Tilknytning og barnehage -En kvalitativ studie av forskjeller mellom profesjoner med hensyn til oppfatninger om, og eventuelt hvordan, tilknytningsteorien bør influere på barnehagedrift.

Master i samfunnsvitenskap med fordypning i sosialt arbeid - Nord universitet 201

Genome sequencing and annotation of Aeromonas sp. HZM

We report the draft genome sequence of Cellulomonas sp. HZM, isolated from a tropical peat swamp forest. The draft genome size is 3,559,280 bp with a G + C content of 73% and contains 3 rRNA sequences (single copies of 5S, 16S and 23S rRNA)

Hvordan har Covid-19 pandemien påvirket elevrelasjoner, skoletrivsel og mobbing hos skoleelever i Tromsø? En kvantitativ undersøkelse basert på rådata fra «Trivsel i Tromsø 1 og 2».

Covid-19-pandemien kom plutselig og overraskende på alle i 2020, og for å begrense sykdom og dødelighet ble Norges befolkning pålagt mange restriksjoner. Det var fra pandemiens start et uttalt mål å begrense konsekvensene for barn og unge i størst mulig grad, men i ettertid ansees ikke det for å ha vært helt vellykket (NOU 2022:5). Dette er en kvantitativ studie basert på rådata fra to tverrsnittsundersøkelser tilknyttet den longitudinelle studien «Trivsel i Tromsø» («Well-being in Tromsø»). Med utgangspunkt i problemstillingen «Hvordan har Covid-19 pandemien påvirket elevrelasjoner, skoletrivsel og mobbing hos skoleelever i Tromsø?» har formålet med studien vært å undersøke elevenes egenrapporterte opplevelser av egen situasjon ett år inn i pandemien, og å sammenligne med data innhentet Pre-Covid. Tverrsnittsundersøkelsen «Trivsel i Tromsø 2» ble gjennomført april 2021(n=1239) og sammenlignet med datasett fra «Trivsel i Tromsø» innhentet vår 2017 (n=972). For å svare på problemstillingen ble fire forskningsspørsmål utarbeidet: 1) Hvordan predikerer elevrelasjon skoletrivsel før og under pandemien?, 2) Har det vært en signifikant endring i elevrelasjon og skoletrivsel før og under pandemien?, 3) Hvordan predikerer mobbing skoletrivsel før og under pandemien? og 4) Har det vært en signifikant endring i mobbing før og under pandemien? Undersøkelsen er basert på to ikke-sannsynlighetsutvalg med respondenter tilhørende 4.-5. trinn, 6.-7. trinn og 8.-10.trinn. Ferdig utarbeidede samlevariabler fra Kindl® og «Life in school» ble benyttet for å undersøke skoletrivsel, elevrelasjoner, klassisk og digital mobbing, samt verbal-, fysisk, sosial- og digital trakassering. Deskriptive analyser, samt korrelasjons- og regresjonsanalyser ble gjennomført i SPSS 28.0. Resultatene i undersøkelsen indiker en sterk samvariasjon mellom skoletrivsel og elevrelasjoner, og svak samvariasjon mellom skoletrivsel og mobbing. Hovedfunnene i studien viser en signifikant nedgang i skoletrivsel fra 2017 til 2021 på alle trinn, samt signifikant økning i mobbing og trakassering på alle trinn. Dette med unntak av sosial trakassering, der var økningen ikke signifikant. Endringene mellom Pre-Covid-gruppen og Covid-gruppen var gjennomgående størst på 8.-10. trinn, og lavest på 4.-5. trinn

Adding complexity to complexity: Gene family evolution in polyploids

Comparative genomics of non-model organisms has resurrected whole genome duplication (WGD) from being viewed as a somewhat obscure process that happens in plants to a primary driver of eukaryotic diversification. The shadow of past ploidy increases has left a strong signature of duplicated genes organized into gene families, even in small genomes that have undergone effectively complete rediploidization. Nevertheless, despite continually advancing technologies and bioinformatics pipelines, resolving the fate of duplicate genes remains a substantial challenge. For example, many important recognition processes are driven not only by allelic expansion through retention of duplicates but also by diversification and copy number variation. This creates technical difficulties with assembly to reference genomes and accurate interpretation of homology. Thus, relatively little is known about the impacts of recent polyploidization and hybridization on the evolution of gene families under selective forces that maintain diversity, such as balancing selection. Here we use a complex of species and ploidy levels in the genus Arabidopsis (A. lyrata and A. arenosa) as a model to investigate the evolutionary dynamics of a large and complicated gene family known to be under strong balancing selection: the receptor-like kinases, which include the female component of genetically controlled self-incompatibility. Specifically, we question: (1) How does diversity of S-receptor kinase (SRK) alleles in tetraploids compare to that in their close diploid relatives? (2) Is there increased trans-specific polymorphism (i.e., sharing of alleles that transcend speciation, characteristic of balancing selection) in tetraploids compared to diploids due to the higher number of copies they carry? (3) Do these highly variable loci show evidence of introgression among extant species/ploidy levels within or outside known zones of hybridization? (4) Is there evidence for copy number variation among paralogs? We use this example to highlight specific issues to consider when interpreting gene family evolution, particularly in relation to polyploids but also more generally in diploids. We conclude with recommendations for strategies to address the challenges of resolving such complex loci in the future, using advances in deep sequencing approaches

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

<p>Abstract</p> <p>Background</p> <p>Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques.</p> <p>Results</p> <p>Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being <it>Lactobacillus</it>, <it>Prevotella </it>and <it>Gardnerella</it>. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500.</p> <p>Conclusions</p> <p>Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.</p

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Masteroppgave i økonomistyring (MSc) 201

Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods

<p>Abstract</p> <p>Background</p> <p>Classification of bacteria within the genus <it>Brucella </it>has been difficult due in part to considerable genomic homogeneity between the different species and biovars, in spite of clear differences in phenotypes. Therefore, many different methods have been used to assess <it>Brucella </it>taxonomy. In the current work, we examine 32 sequenced genomes from genus <it>Brucella </it>representing the six classical species, as well as more recently described species, using bioinformatical methods. Comparisons were made at the level of genomic DNA using oligonucleotide based methods (Markov chain based genomic signatures, genomic codon and amino acid frequencies based comparisons) and proteomes (all-against-all BLAST protein comparisons and pan-genomic analyses).</p> <p>Results</p> <p>We found that the oligonucleotide based methods gave different results compared to that of the proteome based methods. Differences were also found between the oligonucleotide based methods used. Whilst the Markov chain based genomic signatures grouped the different species in genus <it>Brucella </it>according to host preference, the codon and amino acid frequencies based methods reflected small differences between the <it>Brucella </it>species. Only minor differences could be detected between all genera included in this study using the codon and amino acid frequencies based methods.</p> <p>Proteome comparisons were found to be in strong accordance with current <it>Brucella </it>taxonomy indicating a remarkable association between gene gain or loss on one hand and mutations in marker genes on the other. The proteome based methods found greater similarity between <it>Brucella </it>species and <it>Ochrobactrum </it>species than between species within genus <it>Agrobacterium </it>compared to each other. In other words, proteome comparisons of species within genus <it>Agrobacterium </it>were found to be more diverse than proteome comparisons between species in genus <it>Brucella </it>and genus <it>Ochrobactrum</it>. Pan-genomic analyses indicated that uptake of DNA from outside genus <it>Brucella </it>appears to be limited.</p> <p>Conclusions</p> <p>While both the proteome based methods and the Markov chain based genomic signatures were able to reflect environmental diversity between the different species and strains of genus <it>Brucella</it>, the genomic codon and amino acid frequencies based comparisons were not found adequate for such comparisons. The proteome comparison based phylogenies of the species in genus <it>Brucella </it>showed a surprising consistency with current <it>Brucella </it>taxonomy.</p

Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays

Not until recently have custom made high-density oligonucleotide microarrays been available at an affordable price. The aim of this thesis was to design microarrays and analysis algorithms for DNA repair and DNA damage detection, and to apply the methods in real experiments. Thomassen et al. have used their custom designed whole genome-tiling microarrays for detection of transcriptional changes in Escherichia coli after exposure to DNA damageing reagents. The transcriptional changes in E. coli treated with UV light or the methylating reagent MNNG were shown to be larger and to include far more genes than previously reported. To optimize the data analysis for the custom made arrays, Thomassen and coworkers designed their own normalization and analysis algorithms, and showed these more suitable than established methods that are currently applied on custom tiling arrays. Among other findings several novel stress-induced transcripts were detected, of which one is predicted to be a UV-induced short transmembrane protein. Additionally, no upregulation of the previously described UV-inducible aidB is shown. In the MNNG study several genes are shown as downregulated in response to DNA damage although having upstream regulatory sequences similar to the established LexA box A and B. This indicates that the LexA regulon also might control gene repression and that the box A and B sequence can not alone answer for the LexA controlled gene regulation. Thomassen et al. have also custom designed a microarray for oncogenic fusion gene detection. Cancer specific fusion genes are often used to subgroup cancers and to define the optimal treatment, but currently the laboratory detection procedure is both laborious and tedious. In a blinded study on six cancer cell lines proof of principle was shown by detection of six out of six positive controls. The design and analysis methods for this microarray are now being refined to make a diagnostic fusion gene detection tool