genomic Research

NARCIS (Netherlands)

Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often

For bestemmelse af drivhusgasudledning ved udtagning/Ekstensivering af landbrugsjorder på kulstofrige lavbundsjorder

DEFF Research Database (Denmark)

Gyldenkærne, Steen; Greve, Mogens Humlekrog

Sammenfatning: Rapporten beskriver hvordan man kan beregne ændringen i drivhusgasemissionen ved omlægning af landbrugsjord til naturarealer. Rapporten er primært rettet mod tilskudsordningen vedr. udtagning af organiske lavbundsjorde, men kan også anvendes i andre sammenhænge. Rapporten anvender de...

Omsætning af fast ejendom

DEFF Research Database (Denmark)

Edlund, Hans Henrik

Bogen er en systematisk gennemgang af lov om omsætning af fast ejendom, der regulerer ejendomsmægleres virke. Følgende emner er bl.a. behandlet: Hvem kan drive ejendomsmæglervirksomhed og ejendomsmæglernes pligter og ansvar.......Bogen er en systematisk gennemgang af lov om omsætning af fast ejendom, der regulerer ejendomsmægleres virke. Følgende emner er bl.a. behandlet: Hvem kan drive ejendomsmæglervirksomhed og ejendomsmæglernes pligter og ansvar....

The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms.

Science.gov (United States)

Ma, Ji; Yang, Bingxian; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Wang, Xumin

2013-10-10

Mahonia bealei (Berberidaceae) is a frequently-used traditional Chinese medicinal plant with efficient anti-inflammatory ability. This plant is one of the sources of berberine, a new cholesterol-lowering drug with anti-diabetic activity. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of M. bealei. The complete cp genome of M. bealei is 164,792 bp in length, and has a typical structure with large (LSC 73,052 bp) and small (SSC 18,591 bp) single-copy regions separated by a pair of inverted repeats (IRs 36,501 bp) of large size. The Mahonia cp genome contains 111 unique genes and 39 genes are duplicated in the IR regions. The gene order and content of M. bealei are almost unarranged which is consistent with the hypothesis that large IRs stabilize cp genome and reduce gene loss-and-gain probabilities during evolutionary process. A large IR expansion of over 12 kb has occurred in M. bealei, 15 genes (rps19, rpl22, rps3, rpl16, rpl14, rps8, infA, rpl36, rps11, petD, petB, psbH, psbN, psbT and psbB) have expanded to have an additional copy in the IRs. The IR expansion rearrangement occurred via a double-strand DNA break and subsequence repair, which is different from the ordinary gene conversion mechanism. Repeat analysis identified 39 direct/inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Analysis also revealed 75 simple sequence repeat (SSR) loci and almost all are composed of A or T, contributing to a distinct bias in base composition. Comparison of protein-coding sequences with ESTs reveals 9 putative RNA edits and 5 of them resulted in non-synonymous modifications in rpoC1, rps2, rps19 and ycf1. Phylogenetic analysis using maximum parsimony (MP) and maximum likelihood (ML) was performed on a dataset composed of 65 protein-coding genes from 25 taxa, which yields an identical tree topology as previous plastid-based trees, and provides strong support for the sister relationship between Ranunculaceae and Berberidaceae

Fermentering af korn øger fordøjeligheden af næringsstoffer

DEFF Research Database (Denmark)

Pedersen, Anni Øyan; Jørgensen, Henry; Bach Knudsen, Knud Erik

2010-01-01

foderblandingerne med ikke-fermentet korn var dog lavere end normalt, hvilket kan have påvirket resultaterne, så effekten af fermentering er større i dette forsøg, end hvad der normalt kan forventes. Kornet var groft formalet (ca. 30 % under 1 mm), hvilket kan have påvirket resultaterne. Ved finere formaling af...

Bilag til forskningsoversigt - Effekterne af Cooperative Learning

DEFF Research Database (Denmark)

Larsen, Lea Lund

Ved en opsamling af de empiriske studier vedrørende effekten af CL inden for voksenundervisningsfeltet ses en overvægt af studier, som rapporterer en positiv effekt af CL i forhold til de voksne lærendes faglige udbytte. En meta-analyse over 168 amerikanske undersøgelser på universitetsniveau vis...

Læring som improviseret udvikling af praksis

DEFF Research Database (Denmark)

Brinck, Lars

2010-01-01

Med afsæt i forfatterens fænomenografiske studie af amerikanske musikeres oplevelse af det at jamme diskuterer artiklen, hvorvidt jam-bandets spontant improviserende praksis kan give ny forståelse af rytmiske musikeres læring som et overordnet socialt fænomen. Ved at betragte jam-bandets praksis i...

Hvorfor lejere bliver sat ud af deres bolig

DEFF Research Database (Denmark)

Nielsen, Torben Heien; Christensen, Gunvor

Antallet af lejere, der bliver sat ud af deres bolig, er steget fra 1499 i 2002 til 2589 i 2006. Lejere kan blive sat ud af deres bolig, hvis de ikke betaler deres husleje til tiden, eller hvis de ikke overholder husordenen det sted de bor. Denne rapport beskriver årsager til, at lejere bliver sat...... ud af deres boliger og baggrunden for stigningen i antallet af udsættelser. desuden beskriver rapporten konsekvenser af en udsættelse og kommer med en række anbefalinger til indsatsområder. Af afgørende betydning for, at lejere bliver sat ud af deres bolig, er lav indkomst, lavt rådighedsbeløb, stor...

Enzymatisk omestring til produktion af biodiesel

DEFF Research Database (Denmark)

Fjerbæk, Lene

2007-01-01

  Biodiesel er i dag sammen med bioethanol et bud på, hvordan transportsektoren kan nedbringe sin netto CO2-emission til atmosfæren og lagrene af fossilt brændstof kan strækkes. På verdensplan forventes der en produktion af biodiesel på 7,9 mio. tons i 2007. Ved den industrielle fremstilling af...... biodiesel benyttes i dag kemiske katalysatorer såsom H2SO4, NaOH, MeONa eller KOH, der efterfølgende fjernes fra den producerede biodiesel med store mængder vand og derved produceres store mængder spildevand. Ved at benytte enzymer i processen kan man reducere mængden af spildevand, der skal renses. Enzymer...... benyttes ikke i de eksisterende processer, men det forventes, at udviklingen af processerne vil øge deres anvendelse i biodieselproduktion. I artiklen præsenteres fordele og ulemper ved anvendelse af enzymer til biodiesel produktion....

Anvendelse af genmodificerede planter

DEFF Research Database (Denmark)

Møller, F.

I rapporten vurderes mulighederne for at gennemføre velfærdsøkonomiske analyser af anvendelsen af genmodificerede planter. Der gøres rede for kravene til konse-kvensbeskrivelsen og for mulighederne for at prissætte såvel de markedsrelaterede som de ikke-markedsrelaterede konsekvenser. Mulighederne...

Fundering af mindre bygninger

DEFF Research Database (Denmark)

Larsen, J.; Ballisager, C.C.

Denne SBI-anvisning indeholder en gennemgang af de jordbunds- og grundvandsforhold, som er bestemmende for funderingen af en bygning. Specielt gennemgås de betingelser, der skal være opfyldt, for at man på forsvarlig måde kan fundere en mindre bygning i traditionel udformning. Publikationen...

Udvikling af vejledningspraksis i kurser for undervisere i brugen af blended learning-aktiviteter

DEFF Research Database (Denmark)

Stenalt, Maria Hvid; Wichmann-Hansen, Gitte; Rossen, Dorte Sidelmann

Hvert semester tilbyder Center for Undervisning og Læring (CUL) ved School of Business and Social Sciences ved Aarhus Universitet et 1-årig langt kompetenceudviklingsforløb i brugen af blended learning for lektorer og professorer. I løbet af denne periode skal deltagerne gennemføre et indledende...... blended learning-kursusforløb på 5 uger efterfulgt af en udviklings- og afprøvningsfase. Som afslutning skal deltagerne skrive en refleksionsrapport. Forløbet indebærer to vejledningsmøder med en eller flere af de undervisningsudviklere fra CUL, der er ansvarlige for forløbet: 1) Et individuelt...... vejledningsmøde, hvor deltagerne skal finde frem til, hvordan de vil eller kan omlægge deres undervisning til blended learning og 2) et kollektivt vejledningsmøde efter første udviklingsfase, hvor deltagerne modtager feedback på deres igangværende udviklingstiltag fra gruppemedlemmer og undervisningsudviklere. Et...

Videoanalyse af social interaktion

DEFF Research Database (Denmark)

Igennem de sidste 40 år er videooptagelser af praksis blevet anvendt som et redskab i forskning af social interaktion inden for f.eks. læring, design, mediering, kommunikationstræning og i sundhedsvæsenet. Videoanalyse af social interaktion giver et stærkt metodisk, teoretisk og praktisk blik ind i...... videoanalyse og viser, hvordan man som forsker og studerende kan bruge videoanalyse til at undersøge social interaktion. Bogens temaer og spørgsmål udgør således en grundsten i arbejdet med videoanalyse på professions-, universitets- og forskeruddannelser såvel som i forskning mere generelt og omfatter: - de...

Digital innovation af folkeskolernes åbenhed og sammenlignelighed

DEFF Research Database (Denmark)

Andersen, Kim Normann; Henriksen, Helle Zinner; Agger Nielsen, Jeppe

2013-01-01

Denne artikel præsenterer en normativ model (Public Sector Process Rebuilding, PPR), som kan indfange, hvor innovativt offentlige organisationer anvender digitale løsninger. Optag af digital innovation anskues ofte i litteraturen binært – enten er innovationen anskaffet eller ikke anskaffet. Vores...... argument er imidlertid, at optag af digitale innovationer kan gradbøjes. Vores sigte er derfor at få fokus væk fra anskaffelse og mere i retning af udnyttelse af digitaliseringen med henblik på at skabe forbedring af kerneydelserne og gavne slutbrugerne. Med empirisk afsæt i danske folkeskolers tolkning af...

Fluorerede stoffer i mademballage af pap og papir

DEFF Research Database (Denmark)

Trier, Xenia; Cederberg, Tommy Licht; Jensen, Lisbeth Krüger

andre typer af madbokse. Prøverne er blevet analyseret for flere forskellige typer af fluorerede stoffer, der anvendes til at imprægnere disse typer af emballager, så de ikke suger fedt eller vand. I ingen af prøverne er der fundet indhold af fluorerede stoffer, der overstiger analysemetodens...

Chlamydomonas chloroplasts can use short dispersed repeats and multiple pathways to repair a double-strand break in the genome.

Science.gov (United States)

Odom, Obed W; Baek, Kwang-Hyun; Dani, Radhika N; Herrin, David L

2008-03-01

Certain group I introns insert into intronless DNA via an endonuclease that creates a double-strand break (DSB). There are two models for intron homing in phage: synthesis-dependent strand annealing (SDSA) and double-strand break repair (DSBR). The Cr.psbA4 intron homes efficiently from a plasmid into the chloroplast psbA gene in Chlamydomonas, but little is known about the mechanism. Analysis of co-transformants selected using a spectinomycin-resistant 16S gene (16S(spec)) provided evidence for both pathways. We also examined the consequences of the donor DNA having only one-sided or no homology with the psbA gene. When there was no homology with the donor DNA, deletions of up to 5 kb involving direct repeats that flank the psbA gene were obtained. Remarkably, repeats as short as 15 bp were used for this repair, which is consistent with the single-strand annealing (SSA) pathway. When the donor had one-sided homology, the DSB in most co-transformants was repaired using two DNAs, the donor and the 16S(spec) plasmid, which, coincidentally, contained a region that is repeated upstream of psbA. DSB repair using two separate DNAs provides further evidence for the SDSA pathway. These data show that the chloroplast can repair a DSB using short dispersed repeats located proximally, distally, or even on separate molecules relative to the DSB. They also provide a rationale for the extensive repertoire of repeated sequences in this genome.

Aspekter af integrationsindsatsen i 6 kommuner

DEFF Research Database (Denmark)

Rosdahl, Anders

Dette arbejdspapir præsenterer resultaterne af en mindre kvalitativ undersøgelse af kommuners indsats for at bringe nyankomne flygtninge og indvandrere i beskæftigelse. Undersøgelsen er en opfølgning på en kvantitativ benchmarkanalyse, som er gennemført af Amternes og Kommunernes Forskningsinstit...

Modelanalyser af mobilitet og miljø

DEFF Research Database (Denmark)

Christensen, Linda; Gudmundsson, Henrik

Begrebet bæredygtig transport diskuteres og ved hjælp af persontrafikmodellen ALTRANS belyses mulighederne for at fremme bæredygtig udvikling gennem en række scenarier. Desuden præsenteres en mere detaljeret analyse af ændringer i CO2-belastningen ved forbedring af den kollektive trafiks servicen...

Boligboblen pustes op af bankerne

DEFF Research Database (Denmark)

Ravn, Ib

2017-01-01

Den aktuelle boligboble blæses i vejret af bankerne, der gennem opkøb af realkreditobligationer skaber nye penge og dermed presser boligpriserne i vejret - en kreditfinansieret bolig- eller finansboble....

Domesticeringen af Ford i Danmark:Den kulturelle tilegnelse af Ford og fordismen, 1920-1940

OpenAIRE

Wagner, Michael

2009-01-01

Det amerikanske automobilfirma Ford Motor Company med hovedkvarter i Detroit begyndte at drive forretning i Danmark omkring 1906. De første aktiviteter blev konsolideret samme år ved udnævnelsen af motorforhandleren F. Bülow & Co. til salgsagent i Danmark og importør af Ford automobiler til det skandinaviske marked. Dermed havde Ford tidligt fået et stærkt fodfæste i Nordeuropa, som udviklingen i salget af Ford autobiler de næste årtier til fulde skulle demonstrere. Ford Motor Company er ...

Sygeplejestuderendes brug af portfolio i klinisk undervisning

DEFF Research Database (Denmark)

Hjorth, Anne Charlotte Overgaard; Bruhn, Helle

2014-01-01

Brugen af portfolio var mangelfuld, men et udviklingsprojekt i samarbejde med den kommunale sygepleje motiverede både sygeplejestuderende og kliniske vejledere til at anvende læringsdelen af portfolio aktivt.......Brugen af portfolio var mangelfuld, men et udviklingsprojekt i samarbejde med den kommunale sygepleje motiverede både sygeplejestuderende og kliniske vejledere til at anvende læringsdelen af portfolio aktivt....

Monitering, modellering og miljøvurdering af fuldskala afværge af TCE fourening ved stimuleret reduktiv deklorering

DEFF Research Database (Denmark)

Westergaard, Claus; Lemming, Gitte; Janniche, Gry Sander

På Sortebrovej 26 i Tommerup blev der i 2006 gennemført afværgeforanstaltninger ved stimuleret reduktiv deklorering (SRD) ved injektion af donor og bakterier i kildeområdet med henblik på at oprense en forurening med TCE. Kildeområdet befinder sig 10-20 m u. t. i sandet og opsprækket moræneler...... gunstige forhold for nedbrydning af de klorerede ethener ved reduktiv deklorering. Der ses da også en klar dominans af nedbrydningsprodukterne DCE og VC samt ethen og ethan i grundvandet. I nogle boringer, ses dog en stagnerende omsætning af TCE og DCE i grundvandet. Årsagen her til kan være, at donoren...... da også fordoblet fra 2008 til 2010. Der er observeret zoner med betydelig omsætning af TCE, hvor cis-DCE dominerer, og der ses generelt VC og ethen centralt i disse zoner. Koncentrationsniveauet af fermenteringsprodukter er aftaget og består ved en sandslire (B370 K1) alene af acetat og methan...

Vurdering af effekten af en vindmøllepark ved Overgaard på forekomsten af fugle i EF-fuglebeskyttelsesområde nr. 15

DEFF Research Database (Denmark)

Clausen, P.; Larsen, J. K.

forekomsten af en række arter der enten yngler eller raster inden for EF-fuglebeskyttelsesområdet, og er omfattet af EF-fuglebeskyttelsesdirektivets bilag I. Det drejer sig om arterne skarv Phalacrocorax carbo sinensis, blå kærhøg Circus cyaneus, hjejle Pluvialis apricaria, brushane Philomachus pugnax, klyde...

Selektiv avl af racehunde og -katte

DEFF Research Database (Denmark)

Sandøe, Peter; Meyer, Iben Helene Coakley; Fredholm, Merete

2014-01-01

Dette kapitel ser nærmere på de velfærdsmæssige problemstillinger, der opstår som følge af måden, hvorpå racehunde og -katte påvirkes gennem selektiv avl. Først beskrives, hvordan avlen af racehunde og -katte er organiseret. Dernæst gøres der rede for de dyrevelfærdsmæssige konsekvenser heraf....... Selektiv avl af hunde og katte tjener til at vedligeholde en stor racemæssig diversitet. De racemæssige forskelle gør det muligt for mennesker at vælge især hunde, der har nogle egenskaber, som passer til individuelle behov og ønsker. Desværre er der også en række bivirkninger for de pågældende dyrs...... problemer, som knytter sig til selektiv avl af racehunde og -katte, gennemgås og diskuteres mulige praktiske tiltag, som kan trække udviklingen i retning af at reducere forekomsten af disse problemer....

Tema 1: Programmering af robotenheder i grundskolen

Directory of Open Access Journals (Sweden)

Stine Ejsing-Duun

2016-01-01

Full Text Available I denne artikel undersøger vi potentialerne for at lære matematik gennem programmering af robotter. Vi foreslår en model med tre indbyrdes afhængige læringspotentialer, som programmering fordrer. Det omfatter elevens evne til at; (1 tænke i algoritmer, (2 producere viden og artefakter gennem brug af matematik og (3 foretage abstraktion og indkapsling. Programmering er blevet en del af grundskolens læringsmål i flere lande. I Danmark er programmering et læringsmål i forenklede fælles mål for Fysik/Kemi og desuden en del af den nationale undervisningsvejledning for matematik. En analyse af potentialerne i at anvende programmering i forbindelse med disse fag er derfor væsentlig. I denne artikel fokuserer vi på samspillet mellem matematik og programmering gennem litteraturstudier og analyse af empiriske situationer fra undervisning i programmering af LEGO Mindstorms. Teoretisk anvendes den instrumentelle tilgang til teknologi i matematikundervisning. Analysen viser en række måder, hvorpå didaktisk opmærksomhed på epistemisk forhandling kan understøtte læring af matematik gennem programmering.

Realisering af Vision 2020

DEFF Research Database (Denmark)

Bertelsen, Niels Haldor; Hansen, Ernst Jan de Place

Repræsentanter for byggesektoren har på 11 dialogmøder drøftet Erhvervs- og Byggestyrelsens "Vision 2020 - Byggeri med mening". Drøftelserne førte til formulering af en lang række initiativforslag til realisering af visionen. Den mest centrale udfordring bliver at reducere fejl og mangler i...... byggeriet. Branchen lægger også vægt på, at styringen af Vision 2020s reaisering sker i byggesektoren. Initiativforslagene er i rapporten samlet under 3 hovedområder. Det første hovedområde lægger vægt på bygningerne, brugerbehov og det globale samfund. Det andet omhandler processen og leverancesystemet...

Konceptuelt design og udvikling af Intergomus

DEFF Research Database (Denmark)

Ellebæk, P.; Pedersen, T.; Stendal, Karsten

1999-01-01

Denne rapport gennemgår udviklingsforløbet af et træningsapparat til genoptræning af læderede fingre. Rapporten omhandler kun den mekaniske del af udstyret. Opgaven er blevet løst i samarbejde med Ergoterapien på Køge Amtssygehus, Procare, Centret forAvanceret Teknologi og flere afdelinger på RIS...

Offentliggørelse af kursrelevante oplysninger

DEFF Research Database (Denmark)

Werlauff, Erik; Schaumburg-Müller, Peer

2013-01-01

Artiklen analyserer, særligt på baggrund af EU-Domstolens dom af 28. juni 2012 i C-19/11, Daimler AG, hvilken betydning en række mellemliggende trin, der fører frem til en kursrelevant og offentliggørelsespligtig begivenhed, har for tidspunktet for indtrædelsen af pligten til offentliggørelse. De...

Regulering af jødiske kroppe

DEFF Research Database (Denmark)

Schleicher, Marianne

2014-01-01

på teori dels af Michel Foucault om, hvordan kultur sikrer sin egen overlevelse ved at indsamle viden om bl.a. kroppe med henblik på at regulere brugen af dem, dels af Judith Butler, der bl.a. forklarer, hvordan kultur trods alt er åben for såkaldt subversion, idet det bidrager til at udvide og...

En litteraturbaseret gennemgang af mulige velfærdsmæssig betydning af brugen af længerevarende smertelindring til kalve efter afhorning

DEFF Research Database (Denmark)

Herskin, Mette S.; Nielsen, Bodil Højlund

2018-01-01

Dette er et udvidet sammendrag af vidensyntesen. Store dele af vidensyntesen er under review til et videnskabeligt tidsskrift, og kan derfor ikke offentliggøres elektronisk før denne proces er afsluttet. Den fulde rapport kan fremsendes pr. mail. Hvis du gerne vil have den tilsendt, så send en mail...

Kuratering af Samtidskunst

DEFF Research Database (Denmark)

Kuratering af Samtidskunst er den første bogudgivelse i Danmark, der fokuserer på kuratering som fag og praksis. Kuratering spiller en stadig større rolle i samtidskunsten. Bogen er en introduktion til skiftende forståelser af udstillings- og kuratorpraksisser og deres udfordringer, indkredset ge...... Kofod Olsen, Teresa Gleadowe, Helle Ryberg, Kirse Junge-Stevnsborg, Malene Natascha Ratcliffe, Pelin Uran, Jacob Fabricius, Lotte Juul Petersen, Jacob Lillemose, Solvej Helweg Ovesen, Frederikke Hansen & Tone Olaf Nielsen (kuratorisk aktion) og Temporary Services....

Evaluering af kollegial supervision

DEFF Research Database (Denmark)

Petersen, Anne Line Bjerre Folsgaard; Bager, Lene Tortzen; Jørgensen, Mette Eg

2015-01-01

Videoen er en evaluering af arbejdet med en metodisk tilgang til kollegial supervision på VIA Ergoterapeutuddannelsen gennem et par år. Evalueringen sætter fokus på selve metoden, der er anvendt til kollegial supervision. Derudover er der fokus på erfaringer og udbytte af at arbejde systematisk med...... kollegial supervision blandt undervisere på VIA Ergoterapeutuddannelsen....

Effekter af koordineret hjerneskaderehabilitering. Et systematisk litteraturreview

DEFF Research Database (Denmark)

Glintborg, Chalotte; Hansen, Tia G. B.

beskrevet. Der er ingen klar dansk definition af koordination. Begrebet bliver ofte brugt inkonsistent, og koordination er meget forskelligt tilrettelagt. Derfor kan man ikke generelt dokumentere, om koordinatorfunktioner er en sikker vej til forbedring af komplekse rehabiliteringsforløb. Sundhedsstyrelsen......Forskningsprojekt udvikler ny definition af begrebet koordination Som et led i forskningsprojektet ”Bio-psyko-sociale effekter af koordineret hjerneskaderehabilitering” er der udviklet en ny definition af koordinationsbegrebet. Forskningsprojektet ”Bio-psyko-sociale effekter af koordineret...... senhjerneskadeområdet – initiativer, der skal fremme en sammenhængende og helhedsorienteret rehabiliteringsindsats. Men hvad dækker begrebet koordination egentlig over? Det har et nyt forskningsprojekt set på og kommer med et bud på en ny definition. Dansk definition mangler Indholdet i koordination har været upræcist...

Modellering af elforbrug til netanalyse

DEFF Research Database (Denmark)

Østergaard, Jacob

I denne rapport undersøges mulighederne for at etablere en model for elforbruget, der kan anvendes ved analyser af det østdanske transmissionsnet. Rapporten henvender sig til ingeniører og beslutningstagere, der ønsker viden om betydningen af en nøjagtig elforbrugsmodel og om mulighederne for i p...... simuleringsresultater med mindre usikkerhed, og der opnås en integration mellem eksisterende systemer, idet data fra en række systemer bl.a. Panda, elforbrugsprognoser, elforbrugspaneler og stationsprognoser kan udnyttes til etableringen af en model....

Erfaringer fra nedrivning af boligblok i Rødbyhavn

DEFF Research Database (Denmark)

Eriksen, Søren Skibstrup; Hansen, Klaus; Krogh, Hanne

Denne meddelelse indeholder en beskrivelse af nedrivningen af et betonelementbyggeri. Der er foretaget en registrering af energiforbrug i forbindelse med nedrivningen og bortskaffelsen samt en registrering af de miljøbelastende stoffer i bygningsaffaldet. Inden bebyggelsen blev revet ned, blev de...

Genomic characterization of large heterochromatic gaps in the human genome assembly.

Directory of Open Access Journals (Sweden)

Nicolas Altemose

2014-05-01

Full Text Available The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3. The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations.

Overvågning af karplanter i Suserup Skov

DEFF Research Database (Denmark)

Wind, P.

1999-01-01

Vejler, i alt ca. 5.500 ha. Feltstationen blev oprettet i 1978, og siden har observatørerne registreret fuglelivet i Vejlerne og de omgivende arealer foruden vandstand, saltholdighed og drift af området. Tipperne ligger i den sydlige del af Ringkøbing Fjord. Fuglelivet blev fredet i 1898. Reservatet blev...... en samlet fredning af Vadehavet, omfatter øen Langli på 80 ha og vandarealer på i alt ca. 8.000 ha. Øen består af klitter og salte strandenge. Vandområdet er præget af tidevand, hvor vidtstrakte sand- og mudderflader og spredte muslingebanker er synlige ved lavvande. Vorsø ligger i Horsens Fjord...... saltholdighed i Ringkøbing Fjord bevirker, at vandplanter vokser dårligt eller forsvinder. Vandplanter udgør en væsentlig del af føden for visse andefugle og kan derfor have stor betydning for antallet af rastende fugle. Der blev registreret lave antal af knortegå, gråand, pibeand og krikand. Af blishøne blev...

Miljørigtig ombygning af Mallinggård

DEFF Research Database (Denmark)

Hansen, Ernst Jan de Place

2002-01-01

Resume af rapport om den byggetekniske anvendelse af alternativ isolering ved en ombygning af Mallinggårds lade til undervisningslokaler, udarbejdet af Bent Møller fra Rudolf Steiner Skolen i Skanderborg under Energistyrelsens udviklingsprogram "Miljø- og arbejdsmiljøvenlig isolering"...

Et nationalt studie af bankrøveri

DEFF Research Database (Denmark)

Hansen, Maj; Elklit, Ask

11,1 % (n = 41) af ASD og seks måneder efter røveriet led 6,2 % (n = 23) af PTSD. Begge prævalenser var begrænset af kravet om undgåelsessymptomer (ASD uden undgåelse: 14 %, PTSD uden undgåelse: 17,8 %), men ASD diagnosen var især begrænset af kravet om dissociationssymptomer (ASD uden dissociation......: 26,7 %). Hierarkisk regressionsanalyse viste, at 51 % af variansen i PTSD sværhedsgrad blev forklaret af peritraumatisk dissociation, ASD sværhedsgrad, emotionel coping og negative tanker om egen person og evner. ASD sværhedsgrad var den stærkeste prædiktorer for PTSD sværhedsgrad og forudsagde alene...... diagnoser. Særligt ASD sværhedsgrad og negative tanker om egen person og evner synes at kunne forudsige PTSD sværhedsgrad efter bankrøveri. Det anbefales derfor, at ”Acute Stress Disorder Scale” anvendes til at screene for PTSD efter bankrøveri. Fremtidig forskning anbefales at fokusere på udvikling af...

Typebestemmelse af de danske M. bovis stammer

DEFF Research Database (Denmark)

Kokotovic, Branko

Mycoplasma bovis er en af de mest betydningsfulde mykoplasma i kvægbruget på verdensplan. Bakterien findes oftest i forbindelse med mastitis, lunge- og ledbetændelse, men andre kliniske manifestationer kan også forekomme. Der findes ikke præcise, nyere beregninger over konsekvenser af M. bovis...... relateret sygdomme, men det anses, at infektionen hvert år globalt set pålægger en økonomisk byrde til kvægbruget i en multimillion skala. M. bovis blev for første gang påvist i Danmark i 1981 og gennem 1980’erne har bakterien forårsaget store udbrud af mastitis. I de følgende årtier blev bakterien isoleret...... sporadisk fra mange forskellige kvægbesætninger, men på trods af en tilsyneladende stigende forekomst i 1990’erne, blev der ikke registret omfattende sundhedsmæssige problemer som følge af M. bovis smitte. Siden 2011 er M. bovis dog kommet i fokus igen på grund af alvorlige udbrud af især ledbetændelse, men...

E1AF degradation by a ubiquitin-proteasome pathway

International Nuclear Information System (INIS)

Takahashi, Akiko; Higashino, Fumihiro; Aoyagi, Mariko; Yoshida, Koichi; Itoh, Miyuki; Kobayashi, Masanobu; Totsuka, Yasunori; Kohgo, Takao; Shindoh, Masanobu

2005-01-01

E1AF is a member of the ETS family of transcription factors. In mammary tumors, overexpression of E1AF is associated with tumorigenesis, but E1AF protein has hardly been detected and its degradation mechanism is not yet clear. Here we show that E1AF protein is stabilized by treatment with the 26S protease inhibitor MG132. We found that E1AF was modified by ubiquitin through the C-terminal region and ubiquitinated E1AF aggregated in nuclear dots, and that the inhibition of proteasome-activated transcription from E1AF target promoters. These results suggest that E1AF is degraded via the ubiquitin-proteasome pathway, which has some effect on E1AF function

Depressive patienters oplevelse af at modtage ECT

DEFF Research Database (Denmark)

Jensen, Christine Damsbo

Dette studie handler om, hvordan det opleves for den voksne depressive patient at gennemgå et ECT-behandlingsforløb (electroconvulsive therapy). Formålet med projektet er dels at undersøge, hvordan processen omkring ECT-behandlingen udspiller sig og dels at undersøge patienternes oplevelse......, reaktioner og tanker omkring ECT-behandlingen. Studiet bygger på den eksisterende viden om patienters oplevelse af ECT. Metoden er feltforskning med deltagende observation og etnografisk interview. Dette suppleres af to spørgeskemaer. Der blev inkluderet 8 patienter i undersøgelsen. Analysen udspringer af...... konstruktivistisk epistemiologisk vinkel. Ved en teoristyret analyse fremkom 2 overordnede temaer: Anspændthed og tryghed. Disse temaer blev behandlet i en procesorienteret forståelse af ECT-forløbet. Denne proces bestod af: Betingelser, interaktion og konsekvenser. Diskussionen er en kritisk diskussion af fund og...

Breaks in the 45S rDNA Lead to Recombination-Mediated Loss of Repeats

NARCIS (Netherlands)

Warmerdam, Daniel O.; van den Berg, Jeroen; Medema, Rene H.

2016-01-01

rDNA repeats constitute the most heavily transcribed region in the human genome. Tumors frequently display elevated levels of recombination in rDNA, indicating that the repeats are a liability to the genomic integrity of a cell. However, little is known about how cells deal with DNA double-stranded

Overvågning af orkidéer 2000

DEFF Research Database (Denmark)

Wind, P.

resultaterne af orkidéovervågningen (Wind 2001). Hertil kommer præsentationen af projektet og dets resultater efter forløbet af de første tre år (Løjtnant 1991a) og en bearbejdning af projektets resultater for årene 1987-1995 (Wind 1997). I nærværende rapport undersøges skov-hullæbe for en eventuel sammenhæng...... mellem skudanlæggelsen udtrykt ved antallet af blomstrende og vegetative skud i et givet år og nedbørsmængder i august og september året før. Det er en udbredt antagelse at der er en sammenhæng mellem skudanlæggelse og mængden af nedbør det foregående år. Undersøgelser af skov-hullæbe populationer i...... truet og sårbar samt de to arter der er omfattet af Habitatdirektivets bilag 2. I 2000 kan det i forhold til 1999 konstateres at der i 15 bestande er optalt et øget antal skud. I 11 bestande er der noteret en nedgang i antallet af skud sammenlignet med optællingerne i 1999. Af disse er der 2 be...

Digital visualisering i udbygning af Roskilde Universitetscenter

DEFF Research Database (Denmark)

Sørensen, Nils Lykke

Rapporten beskriver tre forsøg med 3D-visualisering i forbindelse med konkurrencer vedrørende udbygning af Roskilde Universitetscenter. Første forsøg var en metode til hurtigt at skabe en række digitale modeller i højt abstraktionsniveau. Forsøget resulterede i 15 små animationer, der blev benyttet...... af dommerkomiteen til volumenstudier af bygningskonkurrencens indsendte forslag. Andet forsøg var afprøvning af et modelleringsarbejde i lavere abstraktionsniveau, som resulterede i en animation af vinderprojektet. I sidste forsøg blev de praktiske erfaringer fra de to første forsøg implementeret hos...

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

Science.gov (United States)

Kang, Jong-Soo; Lee, Byoung Yoon; Kwak, Myounghai

2017-01-01

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

Ekstraktion af æteriske olier fra oregano

DEFF Research Database (Denmark)

Ellitsgaard Jakobsen, Jens; Ankerfeldt, Dorte; Jensen, Morten Busch

2010-01-01

med keratin - Ammoniakforurening reduceres med ny teknologi - Genvinding og genanvendelse af ammoniak fra spildevand og husdyrgødning - Ginseng - en virkningsfuld medicinplante - Ekstraktion af æteriske olier fra oregano "Biotek" er udviklet med udgangspunkt i originalartikler udarbejdet af forskere...

Børn af veteraner

DEFF Research Database (Denmark)

Frederiksen, Signe; Lausten, Mette

Siden starten af 1990’erne har Danmark sendt over 30.000 soldater og andet personel på internationale missioner – langt de fleste til Eks-Jugoslavien, Afghanistan og Irak. Denne undersøgelse handler om de børn, hvis fædre har været udsendt på militære missioner i udlandet. For hvordan håndterer...... spørgsmål er fokus for undersøgelsen. Undersøgelsen bygger på en spørgeskemaundersøgelse blandt børn af veteraner på henholdsvis 7, 11 og 15 år. Undersøgelsen er gennemført for og i samarbejde med Veterancentrets Videncenter, som er en del af Forsvarsministeriets Personalestyrelse....

Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.).

Science.gov (United States)

Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling

2014-06-04

Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Tællinger af vandfugle i Danmark 1998-99

DEFF Research Database (Denmark)

Pihl, S.; Laubek, B.

1999-01-01

Denne rapport præsenterer Miljø- og Energiministeriets seks feltstationer med beskrivelse af deres historie, naturforhold og overvågningsprogram. Resultaterne af fugleobservationer i 1997 beskrives i sammenhæng med tidligere års udvikling. Desuden præsenteres resultater af tre undersøgelser af he...

Om den sociale og symbolske funktion af uddannelsesevalueringer

DEFF Research Database (Denmark)

Nørholm, Morten

Ph.d.-afhandlingen handler om evalueringer, om evalueringer af uddannelse med et fokus og perspektiv som er begrænset til en afdækning af forhold om evalueringer, til en formulering af en teori om evalueringer. I afhandlingens analyser og diskussioner anvendes teorier af Émile Durkheim, Pierre...

Delegation af lovgivningsmagt: risiko for ringere regulering?

DEFF Research Database (Denmark)

Pedersen, Morten Jarlbæk; Christensen, Geert Laier; Ravn, Jacob

2016-01-01

kortsigtetede, politiske incitamenter. Samtidig underlægges delegation ikke samme grad af kvalitetskontrolmekanismer som almindelig lovgivning; dette kunne ellers kompensere for den mere politiserede delegation. En øget brug af bekendtgørelser kan derfor betyde en stigende risiko for regulering af lavere...

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

Science.gov (United States)

Card, Daren C; Schield, Drew R; Reyes-Velasco, Jacobo; Fujita, Matthew K; Andrew, Audra L; Oyler-McCance, Sara J; Fike, Jennifer A; Tomback, Diana F; Ruggiero, Robert P; Castoe, Todd A

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

Science.gov (United States)

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthre K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Biotransformering af pyren i havbørsteormen Nereis virens

DEFF Research Database (Denmark)

Jørgensen, Anne; Giessing, Anders; Juul Rasmussen, Lene

føden og ved overførsel over epithelet. Graden af systemisk akkumulering af PAHer afhænger af optaget men ligeledes af effektiviteten af biotransformering i den pågældende organisme. N. virens er kendt for effektivt at biotransformere PAHer. I nærværende undersøgelse blev biotransformering undersøgt med......-glucuronid er den fase II metabolit der primært produceres ved biotransformering af pyren. Dette indikerer at de vigtigste enzymer i biotransformering af pyren i N. virens er CYP enzymer og glucuronosyl transferase enzymer....

Danskernes brug af nyhedsmedier 2018

DEFF Research Database (Denmark)

Schrøder, Kim Christian; Ørsten, Mark; Eberholst, Mads Kæmsgaard

Hvis der er ét begreb, der i 2018 er blevet slået fast med syvtommersøm i den offentlige debat verden over, så er det ’fake news’! Bekymringen over fænomenet er vokset eksplosivt, samtidig med at det er blevet mere og mere uklart, hvad ’fake news’ egentlig dækker over. I dette års analyse af...... brugen af nyhedsmedier sætter Reuters Institute Digital News Report, og også denne specialrapport om Danmark, analytisk fokus på ’fake news’ og kaster lys over borgernes opfattelse af fænomenet på en måde, så vi får nuancerne i det komplekse begreb med. Et andet emne, der er blevet diskuteret...... for fake news og egne oplevelser af fake news, og danskernes viden om, hvordan nyheder bliver lavet (nyheds-literacy)....

Kontrol af konventionelle våben i Europa

DEFF Research Database (Denmark)

Hoffmann, Rune; Kierulf, John; Pradhan-Blach, Flemming

Rapporten indledes med en historisk gennemgang af tilblivelsen og udviklingen af Traktat om Konventionelle Væbnede Styrker i Europa (CFE), som blev iværksat af NATO og det tidligere Warszawapagten i 1973. Traktaten fastsætter et loft for antallet af kampvogne, pansrede kampkøretøjer, artilleripje...

Kommentarer til love og ændringer af love

DEFF Research Database (Denmark)

Møgelvang-Hansen, Peter

2002-01-01

folkeoplysende foreningsarbejde og Folkeuniversitetet (folkeoplysningsloven) og ophævelse af lov om daghøjskoler m.v. og lov om den fri ungdomduddannelse samt ændring af lov om refusion af udgifter til uddannelse i forbindelse med aktivering m.m. samt ændring af forskellige love (Reform for daghøjskolerne...

Myotonin protein-kinase [AGC]n trinucleotide repeat in seven nonhuman primates

Energy Technology Data Exchange (ETDEWEB)

Novelli, G.; Sineo, L.; Pontieri, E. [Catholic Univ. of Rome (Italy)]|[Univ. of Milan (Italy)]|[Univ. Florence (Italy)] [and others

1994-09-01

Myotonic dystrophy (DM) is due to a genomic instability of a trinucleotide [AGC]n motif, located at the 3{prime} UTR region of a protein-kinase gene (myotonin protein kinase, MT-PK). The [AGC] repeat is meiotically and mitotically unstable, and it is directly related to the manifestations of the disorder. Although a gene dosage effect of the MT-PK has been demonstrated n DM muscle, the mechanism(s) by which the intragenic repeat expansion leads to disease is largely unknown. This non-standard mutational event could reflect an evolutionary mechanism widespread among animal genomes. We have isolated and sequenced the complete 3{prime}UTR region of the MT-PK gene in seven primates (macaque, orangutan, gorilla, chimpanzee, gibbon, owl monkey, saimiri), and examined by comparative sequence nucleotide analysis the [AGC]n intragenic repeat and the surrounding nucleotides. The genomic organization, including the [AGC]n repeat structure, was conserved in all examined species, excluding the gibbon (Hylobates agilis), in which the [AGC]n upstream sequence (GGAA) is replaced by a GA dinucleotide. The number of [AGC]n in the examined species ranged between 7 (gorilla) and 13 repeats (owl monkeys), with a polymorphism informative content (PIC) similar to that observed in humans. These results indicate that the 3{prime}UTR [AGC] repeat within the MT-PK gene is evolutionarily conserved, supporting that this region has important regulatory functions.

Bakteriesensor til on-line identifikation/bestemmelse af mikrobiel drikkevandskvalitet

DEFF Research Database (Denmark)

Bentien, Anders; Tilsted Mogensen, Claus; Østergaard, Else-Marie

Over det meste af verden defineres den mikrobielle drikkevandskvalitet primært på baggrund af grænseværdier for E. coli, coliforme bakterier og kimtal. Anvendelsen af den totale bakteriekoncentration til bestemmelse af mikrobiel drikkevandskvalitet er (af historiske årsager) ikke udbredt og primært...

Genome Architecture and Its Roles in Human Copy Number Variation

Directory of Open Access Journals (Sweden)

Lu Chen

2014-12-01

Full Text Available Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs, are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.

Genlyden af et nej

DEFF Research Database (Denmark)

Östman, Lars

2011-01-01

Europa og den vestlige verden er ramt af en økonomisk krise. Det er en krise, der er anderledes, end den vi har været vant til fx fra 1980'erne.......Europa og den vestlige verden er ramt af en økonomisk krise. Det er en krise, der er anderledes, end den vi har været vant til fx fra 1980'erne....

Optisk scanning af spørgeskemaer

DEFF Research Database (Denmark)

Paulsen, Aksel

/ 1000 felter= 0.370 (95% CI: 0.160-0.729), (p= 0.020)). Der var ingen statistisk forskel mellem optisk scanning (fejl/ 1000 felter= 0.046 (95% CI: 0.001-0.258)) og manuel dobbelt indtastning (p=1.000). Konklusioner: Optisk scanning er et godt alternativ til manuel dobbelt indtastning for spørgeskema med......Formål og baggrund: Patient rapporterede outcomes i form af spørgeskemaer bruges i øgende grad i sundhedssektoren både i klinisk praksis og forskning. Ofte bruges spørgeskemaer i papirformat. Manuel dobbelt indtastning er defineret som guld standard for overføring af data til et elektronisk format......, men processen er tidkrævende. Optisk scanning af spørgeskemaer med automatisk registrering af svar kan være et alternativ, men videre validering af metoden er nødvendig. Design: 200 patienter blev tilfældigt udvalgt fra en kohorte på 5777 patienter der tidligere havde svaret på to forskellige...

En analyse af potentialet for salg af fødevarer gennem Internettet i Danmark og England

DEFF Research Database (Denmark)

Ramus, Kim Bjarne

2001-01-01

I Kim Ramus ph.d.-projekt gennemføres en undersøgelse af danske og britiske forbrugeres holdninger og præferencer til handel med fødevarer på Internettet, hvor formålet er at finde potentialet for salg af fødevarer online. Internettet er ganske udbredt i begge lande, men England er dog et godt st...... stykke foran Danmark med supermarkedskæden Tesco i spidsen, når det gælder salg af fødevarer. I Danmark er der endnu ingen landsdækkende kæder, som for alvor er gået i gang med at sælge fødevarer online.......I Kim Ramus ph.d.-projekt gennemføres en undersøgelse af danske og britiske forbrugeres holdninger og præferencer til handel med fødevarer på Internettet, hvor formålet er at finde potentialet for salg af fødevarer online. Internettet er ganske udbredt i begge lande, men England er dog et godt...

Nye ledelsesudfordringer i forebyggelse af stress i videnarbejdet

DEFF Research Database (Denmark)

Andersen, Vibeke; Ipsen, Christine; Mogensen, Mette

arbejdssituation og muligheder for forebyggelse af arbejdsrelateret stress i vidensarbejdet. – Et kvalitaivt studie af arbejdsrelateret stress i vidensarbejdet. Lyngby, The Technical University of Denmark. Kärreman, Dan, Stefan Svenningson and Mats Alvesson (2003): The Return of the Machine Bureaucracy? Management......Afsættet for projektet ”Forebyggelse af stress i videnarbejdet – mellem begejstring og belastning” er, at der er behov for en ny forståelse af stress i det moderne arbejdsliv, for at kunne arbejde med stressforebyggelse blandt videnarbejdere. I dette paper tager vi udgangspunkt i begrebet...... mangetydighed/ambiguity som en karakteristik af videnarbejdet, da det stiller nogle helt nye udfordringer til hvordan ledelse af videnarbejdet skal foregå, når målet er at forebygge arbejdsrelateret stress. Vi karakteriserer videnarbejdet som mangetydigt og som Alvesson (2004) påpeger, udgør dilemmaerne i...

Nyttigt bidrag til professionalisering af revisionsudvalg

DEFF Research Database (Denmark)

Thomsen, Steen

2009-01-01

Anmeldelse af: KPMG. 2009, Audit Committee Institute. Revisionsudvalg i Praksis. 2. reviderede udgave.......Anmeldelse af: KPMG. 2009, Audit Committee Institute. Revisionsudvalg i Praksis. 2. reviderede udgave....

DVD anmeldelse - En Verden af Lyd og Musik

DEFF Research Database (Denmark)

Holck, Ulla

2006-01-01

Anmeldelse af DVD-udgivelse af Claus Bang (2005): En Verden af Lyd og Musik. Musikterapi for døve, hørehæmmede og multihandicappede børn og unge. Al tale med undertekst eller tegnsprogstolkning. DVD-boks med 3 stk. dobbeltlag DVD beregnet til afspilning på PC. Udgivet af Musikterapi-foreningen En...

En kvantitativ metode til analyse af radio

Directory of Open Access Journals (Sweden)

Christine Lejre

2014-06-01

Full Text Available I den danske såvel som den internationale radiolitteratur er bud på metoder til analyse af radiomediet sparsomme. Det skyldes formentlig, at radiomediet er svært at analysere, fordi det er et medie, der ikke er visualiseret i form af billeder eller understøttet af printet tekst. Denne artikel har til formål at beskrive en ny kvantitativ metode til analyse af radio, der tager særligt hensyn til radiomediets modalitet – lyd struktureret som et lineært forløb i tid. Metoden understøtter dermed både radiomediet som et medie i tid og som et blindt medie. Metoden er udviklet i forbindelse med en komparativ analyse af kulturprogrammer på P1 og Radio24syv lavet for Danmarks Radio. Artiklen peger på, at metoden er velegnet til analyse af ikke kun radio, men også andre medieplatforme samt forskellige journalistiske stofområder.

Degradation of AF1Q by chaperone-mediated autophagy

International Nuclear Information System (INIS)

Li, Peng; Ji, Min; Lu, Fei; Zhang, Jingru; Li, Huanjie; Cui, Taixing; Li Wang, Xing; Tang, Dongqi; Ji, Chunyan

2014-01-01

AF1Q, a mixed lineage leukemia gene fusion partner, is identified as a poor prognostic biomarker for pediatric acute myeloid leukemia (AML), adult AML with normal cytogenetic and adult myelodysplastic syndrome. AF1Q is highly regulated during hematopoietic progenitor differentiation and development but its regulatory mechanism has not been defined clearly. In the present study, we used pharmacological and genetic approaches to influence chaperone-mediated autophagy (CMA) and explored the degradation mechanism of AF1Q. Pharmacological inhibitors of lysosomal degradation, such as chloroquine, increased AF1Q levels, whereas activators of CMA, including 6-aminonicotinamide and nutrient starvation, decreased AF1Q levels. AF1Q interacts with HSPA8 and LAMP-2A, which are core components of the CMA machinery. Knockdown of HSPA8 or LAMP-2A increased AF1Q protein levels, whereas overexpression showed the opposite effect. Using an amino acid deletion AF1Q mutation plasmid, we identified that AF1Q had a KFERQ-like motif which was recognized by HSPA8 for CMA-dependent proteolysis. In conclusion, we demonstrate for the first time that AF1Q can be degraded in lysosomes by CMA. - Highlights: • Chaperone-mediated autophagy (CMA) is involved in the degradation of AF1Q. • Macroautophagy does not contribute to the AF1Q degradation. • AF1Q has a KFERQ-like motif that is recognized by CMA core components

Degradation of AF1Q by chaperone-mediated autophagy

Energy Technology Data Exchange (ETDEWEB)

Li, Peng; Ji, Min; Lu, Fei; Zhang, Jingru [Department of Hematology, Key Laboratory of Cardiovascular Remodeling and Function Research, Qilu Hospital, Shandong University, Jinan 250012 (China); Li, Huanjie; Cui, Taixing; Li Wang, Xing [Research Center for Cell Therapy, Key Laboratory of Cardiovascular Remodeling and Function Research, Qilu Hospital, Shandong University, Jinan 250012 (China); Tang, Dongqi, E-mail: tangdq@sdu.edu.cn [Research Center for Cell Therapy, Key Laboratory of Cardiovascular Remodeling and Function Research, Qilu Hospital, Shandong University, Jinan 250012 (China); Center for Stem Cell and Regenerative Medicine, The Second Hospital of Shandong University, Jinan 250033 (China); Ji, Chunyan, E-mail: jichunyan@sdu.edu.cn [Department of Hematology, Key Laboratory of Cardiovascular Remodeling and Function Research, Qilu Hospital, Shandong University, Jinan 250012 (China)

2014-09-10

AF1Q, a mixed lineage leukemia gene fusion partner, is identified as a poor prognostic biomarker for pediatric acute myeloid leukemia (AML), adult AML with normal cytogenetic and adult myelodysplastic syndrome. AF1Q is highly regulated during hematopoietic progenitor differentiation and development but its regulatory mechanism has not been defined clearly. In the present study, we used pharmacological and genetic approaches to influence chaperone-mediated autophagy (CMA) and explored the degradation mechanism of AF1Q. Pharmacological inhibitors of lysosomal degradation, such as chloroquine, increased AF1Q levels, whereas activators of CMA, including 6-aminonicotinamide and nutrient starvation, decreased AF1Q levels. AF1Q interacts with HSPA8 and LAMP-2A, which are core components of the CMA machinery. Knockdown of HSPA8 or LAMP-2A increased AF1Q protein levels, whereas overexpression showed the opposite effect. Using an amino acid deletion AF1Q mutation plasmid, we identified that AF1Q had a KFERQ-like motif which was recognized by HSPA8 for CMA-dependent proteolysis. In conclusion, we demonstrate for the first time that AF1Q can be degraded in lysosomes by CMA. - Highlights: • Chaperone-mediated autophagy (CMA) is involved in the degradation of AF1Q. • Macroautophagy does not contribute to the AF1Q degradation. • AF1Q has a KFERQ-like motif that is recognized by CMA core components.

SSRscanner: a program for reporting distribution and exact location of simple sequence repeats.

Science.gov (United States)

Anwar, Tamanna; Khan, Asad U

2006-02-20

Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both prokaryotes and eukaryotes. They are distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They are also found at longer lengths (> 6 repeating units) of tracts. Most of the computer programs that find SSRs do not report its exact position. A computer program SSRscanner was written to find out distribution, frequency and exact location of each SSR in the genome. SSRscanner is user friendly. It can search repeats of any length and produce outputs with their exact position on chromosome and their frequency of occurrence in the sequence. This program has been written in PERL and is freely available for non-commercial users by request from the authors. Please contact the authors by E-mail: huzzi99@hotmail.com.

Produktudvikling af fødevarer med Quality Function Deployment

DEFF Research Database (Denmark)

Bech, Anne C.

1998-01-01

Produktudvikling af fødevarer stiller stadig større krav til virksomhedernes kompetencer. QFD filosofien kan bidrage til at skabe en fælles forståelse af grundlaget for udvikling af nye produkter. Udgangspunktet er en forståelse af forbrugernes behov i relation til virksomhedens muligheder...... konkurrentprodukter. Efterfølgende faser handler om at generere forskellige mulige løsninger, inden der træffes valg af løsningsalternativ. Anvendelse af QFD modellen for produktudvikling betyder, at forbrugernes behov er centrale i hele produktudviklingsforløbet, samt at det udviklede produkt sigter mod at opfylde...... væsentlige identificerede behov set fra forbrugernes synspunkt. At virksomheden ser implementering af QFD som en investering, medarbejdernes commitment og målrettet projekt, er væsentlig for en succesfuld implementering af QFD til produktudvikling. QFD tankegangen illustreres med et eksempel på udvikling af...

Innovation af innovation

DEFF Research Database (Denmark)

Harste, Gorm

2009-01-01

, at innovation af innovationen forsøges gennemført på en måde, hvor tiden kræves at forholde sig til sin egen tidslighed i form af fremtid, nutid, fortid og ikke mindst i form af samtidighed. I tiden skal vi iagttage, hvordan vi iagttager tiden. Vi dobbelt-koder tiden på samme måde, som forskning forsker i...... organisationssystemerne. De to typer systemer kan noget helt bestemt med fænomenet tid. De kan synkronisere. Analyseres organisationssystemer ser vi, imidlertid at innovation kræver ro. Stærkt innovative systemer er militærsystemet og kunstsystemet, der også inddrages, og hvor vi ser paradokset mellem innovation og...... involution. Tid er med et medium og ikke et lufttomt rum. Tid er end ikke en gasart, men udgør et solidt fluidum, som samfundet bader i og flyder i, konstant i bevægelse. Reformer forudsætter former, og innovation forudsætter involution. Kun sådan muliggøres evolution....

Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

Directory of Open Access Journals (Sweden)

Komivi Dossa

2017-08-01

Full Text Available The sequencing of the full nuclear genome of sesame (Sesamum indicum L. provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78% were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/, which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

I Frans af Assisis fodspor

DEFF Research Database (Denmark)

Bonde, Lisbeth

2015-01-01

En fodrejse fra Assisi til Rom i Frans af Assisis fodspor sætter gang i tankerne og giver anledning til nye ideer......En fodrejse fra Assisi til Rom i Frans af Assisis fodspor sætter gang i tankerne og giver anledning til nye ideer...

Anbefalinger til organisering af uddannelserne

DEFF Research Database (Denmark)

Andersen, Lars; Andersen, Lars Døvling; Hornemann, Birte C.

2009-01-01

Notatet sammenfatter de diskussioner, som det af fakulteterne nedsatte udvalg vedrørende nye undervisnings- og eksamensformer har haft, og de anbefalinger til en omlægning af vores uddannelsessystem, som udvalget har valgt at give. Notatet er samtidig en begyndelse på en erfaringsudveksling om ny...

Registrering og Benchmarking af Modus 2 Forskning

DEFF Research Database (Denmark)

Duus, Henrik Johannsen; Jørgensen, Jens E.

2004-01-01

Fremvæksten af modus 2 forskning stiller krav om en revurdering af højere læreanstalters evaluerings- og meriteringspraksis. Den endimensionale prioritering af modus 1 forskning såvel som dennes ligeså endimensionale evaluering via publikationer må afvises som utidssvarende. Som en konsekvens her...

NIR: optimerer produktionen af gammeldags modnede sild

DEFF Research Database (Denmark)

Svensson, T.; Bro, Rasmus; Nielsen, Henrik Hauch

2005-01-01

Måling med nærinfrarødt (NIR) lys er et godt supplement til de nuværende metoder til at følge modningen af sild saltede i tønder. Det viser resultaterne af et forskningsprojekt udført i samarbejde mellem Lykkeberg A/S, Danmarks Fiskeriundersøgelser og Den Kgl Veterinær- og Landbohøjskole. Ved hjælp...... af avanceret matematik er det nemt og hurtigt at bestemme modningsgraden af sild direkte fra en NIR måling....

Undersøgelse af udviklingen i maksimale vandstande i den østligste del af Limfjorden Aalborg – Hals

DEFF Research Database (Denmark)

Burcharth, Hans Falk; Røge, Mads Sønderstrup

Udviklingen i maksimalvandstande i den veslige del af Limfjorden har påkaldt sig stor interesse i forbindelse med diskussionen om stigende oversvømmelsesfrekvens relateret til en eventuel klimaændring. Formålet med nærværende undersøgelse er at belyse udviklingen i maksimalvandstande i den østlig...... østligste del af Limfjorden på strækningen fra Aalborg til Hals, en strækning hvor der er lavtliggende områder på begge sider af fjorden. Målinger af højvandstande i Aalborg er foretaget siden 1944 og i Hals siden april 2002....

Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis.

Science.gov (United States)

Fu, Jianmin; Liu, Huimin; Hu, Jingjing; Liang, Yuqin; Liang, Jinjun; Wuyun, Tana; Tan, Xiaofeng

2016-01-01

Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros 'Jinzaoshi' were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. 'Jinzaoshi', support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis.

Directory of Open Access Journals (Sweden)

Jianmin Fu

Full Text Available Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros 'Jinzaoshi' were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp in the cp genome of D. 'Jinzaoshi', support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

Directory of Open Access Journals (Sweden)

Perumal Sampath

Full Text Available Miniature inverted-repeat transposable elements (MITEs are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5 were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1 were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.

Arbejdsmiljøet ved udbud af renovationsarbejde

DEFF Research Database (Denmark)

Busck, Ole Gunni

Forfatteren gennemførte 2003-2005 en undersøgelse for Branchearbejdsmiljådet for transport af danske kommuners praksis i forbindelse med udbud og udlicitering af renovationsopgaver. Formålet var at kortlægge og analysere erfaringerne med varetagelse af arbejdsmiljøhensyn i kommunernes udbud og dr...

Bone marrow mesenchymal stem cells from infants with MLL-AF4+ acute leukemia harbor and express the MLL-AF4 fusion gene

Science.gov (United States)

Catalina, Purificación; Rodríguez, René; Melen, Gustavo J.; Bueno, Clara; Arriero, Mar; García-Sánchez, Félix; Lassaletta, Alvaro; García-Sanz, Ramón

2009-01-01

MLL-AF4 fusion is a hallmark genetic abnormality in infant B-acute lymphoblastic leukemia (B-ALL) known to arise in utero. The cellular origin of leukemic fusion genes during human development is difficult to ascertain. The bone marrow (BM) microenvironment plays an important role in the pathogenesis of several hematological malignances. BM mesenchymal stem cells (BM-MSC) from 38 children diagnosed with cytogenetically different acute leukemias were screened for leukemic fusion genes. Fusion genes were absent in BM-MSCs of childhood leukemias carrying TEL-AML1, BCR-ABL, AML1-ETO, MLL-AF9, MLL-AF10, MLL-ENL or hyperdiploidy. However, MLL-AF4 was detected and expressed in BM-MSCs from all cases of MLL-AF4+ B-ALL. Unlike leukemic blasts, MLL-AF4+ BM-MSCs did not display monoclonal Ig gene rearrangements. Endogenous or ectopic expression of MLL-AF4 exerted no effect on MSC culture homeostasis. These findings suggest that MSCs may be in part tumor-related, highlighting an unrecognized role of the BM milieu on the pathogenesis of MLL-AF4+ B-ALL. MLL-AF4 itself is not sufficient for MSC transformation and the expression of MLL-AF4 in MSCs is compatible with a mesenchymal phenotype, suggesting a differential impact in the hematopoietic system and mesenchyme. The absence of monoclonal rearrangements in MLL-AF4+ BM-MSCs precludes the possibility of cellular plasticity or de-differentiation of B-ALL blasts and suggests that MLL-AF4 might arise in a population of prehematopoietic precursors. PMID:19995953

Udvikling af pille-doserings teknologi

DEFF Research Database (Denmark)

Brændgaard, Rikke; Churchill, Inge-Lise; Bolvig Poulsen, Søren

2015-01-01

Lab. X har i samarbejde med Brønderslev Kommune og Firmaet LT Automation i et idegenereringsforløb omhandlende viden om "pillens vej", indhentet viden om udfordringer og barrierer i forbindelse med udlevering af medicin fra apoteket til den afslutningsvis indtages af borgeren. Formålet med unders...

Delevalueringer af teknologi og velfærd i 4skit

DEFF Research Database (Denmark)

Miller, Tanja; Haslam, Trine Lolk; Abildgaard, Katrine Copmann

Som et led i evaluering af satspuljeprojekt i regi af AMU - Aalborg har CEPRA udført en række delevaluering af udvalgte projekter......Som et led i evaluering af satspuljeprojekt i regi af AMU - Aalborg har CEPRA udført en række delevaluering af udvalgte projekter...

Frisættelse af fødderne

DEFF Research Database (Denmark)

Kirkeby, Ole Fogh

2013-01-01

Kropskultur. Amerikansk journalist og forfatter hævder, at løb - og fødder - giver adgang til livets mening. Anmeldelse af: Christoffer McDougall: Født til løb. Oversat af Jacob Giese efter Born to Run. Forlaget Turbulenz, 400 sider.......Kropskultur. Amerikansk journalist og forfatter hævder, at løb - og fødder - giver adgang til livets mening. Anmeldelse af: Christoffer McDougall: Født til løb. Oversat af Jacob Giese efter Born to Run. Forlaget Turbulenz, 400 sider....

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

Directory of Open Access Journals (Sweden)

Glass John I

2010-07-01

Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

Science.gov (United States)

Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

1997-12-01

Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R.

Distribution af video – lige meget hvordan?

Directory of Open Access Journals (Sweden)

Diba Markus

2009-04-01

Full Text Available Artiklen omhandler løsninger til distribution af video og de faktorer, der kan være udslagsgivende, når man som underviser eller universitet skal vælge, hvilken man vil gøre brug af. De kommercielle løsninger såsom YouTube m.fl. er kendt af de fleste. Hvad færre måske ved er, at der eksisterer alternativer. På europæisk plan har en række institutioner og forskningsnet, herunder det danske, således valgt at lave deres egne løsninger. Der er afgørende forskelle i disse hhv. kommercielle og ikke-kommercielle videodistributionstjenesters tilgange til problemstillinger vedrørende adgangsbegrænsning, ophavsret, metadatering og bevaring samt kvalitetssikring af indhold - forskelle, der for en stor del udspringer af deres respektive opdrag og muligheder for brugerautentificering. Kun de færreste af alternativerne kan bruges af danske studerende og universitetsansatte. Som der argumenteres for i artiklen, er disse problemstillinger imidlertid vigtig baggrundsinformation, når der skal tages stilling til, hvordan man bedst distribuerer videoressourcer. I artiklen beskrives overordnede fællestræk ved hhv. de kommercielle og de ikke-kommercielle distributionsløsninger, og de helt grundliggende forskelle mellem dem diskuteres.

Benchmarking af udsættelser i kommunerne

DEFF Research Database (Denmark)

Christensen, Gunvor; Jeppesen, Anders Gade; Markwardt, Kristoffer

2015-01-01

nuværende tidspunkt stadig mangler relevante forhold i benchmarking-modellen. Eksempelvis antallet af stofmisbrugere, antallet af borgere med psykiatriske indlæggelser samt forekomsten af projekter med henblik på at forebygge udsættelser (fx gældsrådgivning). Disse data er først tilgængelige i 2015....

Brugen af personas hos danske virksomheder - 2012/13

DEFF Research Database (Denmark)

Nielsen, Lene; Nielsen, Kira Storgaard

2013-01-01

Denne rapport er skrevet på baggrund af et projekt initieret og finansieret af InfinIT – Innovationsnetværket for IT. Formålet med projektet er at undersøge hvorledes personas i dag etableres, kommunikeres, anvendes og vedligeholdes i forskellige typer af virksomheder samt etablere et opdateret sæt...... af anbefalinger for deres anvendelse. Virksomheders erfaringer med personas vil blive adresseret fra to forskellige vinkler:. Fokus vil bl.a. være på hvordan personas udvikles og vedligeholdes, om og hvordan de bruges, og hvad de bruges til. Personas er beskrivelser af fiktive brugere og bruges i...... designprocesser. Beskrivelserne er skabt på baggrund af data indsamlet om slutbrugerne. En samling af personas, som regel mellem 2 og 6 beskrivelser, vil i denne rapport benævnes et personasæt. Når personabeskrivelserne indgår i designprocessen bruges de til at få ideer til og beskrive, hvordan brugerne vil...

Svingningsundersøgelse af betonskorsten

DEFF Research Database (Denmark)

Dalgaard, Lars-Bo; Kristensen, Peter

Dette projekt omhandler en teoretisk og en eksperimentel undersøgelse af svingningsforholdene for en 110 meter høj betonskorsten. Skorstenen tilhører I/S Nordjyllands elektricitetsforsyning(NEFO) og er opført i forbindelse med en udbygning af Vendsysselværket med en sektion II med en turbine effe...... på 300 MW. Vendsysselværkets sektion I og II er afbilledet i figur 1.1.1, hvor værket er set fra nordøst med den undersøgte skorsten til højre i billedet. Skorstenen er projekteret af firmaet Rambøll og Hannemann og taget i brug i foråret 1977....

Værdisætning af natur- og kulturgoder. Et metodestudie af betydningen for ændringer i skala og betalingsformat

DEFF Research Database (Denmark)

Hasler, Berit; Jacobsen, Jette Bredahl; Lundhede, Thomas

aggregering og skalaproblemer. Denne rapport beskriver og tester tre af disse problemstillinger. Testene er udført som delundersøgelser ("splitsamples"), hvor det samme spørgeskemamateriale anvendes og ændres separat for hvert split. En undersøgelse af betalingsviljen for restaurering og gennemførelse af et...

Masser af information uden betydning

DEFF Research Database (Denmark)

Brier, Søren

en diskussion af informationsteorien i Tor Nørretranders "Mærk verden" og en skitse til et alternativ baseret på anden ordens kybernetik og semiotik......en diskussion af informationsteorien i Tor Nørretranders "Mærk verden" og en skitse til et alternativ baseret på anden ordens kybernetik og semiotik...

Effekten af absolut kumulation

DEFF Research Database (Denmark)

Kyvsgaard, Britta; Klement, Christian

2012-01-01

Som led i finansloven for 2011 blev regeringen og forligspartierne enige om at undersøge reglerne om strafudmåling ved samtidig pådømmelse af flere kriminelle forhold og i forbindelse hermed vurdere konsekvenserne af at ændre de gældende regler i forhold til kapacitetsbehovet i Kriminalforsorgens...... samlet bødesum ved en absolut kumulation i forhold til en modereret kumulation, som nu er gældende....

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

Directory of Open Access Journals (Sweden)

Charlotte Rehm

Full Text Available In prokaryotes simple sequence repeats (SSRs with unit sizes of 1-5 nucleotides (nt are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4 structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc, Xanthomonas axonopodis pv. citri str. 306 (Xac, and Nostoc sp. strain PCC7120 (Ana. In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

Science.gov (United States)

Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Portræt af litteraturkritikeren som ungt menneske

DEFF Research Database (Denmark)

Schatz-Jakobsen, Claus

2004-01-01

Artiklen præsenterer den amerikanske litteraturkritiker Geoffrey Hartmans tidlige forfatterskab og fremdrager dets selvbiografiske undertekst som nødvendig effekt af den unge Hartmans fascination af den engelske romantiker William Wordsworths forfatterskab.......Artiklen præsenterer den amerikanske litteraturkritiker Geoffrey Hartmans tidlige forfatterskab og fremdrager dets selvbiografiske undertekst som nødvendig effekt af den unge Hartmans fascination af den engelske romantiker William Wordsworths forfatterskab....

Uddrag af Ph.d.-afhandlingen Den groteske modernisme

DEFF Research Database (Denmark)

Lübker, Henrik

2011-01-01

Om forholdet mellem "det groteske" og "den groteske modernisme" eksemplificeret i en læsning af E.A. Poes "The Fall of the House of Usher" og flere af Francis Bacons malerier.......Om forholdet mellem "det groteske" og "den groteske modernisme" eksemplificeret i en læsning af E.A. Poes "The Fall of the House of Usher" og flere af Francis Bacons malerier....

Virkelighedsflugt og masser af sex

DEFF Research Database (Denmark)

Lorentzen, Rasmus Fink

2011-01-01

I artiklen laves en læsning af ungdomsromanen "6" (2010) af Ronni Andersen. Dernæst udfoldes en række litteraturpædagogiske forslag tilen undervisning i romanen i skolens ældste klasser. Arbejdsforslagene er baseret på en kompetencetilgang til danskfaget og rummer fire værksteder hvor eleverne sk...

Forført af hjernen?

DEFF Research Database (Denmark)

Lieberoth, Andreas

2013-01-01

Blandingen af offentlig interesse, gode mediehistorier og smarte sælgere har ført til sejlivede neuromyter, der ikke bare distraherer almindelige mennesker, men også fører til udbredte misforståelser blandt professionelle som lærere og plejepersonale. I bedste fald leder neuromyter til spild af t...

Æstetiseringen af forbruget: En undersøgelse af to udstillinger, hvor branding er kunst - og kunst er branding

DEFF Research Database (Denmark)

Hermansen, Judy

2008-01-01

Æstetiseringen af hverdagen er ét af de helt centrale træk ved det postmoderne forbrugersamfund. Og denne nedbrydning af grænserne mellem kunst og forbrug er det også vigtigt for marketingteorien at udforske. Artiklen analyserer to (kunst?)udstillinger i England, som på hver sin måde tematiserer,...

Breaks in the 45S rDNA Lead to Recombination-Mediated Loss of Repeats

OpenAIRE

Warmerdam, Daniël O.; van den Berg, Jeroen; Medema, René H.

2016-01-01

rDNA repeats constitute the most heavily transcribed region in the human genome. Tumors frequently display elevated levels of recombination in rDNA, indicating that the repeats are a liability to the genomic integrity of a cell. However, little is known about how cells deal with DNA double-stranded breaks in rDNA. Using selective endonucleases, we show that human cells are highly sensitive to breaks in 45S but not the 5S rDNA repeats. We find that homologous recombination inhibits repair of b...

Forhastet regulering af de store

DEFF Research Database (Denmark)

Thomsen, Steen

2013-01-01

Christiansborg gennemfører sandsynligvis en markant skærpet regulering af de store finansielle virksomheder. Det vil virke kontraktivt og medvirke til erhvervslivets kredittørke.......Christiansborg gennemfører sandsynligvis en markant skærpet regulering af de store finansielle virksomheder. Det vil virke kontraktivt og medvirke til erhvervslivets kredittørke....

Ledelse af forandringer i folkeskolen

DEFF Research Database (Denmark)

Kjer, Mikkel; Rosdahl, Anders

2016-01-01

Dette notat bygger på kvalitative interview på seks folkeskoler i efteråret 2015. Skolerne ligger i forskellige egne af landet og i landområder, mindre og store byer. Skolerne er af forskellig størrelse, og deres elevgrundlag, dvs. forældrenes sociale baggrund, varierer også. Notatet bygger primæ...

Håndteringen af musikfiler i krydsfeltet mellem downloading og streaming

DEFF Research Database (Denmark)

Ægidius, Andreas Lenander

remedieringen af musikfilen som stream ud fra den konceptuelle model for et kulturkredsløb, hvori et kulturelt artefakts betydning dannes (Gay mfl., 2013). Kommodificeringer og rekommodificering af musikfiler og håndteringer bliver herved sammenkædet med remediering og konvergens (Bolter & Grusin, 2000; Jenkins...... kommodificerer streamrip med fokus på at gøre filkonverteringer lette at anvende. Sidstnævnte viser jeg med analyse af brugen af software, der ripper musik fra YouTube. Jeg finder modstridende artikulationer af lydkvalitet blandt de tre grupper. Formatet og repræsentationen i diverse platformes brugerflader er...... digitale online musikbrug. Et konkret eksempel herpå er det sammensurium af transkodninger, som følger af YouTubes repræsentation, regulering, produktion af stream og lytternes efterfølgende brug, herunder streamrip. Dette sammensurium af transkodninger betegner jeg som en fonografisk effekt af YouTube...

Miljøoptimering af afvaskning ved tryk med vandfortyndbar flexotrykfarve

DEFF Research Database (Denmark)

Larsen, Henrik Fred; Helweg, Christian; Pedersen, Anne Rathmann

Rapporten beskriver praksis ved afvaskning af vandfortyndbare flexotrykfarver i emballageindustrien og anviser muligheder for indførelse af renere teknologi til reduktion af spildevandsbelastningen. Anbefalingerne omfatter a) udformning af farveværker med henblik på effektiv tømning af farve og e...

Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp).

Science.gov (United States)

Garcia, S A L; Van der Lee, T A J; Ferreira, C F; Te Lintel Hekkert, B; Zapater, M-F; Goodwin, S B; Guzmán, M; Kema, G H J; Souza, M T

2010-11-09

We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units. Five VNTR markers showing multiple alleles were validated with a reference set of isolates from different parts of the world and a population from a banana plantation in Costa Rica. Polymorphism information content values varied from 0.6414 to 0.7544 for the reference set and from 0.0400 and 0.7373 for the population set. Eighty percent of the polymorphism information content values were above 0.60, indicating that the markers are highly informative. These markers allowed robust scoring of agarose gels and proved to be useful for variability and population genetics studies. In conclusion, the strategy we developed to identify and validate VNTR markers is an efficient means to incorporate markers that can be used for fungicide resistance management and to develop breeding strategies to control banana black leaf streak disease. This is the first report of VNTR-minisatellites from the M. fijiensis genome sequence.

Udkantsdanmark: Avisernes (med)produktion af Nordjyllands territorielle stigma

DEFF Research Database (Denmark)

Pristed Nielsen, Helene; Christensen, Sascha

2013-01-01

Artiklen undersøger hvordan Region Nordjylland (NJ) beskrives i medierne og hvordan diskursen om Udkanten dominerer avisernes fremstilling af regionen . Baggrunden herfor er en interesse for social ulighed, og i denne sammenhæng Wacquants begreb om territorielt stigma (1996, 2007). Wacquant føjer...... stigma. I Gunnar Lind Haase Svendsens studie af italesættelsen af ’udkanten’ fra 1996-2011 ses fx en gennem de seneste år stigende anvendelse af termer som ’den rådne banan’ og ’Udkantsdanmark’ i medierne (Svendsen 2013: 12). Dette stigma forbindes med flere dele af Danmark (se bl.a. Arbejderbevægelsens...

Vidensledelse og den sociale dimension i deling af viden

DEFF Research Database (Denmark)

Lauring, Jakob

2004-01-01

imidlertid et alternativt syn på viden som i højere grad inddrager den sociale dimension ved vidensdeling - den socialkonstruktivistiske opfattelse. I denne artikel vil jeg beskæftige mig med den socialkonstruktivistiske opfattelse af viden og beskrive, hvorledes denne synsvinkel kan rette fokus mod nogle...... meget væsentlige problemstillinger ved organisatorisk adfærd, som man ofte kommer til at ignorere, hvis man i for høj grad baserer ledelsen på en funktionalistisk opfattelse af viden. Delingen af viden er en aktuel udfordring for anvendelse af viden i forretningssammenhæng. Det er hovedsageligt det, som...... gør vidensbegrebet interessant i forhold til ledelse af virksomheder. - Fokus på de sociale barrierer for deling af viden Jeg vil i det kommende illustrere, hvilke betydninger den sociale dimension i deling af viden kan have for videnledelse. Det vil jeg gøre gennem beskrivelser af to forskellige...

Analyse og design af produktionssystemer

DEFF Research Database (Denmark)

Johansen, John; Riis, Jens Ove; Arlbjørn, Jan Stentoft

lys, men til vores store glæde og overraskelse har vi erfaret, at dele af materialet stadigvæk er anvendt på en del ingeniør- og økonomiuddannelser i Danmark. Nogle af de tanker og metoder som blev udviklet i ViPSprogrammet har overlevet og opfattes fortsat som relevante og anvendelige også til...

Effektivitet af naturligt drevne radontiltag året rundt

DEFF Research Database (Denmark)

Haker Høegh, Britt; Rasmussen, Torben Valdbjørn

Denne rapport omhandler projektet Effektivitet af naturligt drevne radontiltag året rundt. Projektet er et spireprojekt finansieret af Innovationsnetværket InnoBYG og Forsknings- og Innovationsstyrelsen. Projektet er gennemført af Teknologisk Institut i samarbejde med Statens Byggeforskningsinsti...

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

Science.gov (United States)

Yao, Xiaohong; Tang, Ping; Li, Zuozhou; Li, Dawei; Liu, Yifei; Huang, Hongwen

2015-01-01

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

Produktion og afsætning af nicheprodukter

DEFF Research Database (Denmark)

Jensen, Jonas Baungaard; Hansen, Henning Otte

2016-01-01

. Egnsmærker opnår generelt en merpris på 20-30 pct. Det er dog bemærkelsesværdigt, at landmanden “kun” har omkring 13 pct. af forbrugerkronen på Lammefjords-kartofler. Her er der tale om unikke produkter, hvor det i praksis udelukkende er landmanden og landmandens placering og produktion, som skaber de unikke...

Evaluering af den ernæringsmæssige kvalitet af madordninger i daginstitutioner

DEFF Research Database (Denmark)

Nielsen, Marie Heyn; Lassen, Anne Dahl; Christensen, Lene Møller

Fokus på madordninger i daginstitutioner og kvaliteten heraf har været stigende de seneste år. Mange nye madordninger er etableret i løbet af 2009 og 2010 især i børnehaver og i børnehavegrupper i de integrerede daginstitutioner. I 2009 opstillede Fødevarestyrelsen anbefalinger for den ernæringsm...... fedt samt at servere fisk, grøntsager, kartofler, samt fuldkornsvarianter af ris, pasta og brød mere hyppigt....

Sammenligning af kvaliteten af kommunernes sagsbehandling

DEFF Research Database (Denmark)

Rasmussen, Martin

flere forskellige spørgsmål fra praksis¬undersøgelser i samme sammenligning. Vi foreslår også, at metoder til såkaldte ’multi¬ple sammenligninger’ bruges til dele af undersøgelserne. Det er en ældre og ikke særlig kendt metode, men den er særdeles relevant både i den konkrete anvendelse og i andre...

Undersøgelse af mulighederne for anvendelse af open source Integrated Library Systems (ILS) i universitetsbiblioteket

DEFF Research Database (Denmark)

Greve, Eli; Bøgh Pedersen, Kasper

Dette projekt har til formål, at to biblioteker med meget forskellige profiler gennemfører test af konkrete open source baserede ILS systemer, formidler resultaterne til FFU-bibliotekerne og deres interessenter, og herved bidrager til en nuancering af beslutningsprocesserne i de kommende år omkring...

Anmeldelse af Eigil Lego Andersen: Dirigent og generalforsamling

DEFF Research Database (Denmark)

Werlauff, Erik

2011-01-01

Artiklen er en anmeldelse af advokat, adj. professor, dr. jur. Eigil Lego Andersens juridiske monografi om dirigenten og generalforsamlingen, herunder med lancering af en række nye afstemningsmetoder til brug for generalforsamlingen i (større) aktieselskaber.......Artiklen er en anmeldelse af advokat, adj. professor, dr. jur. Eigil Lego Andersens juridiske monografi om dirigenten og generalforsamlingen, herunder med lancering af en række nye afstemningsmetoder til brug for generalforsamlingen i (større) aktieselskaber....

Forsegling af okklusal dentincaries i permanente molarer

DEFF Research Database (Denmark)

Qvist, Vibeke; Borum, Mette Kit; Dynes Møller, Kirsten

2017-01-01

Der findes ingen eksakte tal for forekomsten af fødevareallergi i den danske befolkning. Den kumulerede forekomst af fødevareallergi hos børn i de første tre leveår skønnes at være på 7-8 %, hvoraf hovedparten vokser sig fra det. Punktprævalensen af diagnosticeret fødevareallergi hos voksne er 3 ...

Succesfulde virksomheder ledes af mænd - Ikke succesfulde af kvinder?

DEFF Research Database (Denmark)

Madsen, Mona Toft; Madsen, Henning; Neergaard, Helle

fra amerikanske og britiske undersøgelser (Schein, 1973, 75, 96; Ryan et al., 2005a) ved at teste dem i et kulturelt miljø karakteriseret af mere feminine ledertræk (Hofstede, 1991). Undersøgelsen tager udgangspunkt i et sæt af person-karakteristika, der er blevet anvendt til at undersøge sammenfald...... mellem mandlige karakteristika og succesfuld ledelse (Schein, 1973, 75, 96). På lige fod med nyere britiske undersøgelser (Ryan et al. 2005a), er den aktuelle undersøgelse imidlertid udvidet til også at omhandle lederes perceptioner i forhold til ledelse i virksomheder uden succes. Resultaterne viser...

Læremiddeltjek af Fandange - dansk for 5. klasse af Trine May og Susanne Arne-Hansen

DEFF Research Database (Denmark)

Christensen, Mette Vedsgaard

2013-01-01

Fandango 5 er skrevet af Trine May og Susanne Arne-Hansen og er første gang udgivet i 2009. Systemet er siden kommet i flere oplag. Fandango – dansk for 5. klasse består af en grundbog (264 sider) Arbejdsbog A (64 sider) Arbejdsbog B (64 sider), en lærervejledning (ca. 220 sider) og en hjemmeside...

Udvikling af en internetsøgestrategi til identifikation af ny medicinsk teknologi inden for prostatacancer

DEFF Research Database (Denmark)

Thygesen, Marianne; Vondeling, Hindrik; Douw, Karla

2007-01-01

internetsider efter efficiens. Her er efficiens forstået som mindst antal minutter brugt pr. fund af information om en ny væsentlig medicinsk teknologi. Resultater: Strategien består af ti sider, som bør benyttes i følgende rækkefølge: YahooHealth, DoctorsGuide, The National Electronic Library for Medicines...

Metodik til studiet af strategiske ledelsesprocesser i organisationer

Directory of Open Access Journals (Sweden)

Jørgen Gulddahl Rasmussen

2010-10-01

Full Text Available Denne artikel handler om at skabe viden om en hverdagspraksis, der sjældent er sat ord på. Den behandler de ledelsesprocesser, der i virksomheder producerer strategi og omsætter sådanne strategier i produktive handlinger. Det er processer, der i små og mellemstore virksomheder er præget af intuition og af meget uformelle samspil mellem virksomhedsledere og medarbejdere. Metodikken er en videreudvikling af de metoder til produktion af kvalitative data, som FIRM-gruppen har eksperimenteret med gennem nogle år. Artiklen kan ses som en afrapportering af et flerårigt metodeudviklingsarbejde. Da erfaringer fra sådanne virksomheder viser, at strategiske processer i høj grad udvikler sig gennem uformel kommunikation, og at lederes intuition spiller en meget stor rolle, arbejder metodikken med en struktureret udviklingsdialog mellem et mindre antal virksomhedsledere med strategiske opgaver og forskere. Denne udviklingsdialog har til formål at følge og forstå de processer, der skaber ledernes egne praksisrelaterede ”teorier” for strategisk handling. Efter en præsentation af temaet gennemgås metodikkens praktiske fremgangsmåde med undersøgelser i en række virksomheder, opbygning af cases i samarbejde med ledere fra disse virksomheder, diskussion af disse og foreløbige konklusioner hen mod de næste trin i metodikken. Artiklen er skrevet samtidigt med arbejdet på et igangværende forskningsprojekt og vil derfor både være en præsentation og en udvikling af muligheder og vanskeligheder i metodikken.

Skattemæsssig kvalifikation af trusts i praksis

DEFF Research Database (Denmark)

Feldthusen, Rasmus Kristian

2013-01-01

Artiklen har til formål at systematisere og redegøre for skattemyndighedernes fremgangsmåde og kvalifikation af trusts i dansk ret. Baggrunden herfor er, at antallet af trust-sager for såvel de administrative myndigheder som domstolene relativt set er vokset betydeligt siden årtusindeskiftet. Ud...... fra en gennemgang af doms- og administrativ praksis kan det konstateres, at kvalifikationen af trusts kan opdeles i fire hovedkategorier, som er væsentlige at have kendskab til, såfremt en skattesag indeholdende trust-elementer måtte være under opsejling. Endvidere inddrages skattestrafferetlig...... praksis på baggrund af en nyligt afsagt landsretsdom vedrørende en offshore trust....

Multitrait, Random Regression, or Simple Repeatability Model in High-Throughput Phenotyping Data Improve Genomic Prediction for Wheat Grain Yield.

Science.gov (United States)

Sun, Jin; Rutkoski, Jessica E; Poland, Jesse A; Crossa, José; Jannink, Jean-Luc; Sorrells, Mark E

2017-07-01

High-throughput phenotyping (HTP) platforms can be used to measure traits that are genetically correlated with wheat ( L.) grain yield across time. Incorporating such secondary traits in the multivariate pedigree and genomic prediction models would be desirable to improve indirect selection for grain yield. In this study, we evaluated three statistical models, simple repeatability (SR), multitrait (MT), and random regression (RR), for the longitudinal data of secondary traits and compared the impact of the proposed models for secondary traits on their predictive abilities for grain yield. Grain yield and secondary traits, canopy temperature (CT) and normalized difference vegetation index (NDVI), were collected in five diverse environments for 557 wheat lines with available pedigree and genomic information. A two-stage analysis was applied for pedigree and genomic selection (GS). First, secondary traits were fitted by SR, MT, or RR models, separately, within each environment. Then, best linear unbiased predictions (BLUPs) of secondary traits from the above models were used in the multivariate prediction models to compare predictive abilities for grain yield. Predictive ability was substantially improved by 70%, on average, from multivariate pedigree and genomic models when including secondary traits in both training and test populations. Additionally, (i) predictive abilities slightly varied for MT, RR, or SR models in this data set, (ii) results indicated that including BLUPs of secondary traits from the MT model was the best in severe drought, and (iii) the RR model was slightly better than SR and MT models under drought environment. Copyright © 2017 Crop Science Society of America.

Rating af banker og banksystemer

DEFF Research Database (Denmark)

Grosen, Anders

2010-01-01

Banksystemer over hele verdenen er med nød og næppe blevet reddet af diverse statslige hjælpepakker. Derfor er der i disse år øget fokus på banker og banksystemers rating. Denne interesse bliver ikke mindre af, at de statslige garantier til bankerne i mange lande udløber i de kommende år. Rating ...

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms

KAUST Repository

Park, Hyo-Young

2017-04-21

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. These proteins also move rapidly and continuously in the nuclei, and their movements are affected by ATP depletion. The U2AF65 proteins are splicing factors that interact with SF1 and U2AF35 proteins to promote U2snRNP for the recognition of the pre-mRNA 3\\' splice site during early spliceosome assembly. We have determined the subcellular localization and movement of these proteins\\' Arabidopsis homologs. It was found that Arabidopsis U2AF65 homologs, AtU2AF65a, and AtU2AF65b proteins interact with AtU2AF35a and AtU2AF35b, which are Arabidopsis U2AF35 homologs. We have examined the mobility of these proteins including AtSF1 using fluorescence recovery after photobleaching and fluorescence loss in photobleaching analyses. These proteins displayed dynamic movements in nuclei and their movements were affected by ATP depletion. We have also demonstrated that these proteins shuttle between nuclei and cytoplasms, suggesting that they may also function in cytoplasm. These results indicate that such splicing factors show very similar characteristics to their human counterparts, suggesting evolutionary conservation.

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms

KAUST Repository

Park, Hyo-Young; Lee, Keh Chien; Jang, Yun Hee; Kim, SoonKap; Thu, May Phyo; Lee, Jeong Hwan; Kim, Jeong-Kook

2017-01-01

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. These proteins also move rapidly and continuously in the nuclei, and their movements are affected by ATP depletion. The U2AF65 proteins are splicing factors that interact with SF1 and U2AF35 proteins to promote U2snRNP for the recognition of the pre-mRNA 3' splice site during early spliceosome assembly. We have determined the subcellular localization and movement of these proteins' Arabidopsis homologs. It was found that Arabidopsis U2AF65 homologs, AtU2AF65a, and AtU2AF65b proteins interact with AtU2AF35a and AtU2AF35b, which are Arabidopsis U2AF35 homologs. We have examined the mobility of these proteins including AtSF1 using fluorescence recovery after photobleaching and fluorescence loss in photobleaching analyses. These proteins displayed dynamic movements in nuclei and their movements were affected by ATP depletion. We have also demonstrated that these proteins shuttle between nuclei and cytoplasms, suggesting that they may also function in cytoplasm. These results indicate that such splicing factors show very similar characteristics to their human counterparts, suggesting evolutionary conservation.

Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes

DEFF Research Database (Denmark)

Peng, Xu; Brügger, Kim; Shen, Biao

2003-01-01

terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also...... recognizes both main families of repeat sequences in S. solfataricus. The recombinant protein, expressed in Escherichia coli, showed the same binding properties to the SRSR repeat as the native one. The SSO454 protein exhibits a tripartite internal repeat structure which yields a good sequence match...... with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure...

Centralisering af FM organisationer

DEFF Research Database (Denmark)

Nielsen, Susanne Balslev

2016-01-01

Centralisering af FM organisationer kan let føre til mange frustrerende arbejds- dage for medarbejdere og deres ledere. Denne artikel giver et bud på hvad kom- muner og andre kan gøre for at komme bedre igennem en omorganisering.......Centralisering af FM organisationer kan let føre til mange frustrerende arbejds- dage for medarbejdere og deres ledere. Denne artikel giver et bud på hvad kom- muner og andre kan gøre for at komme bedre igennem en omorganisering....

Måling af lydisolation og efterklangstid i praksis

DEFF Research Database (Denmark)

Kristensen, J.

Meddelelsen omhandler undersøgelser af mulighederne for at forbedre reproducerbarheden ved måling af luftlydisolation, trinlydniveau og efterklangstid under betingelser, der svarer til måling i den indflytningsfærdige bygning. Der omtales resultater fra måling med to forskellige udformninger af h...

Afståelsesbeskatning ved flytning af DEMPE-funktioner

DEFF Research Database (Denmark)

Kjærsgaard, Louise Fjord; Bundgaard, Jakob

2017-01-01

OECD har i den senest opdaterede version af Transfer Pricing Guidelines fastsat en definition af immaterielle aktiver og har samtidig indført konceptet DEMPE-funktioner, der omfatter visse vigtige funktioner relateret til immaterielle aktiver. SKAT synes at være af den opfattelse, at DEMPE...

Analysis of the a genome genetic diversity among brassica napus, b. rapa and b. juncea accessions using specific simple sequence repeat markers

International Nuclear Information System (INIS)

Tian, H.; Yan, J.; Zhang, R.; Guo, Y.; Hu, S.; Channa, S.A.

2017-01-01

This investigation was aimed at evaluating the genetic diversity of 127 accessions among Brassica napus, B. rapa, and B. juncea by using 15 pairs of the A genome specific simple sequence repeat primers. These 127 accessions could be clearly separated into three groups by cluster analysis, principal component analysis, and population structure analysis separately, and the results analyzed by the three methods were very similar. Group I comprised of mainly B. napus accessions and the most of B. juncea accessions formed Group II, Group III included nearly all of the B. rapa accessions. The result showed that 36.86% of the variance was due to significant differences among populations of species, indicated that abundance genetic diversity existed among the A genome of B. napus, B. rapa, and B. juncea accessions. B. napus, B. rapa, and B. juncea have the abundant genetic diversity in the A genome, and some elite genes can be used to broaden the genetic base of them, especially for B. napus, in future rapeseed breeding program. (author)

Reformationens tøvende omfortolkning af kætterbegrebet

DEFF Research Database (Denmark)

Holm, Bo Kristian; Thomsen, Søren Feldtfos

2012-01-01

Denne artikel undersøger påstanden om en omfortolkning af kætterbegrebet i den lutherske reformation. Der argumenteres for, at det giver god mening at tale om nytænkning af kætterbegrebet hos den unge Luther i form af en internalisering af kætteriet, hvor den enkeltes eget syndige selv udpeges som...

Assembly of Repeat Content Using Next Generation Sequencing Data

Energy Technology Data Exchange (ETDEWEB)

labutti, Kurt; Kuo, Alan; Grigoriev, Igor; Copeland, Alex

2014-03-17

Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.

The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat.

Science.gov (United States)

Naito, Mariko; Ogura, Yoshitoshi; Itoh, Takehiko; Shoji, Mikio; Okamoto, Masaaki; Hayashi, Tetsuya; Nakayama, Koji

2016-02-01

Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we present the complete genome sequence of a clinical strain, OMA14, of this bacterium along with the results of comparative genome analysis with strain 17 of the same species whose genome has also been sequenced, but not fully analysed yet. The genomes of both strains consist of two circular chromosomes: the larger chromosomes are similar in size and exhibit a high overall linearity of gene organizations, whereas the smaller chromosomes show a significant size variation and have undergone remarkable genome rearrangements. Unique features of the Pre. intermedia genomes are the presence of a remarkable number of essential genes on the second chromosomes and the abundance of conjugative and mobilizable transposons (CTns and MTns). The CTns/MTns are particularly abundant in the second chromosomes, involved in its extensive genome rearrangement, and have introduced a number of strain-specific genes into each strain. We also found a novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia and are specifically distributed among the Pre. intermedia-related species. These findings expand our understanding of the genetic features of Pre. intermedia and the roles of CTns and MTns in the evolution of bacteria. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Betydningen af pesticider for forekomsten af vilde bier

DEFF Research Database (Denmark)

Bruus, Marianne; Dupont, Yoko Luise; Grant, Ruth

Både i Danmark og andre steder er der observeret en nedgang i de insekter, der bestøver landmandens afgrøder og de vilde planter. Tilbagegangen falder sammen med, at landbrugsdriften er blevet mere intensiv, og anvendelsen af pesticider er øget. Vi ved imidlertid ikke, hvilken rolle pesticiderne ...

Barriere for Studerendes Læring af Holistisk Systemudvikling

DEFF Research Database (Denmark)

Levinsen, Karin; Madsen, Sabine

Ud fra aktionsforskning af faget Informationsbehandling på bachelorprogrammet HA/DØK ved Copenhagen Business School undersøger vi i denne artikel hvilke barriere de studerende oplever i forbindelse med læring af holistisk systemudvikling og hvorfor. Siden 1980'erne har man i (dele af) litteraturen...

Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

Directory of Open Access Journals (Sweden)

Huaiyong Luo

Full Text Available The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

Science.gov (United States)

Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

2015-01-01

The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

Udførelse af bygningsakustiske målinger

DEFF Research Database (Denmark)

Rasmussen, Birgit; Hoffmeyer, Dan; Olesen, Henrik S.

Denne anvisning definerer og beskriver udførelse af bygningsakustiske målinger m.m. i relation til Bygningsreglement 2015 (BR15), kapitel 6.4, Akustisk Indeklima (Trafik- og Byggestyrelen, 2016). Anvisningen er en opdatering af den første udgave fra 2008. Den nye udgave er ajourført med vejledning...... knyttet til blandt andet de nye standarder med feltmålemetoder for lydisolation. Anvisningen henvender sig primært til personer og firmaer, der udfører bygningsakustiske målinger, men vil også være et vigtigt redskab for rådgivere, udførende og leverandører i forbindelse med projektering af bygninger....... Anvisningen er også relevant for kommunerne i forbindelse med kontrol af opfyldelsen af lydbestemmelserne i bygningsreglementet....

Børns konstruktion af (bi)literacy

DEFF Research Database (Denmark)

Laursen, Helle; Daugaard, Line Møller; Østergaard, Winnie

analyser heraf. Programmet er baseret på et socialsemiotisk teorigrundlag, der indebærer, at tilegnelse af skriftsystemer ses som en proces, hvorigennem børn skaber betydning ud fra den information, der er tilgængelig for dem i de sociale fællesskaber, de indgår i (Kress 1997, 2000, Kenner 2004). For børn....... I dette paper præsenteres programmet, og de indsamlede data analyseres med særligt henblik på at identificere børnenes konstruktion af (bi)literacy og deres fortolkninger af, hvad der konsti-tuerer, og hvad der tæller som literacy...

Identifying uniformly mutated segments within repeats.

Science.gov (United States)

Sahinalp, S Cenk; Eichler, Evan; Goldberg, Paul; Berenbrink, Petra; Friedetzky, Tom; Ergun, Funda

2004-12-01

Given a long string of characters from a constant size alphabet we present an algorithm to determine whether its characters have been generated by a single i.i.d. random source. More specifically, consider all possible n-coin models for generating a binary string S, where each bit of S is generated via an independent toss of one of the n coins in the model. The choice of which coin to toss is decided by a random walk on the set of coins where the probability of a coin change is much lower than the probability of using the same coin repeatedly. We present a procedure to evaluate the likelihood of a n-coin model for given S, subject a uniform prior distribution over the parameters of the model (that represent mutation rates and probabilities of copying events). In the absence of detailed prior knowledge of these parameters, the algorithm can be used to determine whether the a posteriori probability for n=1 is higher than for any other n>1. Our algorithm runs in time O(l4logl), where l is the length of S, through a dynamic programming approach which exploits the assumed convexity of the a posteriori probability for n. Our test can be used in the analysis of long alignments between pairs of genomic sequences in a number of ways. For example, functional regions in genome sequences exhibit much lower mutation rates than non-functional regions. Because our test provides means for determining variations in the mutation rate, it may be used to distinguish functional regions from non-functional ones. Another application is in determining whether two highly similar, thus evolutionarily related, genome segments are the result of a single copy event or of a complex series of copy events. This is particularly an issue in evolutionary studies of genome regions rich with repeat segments (especially tandemly repeated segments).

Læremiddelevaluering af web 2.0 læremidler

DEFF Research Database (Denmark)

Falkesgaard Slot, Marie; Gissel, Stig Toke

2014-01-01

Kapitlet etablerer og afprøver et analyseapparat, der bidrager til at højne kvaliteten af de valg, som foretages af web 2.0-læremidler i danskfaget. I kapitlet fokuseres der på læremiddel evaluering af nogle af de funktioner, som typisk tilskrives web 2.0-værktøjerne, ligesom der gives eksempler på...

FEM-analyse af termiske Spændinger i Svejsning

DEFF Research Database (Denmark)

Hansen, Jan Langkjær

1997-01-01

Undersøgelser af de transiente temperaturfelter og de heraf inducerede spændinger og deformationer som følge af en stumpsøm-svejsning i plader af konstruktionsstål modelleret i henholdsvis 2D plan spændings-/tøjningstilstand og 3D er foretaget ved brug af det generelt anvendelige finite-element p......-element program ABAQUS....

Markedsføring af probiotiske fødevarer: Kan vi lære noget af Gaio og ProViva

DEFF Research Database (Denmark)

Bech-Larsen, Tino; Andersen, Lone Merete Schreiber

2004-01-01

Erfaringerne fra Gaio yoghurt (fra Arla) og ProViva frugtdrik/suppe (fra Skånemejerierne) viser, at der kan være vanskeligt at overbevise forbrugerne om probiotiske fødevarers fortrin. Både Gaio og ProViva har haft succes på deres respektive hjemmemarkeder, men ingen af produkterne har kunnet klare...... den korte tur over øresund. Med afsæt i Gaio og ProViva har MAPP og SIK undersøgt, hvordan forskellige reklame- og mediestrategier påvirker forbrugernes accept af probiotiske fødevarer. Undersøgelsen Undersøgelsen omfattede for det første en analyse af reklamer og nyhedsartikler om de to produkter...

Subregional innovation – indikatorer til optimering af den erhvervsrettede innovationspolitik

DEFF Research Database (Denmark)

Mortensen, Peter Stendahl; Graversen, Ebbe Krogh; Haase, Sanne Schioldann

områder tilgodeses bedst muligt. Desuden kan en differentieret, subregional innovations-politik give erhvervslivet bedre udbytte end en samlet regional eller national innovationspolitik. Selvom Danmark er et lille land, er der store geografiske forskelle internt i landets erhvervsstruktur og i...... virksomhedernes innovationsaktiviteter. Som resultat af en udvidelse af den danske del af CIS 2006-undersøgelsen2 med ekstra virksomheder kan der gives en betydeligt mere nuanceret karak-teristik af virksomheder helt ned på subregionalt niveau. Analysen underbygger, at de innovations-politiske tiltag, der sættes......, lokal brug af resultaterne er nødvendig. Først gennemgås de valgte målepunkter. Det primære er en opdeling i praksis- og forsknings-orientering af virksomheders innovationstilgang, hvorved der identificeres fire grupper af innovationsaktive virksomheder. Det andet er korrektion af de anvendte...

Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae).

Science.gov (United States)

Ma, Qiuyue; Li, Shuxian; Bi, Changwei; Hao, Zhaodong; Sun, Congrui; Ye, Ning

2017-02-01

Ziziphus jujuba is an important woody plant with high economic and medicinal value. Here, we analyzed and characterized the complete chloroplast (cp) genome of Z. jujuba, the first member of the Rhamnaceae family for which the chloroplast genome sequence has been reported. We also built a web browser for navigating the cp genome of Z. jujuba ( http://bio.njfu.edu.cn/gb2/gbrowse/Ziziphus_jujuba_cp/ ). Sequence analysis showed that this cp genome is 161,466 bp long and has a typical quadripartite structure of large (LSC, 89,120 bp) and small (SSC, 19,348 bp) single-copy regions separated by a pair of inverted repeats (IRs, 26,499 bp). The sequence contained 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The genome structure, gene order, GC content, and codon usage are similar to other typical angiosperm cp genomes. A total of 38 tandem repeats, two forward repeats, and three palindromic repeats were detected in the Z. jujuba cp genome. Simple sequence repeat (SSR) analysis revealed that most SSRs were AT-rich. The homopolymer regions in the cp genome of Z. jujuba were verified and manually corrected by Sanger sequencing. One-third of mononucleotide repeats were found to be erroneously sequenced by the 454 pyrosequencing, which resulted in sequences of 1-4 bases shorter than that by the Sanger sequencing. Analyzing the cp genome of Z. jujuba revealed that the IR contraction and expansion events resulted in ycf1 and rps19 pseudogenes. A phylogenetic analysis based on 64 protein-coding genes showed that Z. jujuba was closely related to members of the Elaeagnaceae family, which will be helpful for phylogenetic studies of other Rosales species. The complete cp genome sequence of Z. jujuba will facilitate population, phylogenetic, and cp genetic engineering studies of this economic plant.

Styring af international transfer pricing

DEFF Research Database (Denmark)

Reuther, Peter; Rossing, Christian Plesner

2011-01-01

Nærværende artikel introducerer international transfer pricing, dels som et skatteretligt fænomen og dels som et værktøj til planlægning og økonomisk styring af koncernforbundne selskaber i en multinational virksomhed (MNV). Med udgangspunkt i en case-analyse af MNV’en gives der et konkret eksempel...... på hvordan transfer pricing håndteres i praksis. Artiklens formål er at give et praktisk eksempel på at transfer pricing handler om at efterleve regler, ikke omgå dem. På baggrund af case-analysen argumenteres der for, at såvel akademikere som praktikere bør tage virksomhedens tilgang til...... international transfer pricing i betragtning, når økonomiske styringssystemer i en MNV skal anvendes til planlægning og opfølgning....

Økonomisk vurdering af energibesparende foranstaltninger

DEFF Research Database (Denmark)

Johnsen, Kjeld; Andersen, Hans Skifter

Anvisningen gennemgår detaljeret hvordan man gennemfører analyser af lønsomhed og likviditetsvirkninger som led i udarbejdelsen af det teknisk-økonomiske grundlag for beslutninger om energibesparende investeringer. Anvisningen indeholder blandt andet en række enkle skemaer, der kan lette og syste...

Måling af virksomheders administrative byrder

DEFF Research Database (Denmark)

Langsted, Lars Bo

2004-01-01

Selskabsstyrelsen har offentliggjort rapporten: "Rapport om måling af virksomhedernes administrative byrder ved årsregnskabsloven og rapport om revisionshonorar for B-virksomheder."......Selskabsstyrelsen har offentliggjort rapporten: "Rapport om måling af virksomhedernes administrative byrder ved årsregnskabsloven og rapport om revisionshonorar for B-virksomheder."...

Forekomst af alkohol, narkotika og medicin hos bilister

DEFF Research Database (Denmark)

Bernhoft, Inger Marie

2011-01-01

Inden for rammerne af det fælles-europæiske forskningsprojekt DRUID (DRiving Under the Influence of Drugs, alcohol and medicines) er forekomsten af alkohol og/eller andre stoffer blevet undersøgt i et stort antal europæiske lande, bl.a. i Danmark.......Inden for rammerne af det fælles-europæiske forskningsprojekt DRUID (DRiving Under the Influence of Drugs, alcohol and medicines) er forekomsten af alkohol og/eller andre stoffer blevet undersøgt i et stort antal europæiske lande, bl.a. i Danmark....

En tegning af æstetik 2013

DEFF Research Database (Denmark)

Buhl, Mie; Ejsing-Duun, Stine

2013-01-01

Denne artikel fremstiller skredet fra det individuelle fokus til den sociale forhandling omkring en situation, som er det nye perspektiv indenfor æstetik. Derigennem identificeres tendenser som er med til at udgøre platformen for børn og unges kulturer, hvor det handler om, at et æstetisk system er...... selvproducerende og stiller sig til rådighed for erkendelse. Disse kulturer udfolder sig i formater, som skolen ikke er gearet til at imødekomme. Som eksempel ville DrawSomething vanskeligt kunne begrundes i forhold til billedkunstfagets af ministeriet fastsatte ”fælles mål” – eller kan det? En central udfordring...... er, hvordan der skal arbejdes med æstetiske praksisformer i en nutidig læringskontekst, når børn og unges kulturer udfolder og udvikler sig i formater, der er præget af foranderlighed og flygtighed; af en uendelig skaben for nogen og med nogen og af situationer, der bebos med attituder? Vi diskuterer...

Modellering af ATS forhold på Bjergmarken Renseanlæg

DEFF Research Database (Denmark)

Laursen, Jesper; Rasmussen, Michael R.

Denne rapport indeholder resultaterne af numeriske beregninger af en procestank opereret under ATS-drift på Bjergmarken Renseanlæg.......Denne rapport indeholder resultaterne af numeriske beregninger af en procestank opereret under ATS-drift på Bjergmarken Renseanlæg....

Når ledelse af ledelse rettes mod selvet

DEFF Research Database (Denmark)

Krause-Jensen, Niels Henrik

2012-01-01

Der fokuseres på det nye selvledelsesforhold som ledelse af ledelse er med til at fremkalde. Ud fra et signalement af det nye arbejdsliv beskrives det hvordan ledelse af ledelse skal forvalte en indgriben i medarbejderens selvforhold, hvor både magt og afmagt vil gøre sig gældende....

MSDB: A Comprehensive Database of Simple Sequence Repeats.

Science.gov (United States)

Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh Kumar

2017-06-01

Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Overmæt af islam kontra danskhed

DEFF Research Database (Denmark)

Khawaja, Iram

2013-01-01

Debatindlæg der retter fokus på at, islam og muslimer konstrueres som modbillede til alt det, som danskhed repræsenterer, og at man i denne forbindelse glemmer at definitionen af danskhed gennem negationen af islam sker på bekostning af de mange muslimske borgere, der har skabt en identitet og...... selvforståelse som danske muslimer. Der tales her om de mange mennesker, der har skabt en tilværelse ved at sammentænke danskhed og islam i et forsøg på at overskride kontrasten imellem et fremmed ”dem” og et dansk ”os”. Denne gruppe udgør størstedelen af de herboende unge, voksne og børn, som ikke forstår...

Udtrækning af 10 mm ankerbolte

DEFF Research Database (Denmark)

Hansen, Lars Pilegaard

Denne rapport beskriver forsøg med udtrækning af 10 mm ankerbolte udført af Laboratoriet for Bærende Konstruktioner, Instituttet for Bygningsteknik, Aalborg Universitet. Forsøgene blev udført d. 19. og 21. juni 2001. Forsøgene blev udført dels på Hjørring Sygehus og dels på Laboratoriet.......Denne rapport beskriver forsøg med udtrækning af 10 mm ankerbolte udført af Laboratoriet for Bærende Konstruktioner, Instituttet for Bygningsteknik, Aalborg Universitet. Forsøgene blev udført d. 19. og 21. juni 2001. Forsøgene blev udført dels på Hjørring Sygehus og dels på Laboratoriet....

Undersøgelse af kommunernes administration af bygningsreglementets elevatorkrav

DEFF Research Database (Denmark)

Grangaard, Sidse

Denne rapport undersøger kommunernes praksis omkring administrationen af bygningsreglementets krav om elevator ved nybyggeri og ombygning. Blandt de 26 kommuner, der har deltaget i undersøgelsen, var der generelt konsensus om at stille krav om elevator ved nybyggeri. Kommunerne modtager kun meget...

Overvågning af fugle 1997-98, resultater fra feltstationerne

DEFF Research Database (Denmark)

Vejler, i alt ca. 5.500 ha. Feltstationen blev oprettet i 1978, og siden har observatørerne registreret fuglelivet i Vejlerne og de omgivende arealer foruden vandstand, saltholdighed og drift af området. Tipperne ligger i den sydlige del af Ringkøbing Fjord. Fuglelivet blev fredet i 1898. Reservatet blev...... en samlet fredning af Vadehavet, omfatter øen Langli på 80 ha og vandarealer på i alt ca. 8.000 ha. Øen består af klitter og salte strandenge. Vandområdet er præget af tidevand, hvor vidtstrakte sand- og mudderflader og spredte muslingebanker er synlige ved lavvande. Vorsø ligger i Horsens Fjord...... saltholdighed i Ringkøbing Fjord bevirker, at vandplanter vokser dårligt eller forsvinder. Vandplanter udgør en væsentlig del af føden for visse andefugle og kan derfor have stor betydning for antallet af rastende fugle. Der blev registreret lave antal af knortegå, gråand, pibeand og krikand. Af blishøne blev...

Genome-wide gene expression profiling of low-dose, long-term exposure of human osteosarcoma cells to bisphenol A and its analogs bisphenols AF and S.

Science.gov (United States)

Fic, A; Mlakar, S Jurković; Juvan, P; Mlakar, V; Marc, J; Dolenc, M Sollner; Broberg, K; Mašič, L Peterlin

2015-08-01

The bisphenols AF (BPAF) and S (BPS) are structural analogs of the endocrine disruptor bisphenol A (BPA), and are used in common products as a replacement for BPA. To elucidate genome-wide gene expression responses, estrogen-dependent osteosarcoma cells were cultured with 10 nM BPA, BPAF, or BPS, for 8 h and 3 months. Genome-wide gene expression was analyzed using the Illumina Expression BeadChip. Three months exposure had significant effects on gene expression, particularly for BPS, followed by BPAF and BPA, according to the number of differentially expressed genes (1980, 778, 60, respectively), the magnitude of changes in gene expression, and the number of enriched biological processes (800, 415, 33, respectively) and pathways (77, 52, 6, respectively). 'Embryonic skeletal system development' was the most enriched bone-related process, which was affected only by BPAF and BPS. Interestingly, all three bisphenols showed highest down-regulation of genes related to the cardiovascular system (e.g., NPPB, NPR3, TXNIP). BPA only and BPA/BPAF/BPS also affected genes related to the immune system and fetal development, respectively. For BPAF and BPS, the 'isoprenoid biosynthetic process' was enriched (up-regulated genes: HMGCS1, PDSS1, ACAT2, RCE1, DHDDS). Compared to BPA, BPAF and BPS had more effects on gene expression after long-term exposure. These findings stress the need for careful toxicological characterization of BPA analogs in the future. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimalt design af fødevarer

DEFF Research Database (Denmark)

Bech, Anne C.; Engelund, Erling; Juhl, Hans Jørn

1993-01-01

Udformningen af fødevarer opfattes som et designproblem, det består i at omsætte markedskrav, belyst gennem markedsanalyser, til egenskaber ved de fremstillede produkter under hensyntagen til de dermed forbundne omkostninger. Denne oversættelse af forbrugerønsker antages at kunne ske effektivt ge...

The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

Directory of Open Access Journals (Sweden)

Leila do Nascimento Vieira

Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

Protecting your files on the AFS file system

CERN Multimedia

2011-01-01

The Andrew File System is a world-wide distributed file system linking hundreds of universities and organizations, including CERN. Files can be accessed from anywhere, via dedicated AFS client programs or via web interfaces that export the file contents on the web. Due to the ease of access to AFS it is of utmost importance to properly protect access to sensitive data in AFS. As the use of AFS access control mechanisms is not obvious to all users, passwords, private SSH keys or certificates have been exposed in the past. In one specific instance, this also led to bad publicity due to a journalist accessing supposedly "private" AFS folders (SonntagsZeitung 2009/11/08). This problem does not only affect the individual user but also has a bad impact on CERN's reputation when it comes to IT security. Therefore, all departments and LHC experiments agreed in April 2010 to apply more stringent folder protections to all AFS user folders. The goal of this data protection policy is to assist users in...

Bagsideidræt ramt af skandale

DEFF Research Database (Denmark)

Elbæk, Lars

2008-01-01

Ekspert rystet over sikkerheden - idrætsgren udelukket - redaktør sporløst forsvundet Fyens Bagside Idræt (FBI) er rystet af sin første skandale. Det drejer sig om sikkerheden i den af forbundet indtil i går anerkendte disciplin trampolinbold, hvor flere børn på samme tid hopper i trampolin, mens...... de forsøger at undgå at ramme bolde på samme trampolin. - Det er direkte uansvarligt og jeg er rystet, siger lektor Lars Elbæk fra Institut for Idræt og Biomekanik på Syddansk Universitet. - I overtræder simpelthen samtlige sikkerhedsregler for, hvordan man skal undgå skader på en trampolin...... skader, der opstår i havetrampoliner, sker på baggrund af uhensigtsmæssig brug, siger Lars Elbæk, som har opstillet 12 sikkerhedsanbefalinger, der blandt andet kan ses på www.trampolin.dk . En af disse foranstaltninger er, at kun én person ad gangen hopper i trampolinen: - 75 procent af alle...

Finding atrial fibrillation in stroke patients: Randomized evaluation of enhanced and prolonged Holter monitoring--Find-AF(RANDOMISED) --rationale and design.

Science.gov (United States)

Weber-Krüger, Mark; Gelbrich, Götz; Stahrenberg, Raoul; Liman, Jan; Kermer, Pawel; Hamann, Gerhard F; Seegers, Joachim; Gröschel, Klaus; Wachter, Rolf

2014-10-01

Detecting paroxysmal atrial fibrillation (AF) in patients with ischemic strokes presenting in sinus rhythm is challenging because episodes are often short, occur randomly, and are frequently asymptomatic. If AF is detected, recurrent thromboembolism can be prevented efficiently by oral anticoagulation. Numerous uncontrolled studies using various electrocardiogram (ECG) devices have established that prolonged ECG monitoring increases the yield of AF detection, but most established procedures are time-consuming and costly. The few randomized trials are mostly limited to cryptogenic strokes. The optimal method, duration, and patient selection remain unclear. Repeated prolonged continuous Holter ECG monitoring to detect paroxysmal AF within an unspecific stroke population may prove to be a widely applicable, effective secondary prevention strategy. Find-AFRANDOMISED is a randomized and controlled prospective multicenter trial. Four hundred patients 60 years or older with manifest (symptoms ≥24 hours or acute computed tomography/magnetic resonance imaging lesion) and acute (symptoms ≤7 days) ischemic strokes will be included at 4 certified stroke centers in Germany. Those with previously diagnosed AF/flutter, indications/contraindications for oral anticoagulation, or obvious causative blood vessel pathologies will be excluded. Patients will be randomized 1:1 to either enhanced and prolonged Holter ECG monitoring (10 days at baseline and after 3 and 6 months) or standard of care (≥24-hour continuous ECG monitoring, according to current stroke guidelines). All patients will be followed up for at least 12 months. The primary end point is newly detected AF (≥30 seconds) after 6 months, confirmed by an independent adjudication committee. We plan to complete recruitment in autumn 2014. First results can be expected by spring 2016. Copyright © 2014 Mosby, Inc. All rights reserved.

Udvikling af strategiske alliancer, joint ventures og netværk

DEFF Research Database (Denmark)

Gustafsson, Jeppe; Henriksen, Lars Bo; Larsson, Rune

Rapporten er et resultat af et projekt om virksomhedssamarbejde under Industri- og Handelsstyrelsens program "Ledelse af samarbejde om teknologisk fornyelse". Formålet med projektet har været at bidrage til udvikling af anvendelsesorienterede modeller vedrørende udvikling og ledelse af alliancer ...

Bestemmelse af spormetaller i organisk materiale

DEFF Research Database (Denmark)

Tjell, Jens Christian; Palfeldt, Kirsten

Behovet for pålidelige analysemetoder til bestemmelse af spormetalindhold i organiske materialer, f.eks. planter, slam og dyrevæv er stigende på grund af den stigende erkendelse af disse stoffers betydning for organismers fysiologi, både hvor disse stoffer optræder i uønskede koncentrationer som...... der over de sidste år udviklet en analyseprocedure hvorefter det er muligt at analysere for metallerne Mn, Cu, Ni, Co, Cr, Zn, Cd og Pb i planter, dyrevæv, jord, slam og andre materialer med standardafvigelser på mellem 5 og 10%. Der gøres rede for denne metode....

Optimization of sequence alignment for simple sequence repeat regions

Directory of Open Access Journals (Sweden)

Ogbonnaya Francis C

2011-07-01

Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

Professionel udvikling af naturfagslærere

DEFF Research Database (Denmark)

Krogh, Lars Brian

2016-01-01

& Hollingsworth, 2002) som model for tænkning omkring TPD, samt anvende en mange-lags evalueringsoptik i overensstemmelse med Guskey (2002). Den eksisterende viden om, hvad der skal til for at professionelle udviklingsaktiviteter får virkning opsummeres som afsæt for en drøftelse af TPD-design. Endelig...

Sproget afhænger af stedet

DEFF Research Database (Denmark)

Monka, Malene

2014-01-01

I artiklen præsenteres resultaterne af et ph.d.-projekt ved Nordisk Forskningsinstitut ved Københavns Universitetet, der undersøger sammenhænge mellem sted og sprogforandring. Projektet er en undersøgelse af sprogforandring i virkelig tid, hvor gamle og nye optagelser med 23 informanter fra tre j...

Genome-wide identification, sequence characterization, and protein-protein interaction properties of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat family members in Solanum lycopersicum.

Science.gov (United States)

Zhu, Yunye; Huang, Shengxiong; Miao, Min; Tang, Xiaofeng; Yue, Junyang; Wang, Wenjie; Liu, Yongsheng

2015-06-01

One hundred DDB1 (damaged DNA binding protein-1)-binding WD40-repeat domain (DWD) family genes were identified in the S. lycopersicum genome. The DWD genes encode proteins presumably functioning as the substrate recognition subunits of the cullin4-ring ubiquitin E3 ligase complex. These findings provide candidate genes and a research platform for further gene functionality and molecular breeding study. A subclass of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat domain (DWD) family proteins has been demonstrated to function as the substrate recognition subunits of the cullin4-ring ubiquitin E3 ligase complex. However, little information is available about the cognate subfamily genes in tomato (S. lycopersicum). In this study, based on the recently released tomato genome sequences, 100 tomato genes encoding DWD proteins that potentially interact with DDB1 were identified and characterized, including analyses of the detailed annotations, chromosome locations and compositions of conserved amino acid domains. In addition, a phylogenetic tree, which comprises of three main groups, of the subfamily genes was constructed. The physical interaction between tomato DDB1 and 14 representative DWD proteins was determined by yeast two-hybrid and co-immunoprecipitation assays. The subcellular localization of these 14 representative DWD proteins was determined. Six of them were localized in both nucleus and cytoplasm, seven proteins exclusively in cytoplasm, and one protein either in nucleus and cytoplasm, or exclusively in cytoplasm. Comparative genomic analysis demonstrated that the expansion of these subfamily members in tomato predominantly resulted from two whole-genome triplication events in the evolution history.

Overvågning af influenza A virus i svin - Slutrapport 2015

DEFF Research Database (Denmark)

Krog, Jesper Schak; Hjulsager, Charlotte Kristiane; Larsen, Lars Erik

Denne rapport beskriver resultaterne af overvågning af influenza i svin i Danmark i 2015 og sammenholder resultaterne med dem fra de foregående år og udenlandske studier. Laboratorieundersøgelser og databehandling er udført på DTU Veterinærinstituttet. Indledende screening af prøver for tilstedev......Denne rapport beskriver resultaterne af overvågning af influenza i svin i Danmark i 2015 og sammenholder resultaterne med dem fra de foregående år og udenlandske studier. Laboratorieundersøgelser og databehandling er udført på DTU Veterinærinstituttet. Indledende screening af prøver...... for tilstedeværelsen af influenza A virus er betalt af indsenderne, mens de øvrige analyser er finansieret af FVST’s overvågningsprogram. Slutrapporten er den endelige opgørelse af analyserede indsendelser for det pågældende år. Der kan være mindre afvigelser mellem slutrapport og kvartalsrapporterne....

Anmeldelser af litteratur om den græsk-romerske oldtid

DEFF Research Database (Denmark)

Krasilnikoff, Jens

2007-01-01

Anmeldelse af Neville Morley, "Trade in Classical Antiquity". Key Themes in Ancient History. Cambridge UP, 2007. p.22. Anmeldelse af J. Bingen, "Hellenistic Egypt. Monarchy, Society, economy, Culture", Edinburgh UP, 2007, pp.22-23. Anmeldelse af C. Koehn, "Krieg-Diplomatie-Ideologie. Zur Ausenpol......Anmeldelse af Neville Morley, "Trade in Classical Antiquity". Key Themes in Ancient History. Cambridge UP, 2007. p.22. Anmeldelse af J. Bingen, "Hellenistic Egypt. Monarchy, Society, economy, Culture", Edinburgh UP, 2007, pp.22-23. Anmeldelse af C. Koehn, "Krieg-Diplomatie-Ideologie. Zur...... Ausenpolitik hellenistischer Mittelstaaten", Franz Steiner 2007, pp.24-25. Anmeldelse af A. Kühr,"Als Kadmos nach Boiotien kam. Polis und ethnos im Spiegel thebanischer Gründungsmythen", Franz Steiner 2007, p. 25. P. Low, "Interstate relations in Classical Greece. Morality and Power", Cambridge UP 2007, pp. 26...

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

Science.gov (United States)

Straub, Shannon C K; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

2011-05-04

Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first

Udforskning af dialoger om et regnehul

DEFF Research Database (Denmark)

Lindenskov, Lena

2007-01-01

Med introduktionen af det danske begreb 'regnehuller' om matematikvanskeligheder bliver det muligt at udforske dialoger i klasserummet med brug af værktøjer fra Augusto Boals Forumteater. Principperne i Boals tre faser præsenteres som værktøjer for læreres refleksive praksis. Ud fra datamateriale...

Revisionsklienters anvendelse af serviceleverandører

DEFF Research Database (Denmark)

Kjersgaard, Lisbeth; Kiertzner, Lars

2011-01-01

Artiklen præsenterer det overordnede indhold af den ajourførte ISA 402 om revisionsmæssige overvejelser ved revision af regnskaber for virk somheder, der anvender service-leverandører. Artiklen er opbygget efter de tre grundlæggende elementer i revisionsprocessen - planlægning, udførelse og rappo...

Beskrivelse og modellering af produktionssystemer, Tulip

DEFF Research Database (Denmark)

Jacobsen, Peter

1997-01-01

produktionssystemer til brug ved optimering af drift og planlægning/udvikling af nye produktionssystemer. For at opnå et nødvendigt informationsgrundlag udføres projektet i samarbejde med udvalgte virksomheder.Rapporten er udført i samarbejde med Tulip International A/S i Vejle, hvor den del, der omfatter...

ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants.

Science.gov (United States)

Kapil, Aditi; Rai, Piyush Kant; Shanker, Asheesh

2014-01-01

Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1-6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. Database URL: www.compubio.in/chlorossrdb/ © The Author(s) 2014. Published by Oxford University Press.

Repeat-associated plasticity in the Helicobacter pylori RD gene family.

Science.gov (United States)

Shak, Joshua R; Dick, Jonathan J; Meinersmann, Richard J; Perez-Perez, Guillermo I; Blaser, Martin J

2009-11-01

The bacterium Helicobacter pylori is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two H. pylori strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the H. pylori RD gene family. Each gene of this family is composed of a conserved 3' region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5' region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42 H. pylori strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject's stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by H. pylori-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding H. pylori persistence in its natural host.

detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

Science.gov (United States)

Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

2014-01-01

Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.

Kan man ventilere sig ud af problemer med forhøjet indhold af PCB i indeluften?

DEFF Research Database (Denmark)

Lyng, Nadja

2016-01-01

Vi ser stadig, at byggematerialer fra perioden i nogle tilfælde er årsag til forhøjede koncentrationer af PCB i indeklimaet. Sundhedsstyrelsen har derfor fastsat en vejledende aktionsgrænse på 300 ng/ m ³. Ved koncentrationer over denne grænse anbefales midlertidig afhjælpning som øget rengøring og...... ventilation eller udluftning implementeret straks. Er disse tiltag ikke tilstrækkelige til at nedbringe koncentrationen, anbefales det uden unødig forsinkelse at nedbringe koncentrationen ved kildefjernelse eller indkapsling. Ventilation har betydning for PCB-koncentrationen i indeluften, men kan ventilation...... forurenede lokaler. Da PCB-koncentrationen afhænger af temperaturen, er alle koncentrationer korrigeret for temperatur for at kunne vurdere effekten af ventilation alene....

En bid af ældres hverdagsliv

DEFF Research Database (Denmark)

Bundgaard, Karen Marie; Top Christensen, Boye

2000-01-01

Undersøgelsen har udforsket hjemmeboende ældres egen forståelse og oplevelse af måltiddsaktiviteters betydning, og hvilke behov aktiviteterne dækker hos de ældre. Aktiviteterne har betydninger der knytter sig til maden men aktiviteterne har også betydninger i sig selv. Undersøgelsen er en af fler...

Alu repeats as markers for forensic DNA analyses

Energy Technology Data Exchange (ETDEWEB)

Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Kass, D.H. [Louisiana State Univ., New Orleans, LA (United States)] [and others

1994-01-01

The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 98.9% nucleotide identity with the HS subfamily consensus sequence, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 inch and 3 inch unique flanking DNA sequences from each HS Alu that allow the locus to be assayed for the presence or absence of the Alu repeat. The dimorphic HS Alu sequences probably inserted in the human genome after the radiation of modem humans (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project. HS Alu family member insertions differ from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) in that polymorphisms due to Alu insertions arise as a result of a unique event which has occurred only one time in the human population and spread through the population from that point. Therefore, individuals that share HS Alu repeats inherited these elements from a common ancestor. Most VNTR and RFLP polymorphisms may arise multiple times in parallel within a population.

Sammenligning af laboratorieforsøg med kemiske, biologiske og termiske metoder til oprensning af residual fri fase under grundvandsspejlet i Kærgård Plantage

DEFF Research Database (Denmark)

Christophersen, Mette; Christensen, Jørgen Fjeldsø; Jørgensen, Torben H.

, sulfonamider, barbiturater, anilin, cyanid og kviksølv, og det har resulteret i en meget kompleks forurening. Efter afgravning af 4000 tons meget forurenet jord ned til grundvandsspejlet i to af de seks gruber er næste skridt afprøvning af forskellige metoder til fjernelse af den kraftige grundvandsforurening...

A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAAn Repeats Associated with Friedreich’s Ataxia

Directory of Open Access Journals (Sweden)

Ryan J. McGinty

2017-09-01

Full Text Available Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich’s ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1 of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAAn repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach.

Æstetisk iscenesættelsen af det postindustrielle bylandskab

DEFF Research Database (Denmark)

Kiib, Hans

2013-01-01

det naturskønne, det ruinøse og de pittoreske billede af byen og landskabet spiller en vigtig rolle. Men samtidig iscenesætter den eleverede parkbro byen på en sublim måde forstået som opbyggelse af spændingsfelter mellem den nære og kendte og det fremmede og farlige i en af verdens spektakulære...... kortlægning af parkbroens rolle i bydelens dekonstruktion og nyiscenesættelse i en fremadskuende montage. Det omfatter en æstetisk modstilling af arkitektoniske virkemidler for det skønne, det pittoreske og det sublime og tilsvarende en tregrenet oplevelsespallete hos den besøgende: Den konplemtative væren i...

Ny styring af lærernes autonomi?

DEFF Research Database (Denmark)

Holm, Claus

2015-01-01

Kapitlet ”Ny styring af lærernes autonom?” i bogen Folkeskolen - efter reformen fokuserer på, hvordan en realisering af den vedtagne skolereform og forventningen om en kommende brug af nye forenklede Fælles Mål ud fra en målstyringstænkning ændrer lærernes autonomi til at udøve dømmekraft i...... klasseværelset. Dermed er kapitlets tese, at man ikke – i hvert fald ikke kun – kan tale om et tab af autonomi, men en ændret opfattelse og indhold heraf. Opgaven er derfor at indkredse, hvordan danske læreres autonomi til at udøve professionel dømmekraft forandrer sig, hvis man realiserer idéen om en...... læringsmålstyret undervisning, konkret i form af forenklede Fælles Mål. Og netop spørgsmålet om lærerens autonomi til at udøve professionel dømmekraft bliver i sammenhæng med styring heraf et centralt emne og problematik at afklare. Ikke kun i dansk sammenhæng, men også internationalt....

Lokal integration af førtidspensionister

DEFF Research Database (Denmark)

Jacobsen, Joannes; Lindstrøm, Maia

Denne rapport kortlægger livsvilkårene for en bred gruppe af førtidspensionister med fokus på deres hverdag og de vilkår, som omgiver dem. Derudover identificerer rapporten en gruppe af førtidspensionister, der selv ønsker mere social interaktion og indhold i hverdagen. Undersøgelsen viser, at de...

Arbejdsmiljø ved udbud af busdrift

DEFF Research Database (Denmark)

Wiegmann, Inger-Marie; Mathiesen, Karin; Hasle, Peter

En undersøgelse af sammenhængen mellem arbejdsmiljø og udbud af busdrift i tre trafikselskabet. Resultaterne peger på at arbejdsmiljøet går fra udelukkende til at være et anliggende mellem arbejdsgiver og arbejdstager til et trepartsforhold hvor også udbyder (trafikselskabet) får et ansvar og har...

Breaks in the 45S rDNA Lead to Recombination-Mediated Loss of Repeats

Directory of Open Access Journals (Sweden)

Daniël O. Warmerdam

2016-03-01

Full Text Available rDNA repeats constitute the most heavily transcribed region in the human genome. Tumors frequently display elevated levels of recombination in rDNA, indicating that the repeats are a liability to the genomic integrity of a cell. However, little is known about how cells deal with DNA double-stranded breaks in rDNA. Using selective endonucleases, we show that human cells are highly sensitive to breaks in 45S but not the 5S rDNA repeats. We find that homologous recombination inhibits repair of breaks in 45S rDNA, and this results in repeat loss. We identify the structural maintenance of chromosomes protein 5 (SMC5 as contributing to recombination-mediated repair of rDNA breaks. Together, our data demonstrate that SMC5-mediated recombination can lead to error-prone repair of 45S rDNA repeats, resulting in their loss and thereby reducing cellular viability.

Udvikling og afprøvning af it-støttet vejledning af lærerstuderende i praktik

DEFF Research Database (Denmark)

Clemens, Heidie

2011-01-01

samarbejdet mellem læreruddannelsen og praktikinstitutionerne omkring vejledning af de studerende i praktikken via Skype eller VIAs platform og at afprøve en vejledningsform, der har karakter af procesvejledning. Erfaringer med at afprøve den virtuelle mødeform i denne sammenhæng muliggør mødet mellem...

Telefonitis: unge danskeres brug af telefonen i IT-tidsalderen

Directory of Open Access Journals (Sweden)

Gitte B. Stald

2000-09-01

Full Text Available Den udbredte brug af mobiltelefoner har sat fornyet fokus på telefonens betydning i vores tid. Som følge af den informationsteknologiske udvikling ændrer telefonen karakter fra at være en kanal for kommunikation til at være et medie for flere funktioner, samtidig med at dens konkrete og sym- bolske betydning forstærkes. Dette kan i særlig grad aflæses i større børns og unges brug af telefonen, der dels er karakteriseret ved stor selvfølgelig- hed, dels ved at have en betydning, der rækker ud over funktioner: den er markør af ungdomskultur, den er garant for tryghed, og den muliggør fast- holdelse af sociale og personlige relationer. Telefonen befordrer etablering- en af et virtuelt rum, hvor intimitet og fortrolighed er mulig. Set i lyset af den informationsteknologiske udvikling, der har bragt e-mail, chat og andre for- mer for on- og offline kommunikation ind i de fleste unge danskeres tilvæ- relse, er det interessant, at telefonen har fastholdt og endog forstærket sin betydning.

Anmeldelse af: Afghantsy. The Russians in Afghanistan 1979-89

DEFF Research Database (Denmark)

Vestenskov, David

2012-01-01

Baseret på nyligt afklassificeret materiale fra arkiverne i Moskva samt fremstillinger af russiske historikere, tegnes et anderledes og mere nuanceret billede af de sovjetiske erfaringer fra Afghanistan. De første spadestik til opgøret med den amerikanske stempling af den sovjetiske ageren i...

Antitrombotisk behanding af patienter med valvulær atrieflimren

DEFF Research Database (Denmark)

Bovin, Ann; Christensen, Thomas Decker; Grove, Erik Lerkevang

2017-01-01

with valvular AF. Although the definition of valvular AF is disputed, the lack of evidence regarding the use of NOACs for these patients is not. We discuss the definition of valvular AF, the risk of thromboembolism, and the antithrombotic treatment for stroke prevention in these patients....

Flexicurity - afklaring af et begreb i bevægelse

DEFF Research Database (Denmark)

Larsen, Flemming; Madsen, Per Kongshøj; Bredgaard, Thomas

2007-01-01

Flexicurity er et begreb på vandring. Det blev opfundet i Holland i midten af 1990erne, og er siden blevet en samlebetegnelse for det danske arbejdsmarkedssystem. Aktuelt er opnåelse af flexicurity blevet til topprioriteten for EU-kommissionens forsøg på reformer af arbejdsmarkedsområdet. Dermed...... bliver det et begreb som alle medlemslande er tvunget til at forholde sig til. Flexicurity er med andre ord en retorisk succes. I denne artikel søger vi at dokumentere begrebets sejrsvandring. Den politiske og akademiske omfavnelse af flexicurity indebærer imidlertid en risiko for at begrebet udvandes......, og bliver meningsløst. Vi diskuterer derfor forskellige definitioner af flexicurity for at opnå en større klarhed over, hvad der bør og kan forstås ved flexicurity, og giver til slut et bud på en ny forståelse af flexicurity som analytisk begreb....

Randomiseret klinisk undersøgelse af effekten af kognitiv adaptationstræning: design og metodediskussion

DEFF Research Database (Denmark)

Hansen, Jens Peter; Østergaard, Birte; Nordentoft, Merete

2009-01-01

  Kognitiv adaptations træning er afprøvet gennem randomiserede studier i udlandet, men er ikke afprøvet på nydebuterede patienter, som modtager intensiv pleje og behandling. I denne artikel præsenteres et forskningsprojekt, som skal afgøre om kognitiv adaptations træning er velegnet i en dansk...... kontekst som supplement til nuværende tilbud til patienter med debuterende skizofreni. Studiet gennemføres som et randomiseret multicenter forsøg, hvor 164 konsekutivt inkluderede patienter fordeles til henholdsvis kognitiv adaptations træning og standardbehandling. Effekten af interventionen evalueres med......, fordelingsprocedure, bortfald, udvælgelse af patienter og sammenlignelighed mellem tilknyttede centre. Dette studie er det første studie, hvor kognitiv adaptations træning sammenlignes med et ambulant tilbud bestående af psykiatrisk behandling kombineret med hyppige hjemmebesøg ved distriktssygeplejersker. Studiet...

The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

Science.gov (United States)

Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

2014-04-01

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

Pædagogers formidling af naturen i naturbørnehaver

DEFF Research Database (Denmark)

Ejbye-Ernst, Niels

2012-01-01

, interviews, andenordensrefleksioner og udsagn fra 500 pædagoger) giver mulighed for triangulering af resultaterne (Denzin & Lincoln 1998) og dermed mulighed for at belyse området alsidigt. I forskningsprojektets sigte indgår både en analyse af feltet gennem gennemgribende iagttagelser af pædagogers...

Retsbeskyttelsen af fostre og befrugtede æg

DEFF Research Database (Denmark)

Herrmann, Janne Rothmar

tydeliggøres og analyseres forskellige problemstillinger: -Abort og fosterreduktion - Fosterdiagnostik - Fosteret som patient og forsøgsperson - Anvendelse af føtale celler og væv - Fosterets status som afdød - Fertilitetsbehandling og sortering af befrugtede æg - Fertilitetsturisme - Stamcelleforskning...

Selskaberne er en del af staten

DEFF Research Database (Denmark)

Hein Jessen, Mathias

2016-01-01

Lækket af Panama Papers fremhæver endnu engang den paradoksale rolle, ikke mindst multinationale selskaber spiller i politik og økonomi: De er både skabt af staten, og fremstår stadig som uden for og i opposition til staten. Hvis vi vil gøre noget ved problemet, må vi forstå, hvordan stat og...

Omrids af en trækultur

DEFF Research Database (Denmark)

Rauff Greisen, Johannes

2007-01-01

høje prioritering af de fysiske rammer kan aflæses i de store linjer såvel som i de redelige detaljer. Artiklens spørgsmål er, hvorledes håndværkstraditionens kvaliteter og kerne kan overleveres til det moderne byggeri, der også i Vorarlberg i stigende grad præges af industrialiseringen, samt i hvilke...

AF Sites

Science.gov (United States)

AF Bands Air Force Band Recordings Air National Guard Band of the Midwest Air National Guard Band of U.S. Air Force Bands U.S. Air Force Heartland of America Band U.S. Air Force Heritage of America Band U.S. Air Forces in Europe Band US Air Forces Central Command Band Medical 42d Medical Group 59th

Arbejdsformer under anvendelse af 4. generationsværktøjer

DEFF Research Database (Denmark)

Christensen, Søren; Grønbæk, Kaj; Rolskov, Tove

En belysning af sammenhængen mellem arbejdsformer og anvendelse af 4. generationsværktøjer i systemudvikling -- baseret på en undersøgelse af 9 systemudviklingsprojekter og et litteraturstudium...

Logning af teledata i lyset af Tele2-dommen

DEFF Research Database (Denmark)

Lentz, Lene Wacher

2017-01-01

De danske teleudbydere har siden 2007 været underlagt en pligt efter logningsbekendtgørelsen til at registrere data om al telekommunikation for at sikre at data er tilgængelige ved en eventuel senere efterforskning. Logningspligten må nu revideres og i vidt omfang afvikles som følge af EU-domstol...

Opfattelser af integration blandt unge med migrantbaggrund

DEFF Research Database (Denmark)

Skytte, Marianne; Bryderup, Inge

2014-01-01

I artiklen formidles analyser af otte interview med unge med migrantbaggrund. Der er fokus på de unges oplevelser og opfattelser af integration. Der er tale om komplekse processer og vekselvirkninger i forholdet mellem de samfundsmæssige kategoriseringer og individernes selvopfattelser. De unge o...

Studerendes mulighed for opnåelse af kompetence til udvikling af professionen i positionen mellem central styring og decentral autonomi

DEFF Research Database (Denmark)

Dau, Susanne

Dette paper bygger på et casestudie af implementeringen af blended læring i to professionsuddannelser ved University College Nord i Danmark. I paperet afdækkes studerendes udfordringer i positionen mellem central styring og decentral autonomi: 1) På den ene side de ydre styringsbetingelser, og...... kompetencemål skal de studerendes opnå selvstyret læring for at kvalificere sig til kommende profession, videreuddannelse, livslang læring og professionsudvikling. Denne kvalificering kan være i risiko for at blive undergravet af den centrale styring. På baggrund heraf undersøges problemstillingen: Hvordan......, praktikken og de studerendes fremtidige professionspraksis. Det anbefales, at der arbejdes både centralt og decentralt med at minimere de studerendes dilemmaposition mellem central styring og autonomi til gavn for samfundet og brugerne af de professionelles ydelser....

Breaks in the 45S rDNA Lead to Recombination-Mediated Loss of Repeats.

Science.gov (United States)

Warmerdam, Daniël O; van den Berg, Jeroen; Medema, René H

2016-03-22

rDNA repeats constitute the most heavily transcribed region in the human genome. Tumors frequently display elevated levels of recombination in rDNA, indicating that the repeats are a liability to the genomic integrity of a cell. However, little is known about how cells deal with DNA double-stranded breaks in rDNA. Using selective endonucleases, we show that human cells are highly sensitive to breaks in 45S but not the 5S rDNA repeats. We find that homologous recombination inhibits repair of breaks in 45S rDNA, and this results in repeat loss. We identify the structural maintenance of chromosomes protein 5 (SMC5) as contributing to recombination-mediated repair of rDNA breaks. Together, our data demonstrate that SMC5-mediated recombination can lead to error-prone repair of 45S rDNA repeats, resulting in their loss and thereby reducing cellular viability. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Forekomst af resistente bakterier og forbrug af antibiotika til hunde

DEFF Research Database (Denmark)

Pedersen, Karl; Pedersen, Kristina; Jensen, Helene

2007-01-01

), Pasteurella multocida (n=25), Bordetella bronchiseptica (n=14), Proteus spp. (n=29), og E. coli (n=449). I undersøgelsen anvendtes data fra VetStat databasen. Størstedelen af de antibiotika, der bruges til hunde er bredspektrede. Penicilliner med udvidet spektrum, cephalosporiner samt sulphonamider...

Transkateterlukning af venstre atriums aurikel til forebyggelse af apoplexia cerebri

DEFF Research Database (Denmark)

Loupis, Anastasia M; De Backer, Ole; Ihlemann, Nikolaj

2014-01-01

In patients with atrial fibrillation (AF) and increased risk of stroke, oral anticoagulation (OAC) is the standard treatment for stroke prevention - however, this therapy also carries a high risk of bleeding. Percutaneous closure of the left atrial appendage (LAA) has been suggested to be an alte...

“All That Jazz” - bagsiden af showbizz

DEFF Research Database (Denmark)

Eigtved, Michael

2017-01-01

Artiklen, der er skrevet til programmet ifbm premieren på musicalen Chicago på Det Ny Teater beskriver den tendens i broadwaymusicals, som begynder i slutningen af 1960’erne med bla forestillingen Cabaret, hvor det er skyggesiden af underholdningens industrien, der selvrefleksivt er emnet for for...

Anvendelse af webkonference på Syddansk Universitet

DEFF Research Database (Denmark)

Kjær, Christopher; Christensen, Inger-Marie F.; Blok, Rasmus

2009-01-01

Artiklen videregiver en række praktiske erfaringer med anvendelse af webkonferencesystemet Adobe Connect Pro i forbindelse med undervisning på Syddansk Universitet (SDU). Via tre pilotprojekter fra forskellige fagområder præsenteres de første konkrete og indledende erfaringer med anvendelsen af det...

Building a model: developing genomic resources for common milkweed (Asclepias syriaca with low coverage genome sequencing

Directory of Open Access Journals (Sweden)

Weitemier Kevin

2011-05-01

Full Text Available Abstract Background Milkweeds (Asclepias L. have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L. could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp and 5S rDNA (120 bp sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp, with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae unigenes (median coverage of 0.29× and 66% of single copy orthologs (COSII in asterids (median coverage of 0.14×. From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites and phylogenetics (low-copy nuclear genes studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species

Ingeniørens rolle ved skabelse af innovative koncepter

DEFF Research Database (Denmark)

McAloone, Tim C.

2007-01-01

sågar også konkurrencer for skolebørn. En af årsagerne til konkurrencerne, er, at mange virksomheder anser konceptudviklingsaktiviteten for værende af stigende vigtighed. Det er interessant at bemærke, når man studerer disse forskellige konkurrencers rammer, regler og mål, at fællesnævneren for alle...... "innovative koncepter"? Først vedrørende en forståelse af "innovation" i den industrielle kontekst. Udover den relativt sikre og simplistiske definition af: innovation = opfindelse + markedsmæssig succes, er der kun ganske få forsøg i den danske industrikontekst på at definere målene for, eller aktiviteterne...... skabt (kerne produktindhold). Indtil videre er der ikke blevet leveret nogle af disse pc?er, så den kan stadig betragtes som et koncept. Men man har i hvert fald gjort sit bedste for at overveje alle teknologiske, sociale og design-aspekter af konceptet. Moralen her er, at vi ingeniører skal skærpe...

Variable presence of the inverted repeat and plastome stability in Erodium.

Science.gov (United States)

Blazier, John C; Jansen, Robert K; Mower, Jeffrey P; Govindu, Madhu; Zhang, Jin; Weng, Mao-Lun; Ruhlman, Tracey A

2016-06-01

Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts. © The Author 2016

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Science.gov (United States)

Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H.

2014-01-01

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L. Genome

Directory of Open Access Journals (Sweden)

Navdeep Gill

2014-04-01

Full Text Available Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

Repeat-Associated Plasticity in the Helicobacter pylori RD Gene Family▿ †

Science.gov (United States)

Shak, Joshua R.; Dick, Jonathan J.; Meinersmann, Richard J.; Perez-Perez, Guillermo I.; Blaser, Martin J.

2009-01-01

The bacterium Helicobacter pylori is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two H. pylori strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the H. pylori RD gene family. Each gene of this family is composed of a conserved 3′ region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5′ region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42 H. pylori strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject's stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by H. pylori-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding H. pylori persistence in its natural host. PMID:19749042

Lukning og indskrænkninger af virksomheder

DEFF Research Database (Denmark)

Pico Geerdsen, Peter; Høgelund, Jan; Larsen, Mona

Der tales meget om de negative konsekvenser af globalisering. I denne rapport søger forfatterne at vurdere risikoen for svagere tilknytning til arbejdsmarkedet og forringet indkomstudvikling blandt fratrådte lønmodtagere i de dele af industrien, der er særligt udsat for konkurrence fra...

The diversity and evolution of Wolbachia ankyrin repeat domain genes.

Directory of Open Access Journals (Sweden)

Stefanos Siozios

Full Text Available Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.

Digitalisering af undervisning

DEFF Research Database (Denmark)

Christiansen, René B.; Hansen, Søren; Rossen, Svend

2010-01-01

Rapporten er et bestillingsarbejde fra FU (Forskning og Udvikling) og viser en række eksempler på hvorledes undervisningsforløb kan konstrueres online. Herunder ved brug af både LMS-systemer og web 2.0-værktøjer...

Mononucleotide repeats are asymmetrically distributed in fungal genes

NARCIS (Netherlands)

Passel, van M.W.J.; Graaff, de L.H.

2008-01-01

ABSTRACT: BACKGROUND: Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the distribution of sequence repeats, which are notoriously variable and can disrupt the reading frame in genes, showed that

The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus

Directory of Open Access Journals (Sweden)

Huynh Minh

2009-11-01

Full Text Available Abstract Background There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial genome. Results The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals. Conclusion The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial