379 research outputs found
A genome-wide analysis of promoter-mediated phenotypic noise in <i>Escherichia coli</i>
No full textGene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as "phenotypic noise." In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alone.</p
Fabry-Perot-cavity-based refractometry without influence of mirror penetration depth
No full textAssessments of refractivity in a Fabry-Perot (FP) cavity by refractometry often encompass a step in which the penetration depth of the light into the mirrors is estimated to correct for the fraction of the cavity length into which no gas can penetrate. However, as it is currently carried out, this procedure is not always coherently performed. Here, we discuss a common pitfall that can be a reason for this and provide a recipe on how to perform FP-cavity-based refractometry without any influence of mirror penetration depth.Errata: C. Forssén, I. Silander, J. Zakrisson, M. Zelan, and O. Axner , "Retraction: “Fabry–Perot-cavity-based refractometry without influence of mirror penetration depth” [J. Vac. Sci. Technol. B 39, 065001 (2021)]", Journal of Vacuum Science & Technology B 40, 037001 (2022) https://doi.org/10.1116/6.0001829</p
To act or not to act? : A study about how France, Belgium and Rwanda acted in the genocide in Rwanda 1994.
No full textFolkmordet i Rwanda 1994 pågick under tre månader och är ett av de mest brutala folkmorden som har utförts under modern tid. Under dessa tre månader dödades ca 800 000 personer och takten i mördandet i Rwanda var fem gånger högre än vad dödandet var under Förintelsen. Till en början trodde omvärlden att det var ett inbördeskrig i Rwanda, vilket var en lögn. Den tidigare forskningen kring folkmordet i Rwanda 1994 bekräftar att FN som organisation misslyckades med att genomföra sitt uppdrag i Rwanda – men det visade sig också att vissa medlemsländer i FN kunde ha agerat annorlunda. Syftet med studien är att med utgångspunkt i FN-dokument undersöka hur Frankrike, Belgien och Rwanda agerade under och efter folkmordet i Rwanda 1994. Studiens källmaterial bestod av officiella FN-dokument som har publicerats i sin helhet i boken The United Nations and Rwanda 1993 – 1996 som FN utgav 1996. Studien präglades utav en kvalitativ textanalys, vilket syftar till att undersöka och analysera vad som faktiskt står i källmaterialet. Resultatet utav studien visade att både Frankrike och Belgiens ”icke-agerande” resulterade i att folkmordet i Rwanda inte stoppades tillräckligt fort. Både Frankrike och Belgien har en historia i Rwanda, vilket borde ha spelat en stor roll i hur de båda borde ha agerat. Resultatet visade också att Rwanda inte kunde sätta stopp för folkmordet själva eftersom Rwandas dåvarande regering var i konflikt med RPF. Det hade behövts ett agerande från FN, men speciellt från Frankrike och Belgien. Detta eftersom att de två medlemsländerna hade vetskap om bakomliggande orsaker till varför folkmordet utfördes under 1994
DEBATTEN OM NF OCH DESS SANKTIONSSYSTEM – VILHELM LUNDSTEDT OCH HANS ANTAGONISTER
No full textUnder år 2008 har det som bekant inte ens varit möjligt att inom Förenta Nationernas säkerhetsråd enas om sanktioner mot regimen i Zimbabwe. Denna uppsats tar dock sikte på en debatt som utspelade sig över 70 år tidigare i samband med den så kallade Abessinienkrisen
Automatic topic detection strategy for information retrieval in spoken document
No full textThis paper suggests an alternative solution for the task of spoken document retrieval (SDR). The proposed system runs retrieval on multi-level transcriptions (word and phone) produced by word and phone recognizers respectively, and their outputs are combined. We propose to use latent Dirichlet allocation (LDA) model for capturing the semantic information on word transcription. The LDA model is employed for estimating topic distribution in queries and word transcribed spoken documents, and the matching is performed at the topic level. Acoustic matching between query words and phonetically transcribed spoken documents is performed using phone-based matching algorithm. The results of acoustic and topic level matching methods are compared and shown to be complementary
Characterisation of epigenomic variation in natural isolates of E. coli : a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D in Genetics, Massey University, College of Science, School of Natural Sciences, Auckland
No full textDNA methylation is ubiquitous in bacteria and has a range of roles including self versus non-self recognition, DNA repair, and regulation of gene expression in response to internal and external cues. Regulation of gene expression by DNA methylation can lead to the establishment of phenotypic variation in otherwise isogenic populations. Until recently methods for the genome-wide study of DNA methylation in bacteria have been limited and therefore the full extent of DNA methylation's role in bacterial genomes is not well understood.
In this thesis I use Oxford Nanopore Technologies sequencing to investigate the presence and activity of DNA methyltransferase in natural isolates of E. coli. The first aim of this thesis is to produce high quality genome assemblies that can be used to determine methylation patterns. To achieve this, in Chapter 2 I first use in silico methods to quantify the effects of different read length characteristics on assembly quality. I then optimise DNA isolation and library prep methods to obtain high quality DNA.
In Chapter 3 I apply the results of Chapter 2 to sequence 49 natural isolates of E. coli from across the E. coli clade. I next benchmark five genome assembly methods for assembly accuracy. I base accuracy on five metrics designed to measure both the overall structural accuracy and the sequence accuracy of each assembly. The large number of isolates (49) used in this study, allows identification of the strengths associated with each assembly method. These results quantitatively describe best practices for bacterial genome assembly and highlight the current variability in genome assembly accuracy and therefore the importance of tailoring assembly methods to the study objectives.
Finally, in chapter 4 I use the data produced in Chapter 3 to investigate DNA methylation in three E. coli natural isolates. After in silico identification of all the methyltransferases in each genome, I show that the activity of all predicted methyltransferases can be detected, as well as the activity of unexpected putative methyltransferases which are present in our isolates. Finally, I show that the genome wide DNA methylation patterns show consistent differences across growth conditions. These results suggest that E. coli exhibits transient DNA methylation patterns depending on growth environment and state.
Overall this thesis establishes methods for assessing genome assemblies and broadens our understanding of genome wide DNA methylation patterns and the dynamics of these patterns in E. coli. Additionally this work provides insight into the possibility of transient epigenetic differentiation in E. coli which is reflected in the DNA methylation patterns across the genome
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