Movement of a prawn a Hidden Markov Model approach

Abstract This thesis presents the basic theory for hidden Markov models and standard inference algorithms for these. The performance for these algorithms are examined with the help of a small test problem and the algorithms are found to operate properly. An application of hidden Markov models for modelling the movements of a prawn is implemented. This model is shown to be significantly better to use for the problem than a more simple model, where all movements are independent. The model also proves useful for finding the time points for where the prawn changed direction. As a brief example of how this model can be used, logistic regression is used to find that the distance to neighbouring prawns have an effect on the probability of changing direction

Kreativitetens kugghjul - En studie om management av kreativitet

Syftet är att identifiera, beskriva och analysera viktiga aspekter för management av kreativitet i upplevelseföretag. Frågeställningar: Hur används kreativitet i upplevelseföretag? Vilka aspekter främjar organisatorisk kreativitet i upplevelseföretag? Hur hanterar ledare i upplevelseföretag kreativitet? Slutsatser: En organisations kreativitet skapas genom dess samspel mellan individer, grupp och organisatoriska egenskaper och studien har visat att ledaren har stor påverkan på detta samspel. Eftersom kreativitet är nödvändigt för alla företag i någon form blir ledarens uppgifter att främja kreativitet och använda den så att den gynnar företaget viktiga. Dessutom behöver ledaren ständigt bedöma kreativa idéer och handlingar för att besluta om vad som är värt att uppmärksamma. Det har visat sig att kreativitet i upplevelseföretag används dels i det dagliga arbetet och dess servicemöten, samt i utformandet och utvecklandet av upplevelseerbjudanden. Ägandeförhållanden har visat sig påverka hur kreativiteten kommer till uttryck och används. Det har blivit tydligt att det komplexa samspel som organisationer består av, i kombination med ledarens egenskaper, innebär att alla företag är unika och att det därför är svårt att finna ett framgångsrecept som är tillämpbart för alla upplevelseföretag

De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning

Background We introduce DESMAN for De novo Extraction of Strains from MetAgeNomes. Metagenome sequencing generates short reads from throughout the genomes of a microbial community. Increasingly large, multi-sample metagenomes, stratified in space and time are being generated from communities with thousands of species. Repeats result in fragmentary co-assemblies with potentially millions of contigs. Contigs can be binned into metagenome assembled genomes (MAGs) but strain level variation will remain. DESMAN identifies variants on core genes, then uses co-occurrence across samples to link variants into strain sequences and abundance profiles. These strain profiles are then searched for on non-core genes to determine the accessory genes present in each strain. Results We validated DESMAN on a synthetic twenty genome community with 64 samples. We could resolve the five E. coli strains present with 99.58% accuracy across core gene variable sites and their gene complement with 95.7% accuracy. Similarly, on real fecal metagenomes from the 2011 E. coli (STEC) O104:H4 outbreak, the outbreak strain was reconstructed with 99.8% core sequence accuracy. Application to an anaerobic digester metagenome time series reveals that strain level variation is endemic with 16 out of 26 MAGs (61.5%) examined exhibiting two strains. In almost all cases the strain proportions were not statistically different between replicate reactors, suggesting intra-species niche partitioning. The only exception being when the two strains had almost identical gene complement and, hence, functional capability. Conclusions DESMAN will provide a provide a powerful tool for de novo resolution of fine-scale variation in microbial communities. It is available as open source software from https://github.com/chrisquince/DESMAN

Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen cycling genes at two contrasting estuarine sites

Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.Peer reviewe

Targeted metagenomics of active microbial populations with stable-isotope probing

The ability to explore microbial diversity and function has been enhanced by novel experimental and computational tools. The incorporation of stable isotopes into microbial biomass enables the recovery of labeled nucleic acids from active microorganisms, despite their initial abundance and culturability. Combining stable-isotope probing (SIP) with metagenomics provides access to genomes from microorganisms involved in metabolic processes of interest. Studies using metagenomic analysis on DNA obtained from DNA-SIP incubations can be ideal for the recovery of novel enzymes for biotechnology applications, including biodegradation, biotransformation, and biosynthesis. This chapter introduces metagenomic and DNA-SIP methodologies, highlights biotechnology-focused studies that combine these approaches, and provides perspectives on future uses of these methods as analysis tools for applied and environmental microbiology

AMBER: Assessment of Metagenome BinnERs

Meyer F, Hofmann P, Belmann P, et al. AMBER: Assessment of Metagenome BinnERs. GigaScience. 2018;7(6): giy069

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. It automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat

Effect of sulfate on carbon monoxide conversion by a thermophilic syngas-fermenting culture dominated by a Desulfofundulus species

A syngas-degrading enrichment culture, culture T-Syn, was dominated by a bacterium closely related to Desulfofundulus australicus strain AB33T (98% 16S rRNA gene sequence identity). Culture T-Syn could convert high CO concentrations (from pCO 34 kPa to pCO 170 kPa), both in the absence and in the presence of sulfate as external electron acceptor. The products formed from CO conversion were H2 and acetate. With sulfate, a lower H2/acetate ratio was observed in the product profile, but CO conversion rates were similar to those in the absence of sulfate. The ability of D. australicus strain AB33T to use CO was also investigated. D. australicus strain AB33T uses up to 40% CO (pCO 68 kPa) with sulfate and up to 20% CO (pCO 34 kPa) without sulfate. Comparison of the metagenome-assembled genome (MAG) of the Desulfofundulus sp. from T-Syn culture with the genome of D. australicus strain AB33T revealed high similarity, with an ANI value of 99% and only 32 unique genes in the genome of the Desulfofundulus sp. T-Syn. So far, only Desulfotomaculum nigrificans strain CO-1-SRB had been described to grow with CO with and without sulfate. This work further shows the carboxydotrophic potential of Desulfofundulus genus for CO conversion, both in sulfate-rich and low-sulfate environments.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER307 000004) by the European Regional Development Fund under the scope of Norte 2020 – Programa Operacional Regional do Norte. The financial support from FCT and European Social Fund (POPH-QREN) through the grant PD/BD/128030/2016 given to AA and through the project INNOVsyn – Innovative strategies for syngas fermentation (POCI-01-0145-FEDER-031377) is gratefully acknowledged. Research of AS and DS was supported a Gravitation grant (024.002.002) of the Netherlands Ministry of Education, Culture and Science.info:eu-repo/semantics/publishedVersio