Gene duplicability of core genes is highly consistent across all angiosperms

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes

A study of the regulation of undecylprodigiosin biosynthesis in Streptomyces coelicolor A3(2)

Undecylprodigiosin is one of four secondary metabolites with antibacterial activity produced by S. coelicolor A3(2). The overall aim of this study was to further investigate the control of biosynthesis of the secondary metabolite undecylprodigiosin (Red) in Streptomyces coelicolor A3(2). Proline transport mutants (Put-) were isolated, and the over-production of Red was observed in these strains. It was hypothesised that Red biosynthesis is essential as a shunt for excess proline in the Put- mutants. Red biosynthesis was abolished by disrupting the redX structural gene in a Put- mutant. The Put- RedX- mutants were viable, demonstrating that Red is not essential in Pur mutants. Si nuclease mapping of redD and redX genes in a Put- mutant revealed that red genes are transcribed earlier in the growth phase of Put- mutants compared to the progenitor strain J802. Pwb (pigmented whilst bid) mutants had been isolated due to their ability to produce Red in a b1dA background. The regions believed to contain the mutations of Pwb-6, Pwb-9, Pwb-16 and Pwb+ were sub-cloned and sequence data obtained. An open reading frame was identified which is predicted to encode a protein showing homology to the UhpA-LuxR family of regulators. The open reading frame, contains an in-frame TTA codon. It is proposed that this gene, named redZ, mediates the b1dA dependence of Red biosynthesis. The Pwb-6 mutation was located to the putative -35 promoter region. The mutation makes the promoter more similar to the enteric bacterium major sigma factor promoter -35 consensus sequence. It is anticipated that greater transcription from the promoter causes the Pwb phenotype. Introduction of the Pwb-9 redZ gene into antibiotic biosynthesis mutants, absA and absB, did not result in Red biosynthesis

Identification, antimicrobial susceptibility and functionality of potentially probiotic bifidobacteria

Om een wetenschappelijk verantwoord probiotisch product op de markt te introduceren is het van uitermate groot belang dat de gebruikte probiotische stammen correct geïdentificeerd zijn en onderworpen worden aan grondig onderzoek naar hun veiligheid en functionaliteit vooraleer klinische studies worden aangevat en voor eigenlijke commercialisering van het product. Enkel op die manier kunnen probiotische producten met lange-termijn perspectieven succesvol geïntroduceerd worden. Dit doctoraat had tot doel nieuwe en bestaande technieken te evalueren en optimaliseren voor microbiële kwaliteitscontrole van probiotische producten evenals voor het verschaffen van wetenschappelijke informatie gerelateerd aan de veiligheid en functionaliteit van commercieel gebruikte en humane referentie stammen van het genus Bifidobacterium. Dit omvatte de kwalitatieve en kwantitatieve microbiële analyse van wereldwijd verzamelde probiotische producten die beweerden bifidobacteriën te bevatten, gebruik makende van zowel kweekahankelijke als kweekonafhankelijke methoden. Op basis van deze resultaten werd een subset probiotische product isolaten geselecteerd die samen met humane referentie stammen van het genus Bifidobacterium onderzocht werden naar de aanwezigheid van atypische antibiotica resistenties, naar hun immuunmodulerende eigenschappen en hun capaciteit om transit doorheen het gastrointestinaal stelsel te overleven

CLEVER: Clique-Enumerating Variant Finder

Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals. Here we present a novel internal segment size based approach, which organizes all, including also concordant reads into a read alignment graph where max-cliques represent maximal contradiction-free groups of alignments. A specifically engineered algorithm then enumerates all max-cliques and statistically evaluates them for their potential to reflect insertions or deletions (indels). For the first time in the literature, we compare a large range of state-of-the-art approaches using simulated Illumina reads from a fully annotated genome and present various relevant performance statistics. We achieve superior performance rates in particular on indels of sizes 20--100, which have been exposed as a current major challenge in the SV discovery literature and where prior insert size based approaches have limitations. In that size range, we outperform even split read aligners. We achieve good results also on real data where we make a substantial amount of correct predictions as the only tool, which complement the predictions of split-read aligners. CLEVER is open source (GPL) and available from http://clever-sv.googlecode.com.Comment: 30 pages, 8 figure

Using a zebrafish model to examine the importance of the stringent response for Staphylococcus aureus pathogenesis

Staphylococcus aureus is a human commensal organism with the potential to become opportunistic given the right conditions. During infection, bacteria are exposed to stresses like nutrient limitation, which they respond to by inducing the stringent response. This is a conserved bacterial reaction to stress that ultimately shuts down macromolecular processes to promote bacterial survival, achieved by the production of the nucleotide signalling molecule guanosine penta-/tetraphosphate ((p)ppGpp). The S. aureus genome encodes three (p)ppGpp synthetases: Rel, RelP and RelQ. (p)ppGpp produced by these synthetases contributes to bacterial pathogenesis in a number of species. In this study, a toolbox of S. aureus strains was constructed to improve understanding of how the stringent response is important for the survival and virulence of S. aureus in vitro and in vivo. To elucidate the mechanism behind the requirement of (p)ppGpp for intracellular survival in vitro, the S. aureus strains were exposed to stress conditions typically found in a phagolysosome. A (p)ppGpp0 mutant was observed to be more susceptible to hydrogen peroxide, itaconic acid and hypochlorous acid whereas an overproduction of (p)ppGpp increased the tolerance of S. aureus to these stressors. RelP alone could complement itaconic acid stress while both Rel and RelP could have a role in the tolerance of S. aureus to hydrogen peroxide. Systemic infection of zebrafish embryos with a (p)ppGpp0 mutant revealed increased survival of embryos when compared to embryos infected with the wildtype, which is likely due to a virulence defect as the (p)ppGpp0 mutant replicated at a similar rate to the wildtype in vivo. (p)ppGpp overproduction also resulted in an increased survival of embryos. Complementation experiments revealed that Rel is a key (p)ppGpp synthetase during infection, but that RelP and RelQ may be sufficient in the absence of Rel. Taken together, these results demonstrate a role of (p)ppGpp for S. aureus pathogenesis within a zebrafish embryo systemic infection model, with in vitro experiments showing that the stringent response is required for survival during stress

Testimonial of Professional Contributions in the Biotechnology Field (1991-2019). Pulmonary Infectious Agents Streptococcus pneumoniae and Mycobacterium tuberculosis

Relatório elaborado nos termos do Despacho n.º 20/2010 para obtenção do Grau de Mestre em Biotecnologia por Licenciados “Pré-Bolonha”Pulmonary infectious diseases, like pneumonia and tuberculosis, have been pervasive throughout the world for centuries; they kill millions of people annually worldwide and pose an increased threat when associated with antibiotic resistance and viral co-infections such as influenza and, more recently, Covid-19. This professional activity report summarizes some of my work in the last three decades, using biotechnology to type, characterize or detect two major bacterial infectious agents, Streptococcus pneumoniae and Mycobacterium tuberculosis. Strain typing techniques, like Pulsed Field Gel Electrophoresis and Penicillin Binding Protein patterns, were used to identify Streptococcus pneumoniae clones from different geographic areas in the early-1990s, showing strong evidence of clonal dissemination locally and across the globe, from Spain to Iceland and to the United States. In the mid-1990s, an in vivo expression technology system based on a promoter-trap was constructed to enable the identification of Mycobacterium tuberculosis genes upregulated in human macrophages, through selection for antibiotic resistance. This work led to the identification of eight genes likely relevant for Mycobacterium tuberculosis virulence. Several were later confirmed to be required for infection or survival in the host. A single-step molecular diagnostic real-time PCR assay for the detection of multidrug resistant Mycobacterium tuberculosis was commercialized in the late 2000s, with great impact in the detection of tuberculosis, especially in developing countries. The mechanism of the assay is presented here as published by its inventors, as well as with my role in the industry, from the development of processes for production and quality control, to regulation-compliant distribution, troubleshooting and development of improvements.As doenças infeciosas pulmonares, como a pneumonia e a tuberculose, têm tido, durante séculos uma prevalência mundial significativa, matando milhões de pessoas anualmente e representando uma ameaça crescente quando associadas à resistência a antibióticos ou coinfeções virais, como a gripe e, recentemente, o Covid-19. Este relatório de atividade profissional resume parte do meu trabalho nas últimas três décadas, usando técnicas de biotecnologia para identificar, caracterizar ou detetar dois importantes agentes infeciosos de origem bacteriana, Streptococcus pneumoniae e Mycobacterium tuberculosis. Técnicas de identificação de estirpes, como eletroforese tipo Pulsed Field e padrões de proteínas com afinidade à penicilina, foram usadas para identificar clones de Streptococcus pneumoniae de diferentes áreas geográficas no início da década de 90, mostrando forte evidência de disseminação, não só a nível local, mas também através do globo, nomeadamente, de Espanha para a Islândia e Estados Unidos. Em meados da década de 90, um sistema de expressão in vivo foi construído para permitir a identificação de genes de Mycobacterium tuberculosis com expressão elevada em macrófagos humanos, através de seleção por resistência a antibióticos. Este trabalho levou à identificação de oito genes com probabilidade de serem relevantes para a virulência de Mycobacterium tuberculosis; vários posteriormente confirmados como necessários para a infeção ou sobrevivência no hospedeiro. Mais recentemente, foi comercializado um teste de real-time PCR para diagnóstico molecular de Mycobacterium tuberculosis com multirresistência a antibióticos, com grande impacto na deteção da tuberculose, principalmente em certos países em desenvolvimento. O mecanismo de deteção é apresentado aqui conforme publicado pelos seus inventores, bem como o meu papel na indústria de diagnósticos moleculares, desde o desenvolvimento de processos de produção e controle de qualidade, até a distribuição em conformidade com os respetivos regulamentos, passando por resolução de problemas e desenvolvimento de melhorias

Asynchronous and Multiprecision Linear Solvers - Scalable and Fault-Tolerant Numerics for Energy Efficient High Performance Computing

Asynchronous methods minimize idle times by removing synchronization barriers, and therefore allow the efficient usage of computer systems. The implied high tolerance with respect to communication latencies improves the fault tolerance. As asynchronous methods also enable the usage of the power and energy saving mechanisms provided by the hardware, they are suitable candidates for the highly parallel and heterogeneous hardware platforms that are expected for the near future

Catalysis and biocatalysis program

The annual report presents the fiscal year (FY) 1990 research activities and accomplishments for the Catalysis and Biocatalysis Program of the Advanced Industrial Concepts Division (AICD), Office of Industrial Technologies of the Department of Energy (DOE). The mission of the AICD is to create a balanced program of high risk, long term, directed interdisciplinary research and development that will improve energy efficiency and enhance fuel flexibility in the industrial sector. The Catalysis and Biocatalysis Program's technical activities were organized into five work elements: the Molecular Modeling and Catalysis by Design element; the Applied Microbiology and Genetics element; the Bioprocess Engineering element; the Separations and Novel Chemical Processes element; and the Process Design and Analysis element