Gabriele Romagnoli

Gabriele Romagnoli

Leiden, Zuid-Holland, Nederland
31K volgers Meer dan 500 connecties

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Creative, Technologist, Storyteller... in any order you like 😉

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Artikelen van Gabriele

  • How to Make Procedural Generation Look Good

    How to Make Procedural Generation Look Good

    In this episode, we dive into the creative mind of Oskar Stålberg, the developer behind many acclaimed indie successes…

    1 commentaar
  • How to pick the best GenAI tool for images

    How to pick the best GenAI tool for images

    In this episode, we sit down with Sachin Kamath↗️ and unpack the world of AI-generated images. We explore his favorite…

    4 commentaren
  • HOLOGATE's Journey from VR Games to Military Trainings

    HOLOGATE's Journey from VR Games to Military Trainings

    In this issue we explore with HOLOGATE ’s CEO Leif Arne Petersen how they went from becoming a world leader in the LBE…

    1 commentaar
  • Deep Dive into Microsoft's XR and AI Strategy with Alex Karim

    Deep Dive into Microsoft's XR and AI Strategy with Alex Karim

    In this issue we discuss with Alex Karim , AI Architect at Microsoft, how to deploy XR and AI technologies in big and…

    5 commentaren
  • The Only Open Source AR Glasses Powered by AI

    The Only Open Source AR Glasses Powered by AI

    After the tumultous release of the Humane AI pin and the Rabbit R1 the space of AI wearables heated up. In this issue…

    1 commentaar
  • How Retropolis got 4.9 ⭐ on the Meta Store

    How Retropolis got 4.9 ⭐ on the Meta Store

    Today we will Learn about the origins, challenges, and success of Retropolis: a story-driven point-and-click adventure…

    1 commentaar
  • The Environmental Impact of AI Quantified

    The Environmental Impact of AI Quantified

    In this issue, we delve into the critical impact that training and running AI models is having on the environment and…

  • The Truth About AI in Game Development

    The Truth About AI in Game Development

    In this episode, we will give a pragmatic look at the current state of AI in Game development with Tommy Thompson , a…

    1 commentaar

Activiteit

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Ervaring

  • ShapesXR grafisch
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    Netherlands

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    Berlin, Germany

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    Netherlands

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    Netherlands

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    Netherlands

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    Leiden

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    Leiden

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    Leiden

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    Delft Area, Netherlands

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    Nottingham, United Kingdom

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    Singapore

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    Rome Area, Italy

Opleiding

  • University of Rome "La Sapienza"

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    Graduated with Honors.
    Dissertion title: "Synchronous protein cycling in batch cultures of the yeast Saccharomyces cerevisiae at log growth phase"

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    Graduated with Honors.
    Dissertion title "Optimization of recombinant fungal laccase production with strains of the yeast Kluyveromyces lactis from the pyruvate decarboxylase promoter"

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    Grade: 110/110

Publicaties

  • An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme

    Molecular Microbiology

    Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologues of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to functionally complement the corresponding deletion in S. cerevisiae. Surprisingly, deletion of the single K. lactis arginase gene KlCAR1 did not completely…

    Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologues of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to functionally complement the corresponding deletion in S. cerevisiae. Surprisingly, deletion of the single K. lactis arginase gene KlCAR1 did not completely abolish growth on arginine as nitrogen source. Growth rate of the deletion mutant strongly increased during serial transfer in shake-flask cultures. A combination of RNAseq-based transcriptome analysis and 13C-15N-based flux analysis was used to elucidate the arginase-independent pathway. Isotopic 13C15N-enrichment in γ-aminobutyrate revealed succinate as the entry point in the TCA cycle of the alternative pathway. Transcript analysis combined with enzyme activity measurements indicated increased expression in the Klcar1Δ mutant of a guanidinobutyrase (EC.3.5.3.7), a key enzyme in a new pathway for arginine degradation. Expression of the K. lactis KLLA0F27995g (renamed KlGBU1) encoding guanidinobutyrase enabled S. cerevisiae to use guanidinobutyrate as sole nitrogen source and its deletion in K. lactis almost completely abolish growth on this nitrogen source. Phylogenetic analysis suggests that this enzyme activity is widespread in fungi.

    Andere auteurs
  • Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose

    Yeast

    Phenylethanol has a characteristic rose-like aroma that makes it a popular ingredient in foods, beverages and cosmetics. Microbial production of phenylethanol currently relies on whole-cell bioconversion of phenylalanine with yeasts that harbour an Ehrlich pathway for phenylalanine catabolism. Complete biosynthesis of phenylethanol from a cheap carbon source, such as glucose, provides an economically attractive alternative for phenylalanine bioconversion. In this study, synthetic genetic array…

    Phenylethanol has a characteristic rose-like aroma that makes it a popular ingredient in foods, beverages and cosmetics. Microbial production of phenylethanol currently relies on whole-cell bioconversion of phenylalanine with yeasts that harbour an Ehrlich pathway for phenylalanine catabolism. Complete biosynthesis of phenylethanol from a cheap carbon source, such as glucose, provides an economically attractive alternative for phenylalanine bioconversion. In this study, synthetic genetic array (SGA) screening was applied to identify genes involved in regulation of phenylethanol synthesis in Saccharomyces cerevisiae. The screen focused on transcriptional regulation of ARO10, which encodes the major decarboxylase involved in conversion of phenylpyruvate to phenylethanol. A deletion in ARO8, which encodes an aromatic amino acid transaminase, was found to underlie the transcriptional upregulation of ARO10 during growth, with ammonium sulphate as the sole nitrogen source. Physiological characterization revealed that the aro8Δ mutation led to substantial changes in the absolute and relative intracellular concentrations of amino acids. Moreover, deletion of ARO8 led to de novo production of phenylethanol during growth on a glucose synthetic medium with ammonium as the sole nitrogen source. The aro8Δ mutation also stimulated phenylethanol production when combined with other, previously documented, mutations that deregulate aromatic amino acid biosynthesis in S. cerevisiae. The resulting engineered S. cerevisiae strain produced >3 mm phenylethanol from glucose during growth on a simple synthetic medium. The strong impact of a transaminase deletion on intracellular amino acid concentrations opens new possibilities for yeast-based production of amino acid-derived products

    Andere auteurs
  • Functional analysis and transcriptional regulation of two orthologs of ARO10, encoding broad-substrate-specificity 2-oxo-acid decarboxylases, in the brewing yeast Saccharomyces pastorianus CBS1483

    Fems yeast research

    The hybrid genomes of Saccharomyces pastorianus consist of subgenomes simi-
    lar to those of S. cerevisiae and S. eubayanus, and impact of the genome struc-
    ture on flavour production and its regulation is poorly understood. This study
    focuses on ARO10, a 2-oxo-acid decarboxylase involved in production of
    higher alcohols. In S. pastorianus CBS1483, four ARO10 copies were identified,
    three resembled S. cerevisiae ARO10 and one S. eubayanus ARO10. Substrate
    specificities of lager…

    The hybrid genomes of Saccharomyces pastorianus consist of subgenomes simi-
    lar to those of S. cerevisiae and S. eubayanus, and impact of the genome struc-
    ture on flavour production and its regulation is poorly understood. This study
    focuses on ARO10, a 2-oxo-acid decarboxylase involved in production of
    higher alcohols. In S. pastorianus CBS1483, four ARO10 copies were identified,
    three resembled S. cerevisiae ARO10 and one S. eubayanus ARO10. Substrate
    specificities of lager strain (Lg)ScAro10 and LgSeubAro10 were compared by
    individually expressing them in a pdc1D-pdc5D-pdc6D-aro10D-thi3D S. cerevisiae
    strain. Both isoenzymes catalysed decarboxylation of the 2-oxo-acids derived
    from branched-chain, sulphur-containing amino acids isoleucine, and prefera-
    bly phenylpyruvate. Expression of both alleles was induced by phenylalanine,
    however in contrast to the S. cerevisiae strain, the two genes were not induced
    by leucine. Additionally, LgSeubARO10 showed higher basal expression levels
    during growth with ammonia. ARO80, which encodes ARO10 transcriptional
    activator, is located on CHRIV and counts three Sc-like and one Seub-like cop-
    ies. Deletion of LgSeubARO80 did not affect LgSeubARO10 phenylalanine
    induction, revealing ‘trans’ regulation across the subgenomes. ARO10 transcript
    levels showed a poor correlation with decarboxylase activities. These results
    provide insights into flavour formation in S. pastorianus and illustrate the
    complexity of functional characterization in aneuploid strains.

    Andere auteurs
    Publicatie weergeven
  • Substrate specificity of thiamine-pyrophosphate-dependent 2-oxo-acid decarboxylases in Saccharomyces cerevisiae

    Fusel alcohols are precursors and contributors to flavour and aroma compounds in fermented beverages and some are under investigation as biofuels. Decarboxylation of 2-oxo acids is a key step in the Ehrlich pathway for fusel alcohol production. In Saccharomyces cerevisiae, five genes share sequence similarity with genes encoding thiamine-pyrophosphate-dependent 2-oxo-acid decarboxylases (2ODCs). PDC1, PDC5 and PDC6 encode differentially regulated pyruvate-decarboxylase isoenzymes, ARO10…

    Fusel alcohols are precursors and contributors to flavour and aroma compounds in fermented beverages and some are under investigation as biofuels. Decarboxylation of 2-oxo acids is a key step in the Ehrlich pathway for fusel alcohol production. In Saccharomyces cerevisiae, five genes share sequence similarity with genes encoding thiamine-pyrophosphate-dependent 2-oxo-acid decarboxylases (2ODCs). PDC1, PDC5 and PDC6 encode differentially regulated pyruvate-decarboxylase isoenzymes, ARO10 encodes a 2-oxo-acid decarboxylase with broad substrate specificity and THI3 has not yet been shown to encode an active decarboxylase. Despite the importance of fusel alcohol production in S. cerevisiae, substrate specificities of these five 2ODCs have not been systematically compared. When the five 2ODCs were individually overexpressed in a pdc1∆ pdc5∆ pdc6∆ aro10∆ thi3∆ strain, only Pdc1, Pdc5 and Pdc6 catalyzed decarboxylation of the linear-chain 2-oxo acids pyruvate, 2-oxo-butanoate and 2-oxo-pentanoate in cell extracts. Presence of a Pdc isoenzyme was also required for production of n-propanol and n-butanol in cultures grown on threonine and norvaline, respectively, as nitrogen sources. These results demonstrate the importance of pyruvate decarboxylases in the natural production of n-propanol and n-butanol by S. cerevisiae. No decarboxylation activity was found for Thi3p with any of the substrates tested. Only Aro10p and Pdc5p catalyzed the decarboxylation of the aromatic substrate phenylpyruvate, with Aro10p showing superior kinetic properties. Aro10, Pdc1, Pdc5 and Pdc6 exhibited activity with all branched-chain and sulfur-containing 2-oxo acids tested, but with markedly different decarboxylation kinetics. The high affinity of Aro10p identified it as key contributor to production of branched-chain and sulfur-containing fusel alcohols.

    Andere auteurs
    Publicatie weergeven
  • Resolving phenylalanine metabolism sheds light on natural synthesis of penicillin G in Penicillium chrysogenum

    Eukaryotic cell (impact factor: 3.81)

    Industrial production of penicillin G by Penicillium chrysogenum requires supplementation of the growth medium with the side-chain precursor phenylacetate. Growth of P.chrysogenum with phenylalanine as sole nitrogen source resulted in extracellular production of phenylacetate and penicillin G. To analyse this 'natural' pathway for penicillin G production, chemostat cultures were switch to (13)C(9)-phenylalanine as nitrogen source. Quantification and modelling of the dynamics of labelled…

    Industrial production of penicillin G by Penicillium chrysogenum requires supplementation of the growth medium with the side-chain precursor phenylacetate. Growth of P.chrysogenum with phenylalanine as sole nitrogen source resulted in extracellular production of phenylacetate and penicillin G. To analyse this 'natural' pathway for penicillin G production, chemostat cultures were switch to (13)C(9)-phenylalanine as nitrogen source. Quantification and modelling of the dynamics of labelled metabolites indicated that phenylalanine was: i) incorporated in nascent protein, ii) transaminated to phenylpyruvate and further converted by oxidation or by decarboxylation and iii) hydroxylated to tyrosine and subsequently metabolized via the homogentisate pathway. Involvement of the homogentisate pathway was supported by comparative transcriptome analysis of P. chrysogenum cultures grown with phenylalanine and (NH(4))(2)SO(4) as nitrogen source. This transcriptome analysis also enabled the identification of two putative 2-oxo acid decarboxylase genes (Pc13g9300 and Pc18g01490). cDNAs of both genes were cloned and expressed in the 2-oxo-acid-decarboxylase-free Saccharomyces cerevisiae strain CEN.PK711-7C (pdc1,5,6Δ aro10Δ thi3Δ). Introduction of Pc13g09300 restored growth of this S. cerevisiae mutant on glucose and phenylalanine, thereby demonstrating that Pc13g09300 encodes a dual substrate pyruvate and phenylpyruvate decarboxylase, which plays a key role in an Ehrlich-type pathway for production of phenylacetate in P. chrysogenum. These results provide a basis for metabolic engineering of P. chrysogenum for production of the penicillin G side-chain precursor phenylacetate

    Andere auteurs
    • Tania Veiga
    • Daniel Solis-Escalante
    • Angela Ten Pierick
    • Mark Hanemaaijer
    • Amit T Deshmukh
    • Aljoscha Wahl
    • Jack T Pronk
    • Jean-Marc Daran
    Publicatie weergeven
  • Synchronous protein cycling in batch cultures of the yeast Saccharomyces cerevisiae at log growth phase

    Experimental cell research (impact factor: 3.59)

    The assumption that cells are temporally organized systems, i.e. showing relevant dynamics of their state variables such as gene expression or protein and metabolite concentration, while tacitly given for granted at the molecular level, is not explicitly taken into account when interpreting biological experimental data. This conundrum stems from the (undemonstrated) assumption that a cell culture, the actual object of biological experimentation, is a population of billions of independent…

    The assumption that cells are temporally organized systems, i.e. showing relevant dynamics of their state variables such as gene expression or protein and metabolite concentration, while tacitly given for granted at the molecular level, is not explicitly taken into account when interpreting biological experimental data. This conundrum stems from the (undemonstrated) assumption that a cell culture, the actual object of biological experimentation, is a population of billions of independent oscillators (cells) randomly experiencing different phases of their cycles and thus not producing relevant coordinated dynamics at the population level. Moreover the fact of considering reproductive cycle as by far the most important cyclic process in a cell resulted in lower attention given to other rhythmic processes. Here we demonstrate that growing yeast cells show a very repeatable and robust cyclic variation of the concentration of proteins with different cellular functions. We also report experimental evidence that the mechanism governing this basic oscillator and the cellular entrainment is resistant to external chemical constraints. Finally, cell growth is accompanied by cyclic dynamics of medium pH. These cycles are observed in batch cultures, different from the usual continuous cultures in which yeast metabolic cycles are known to occur, and suggest the existence of basic, spontaneous, collective and synchronous behaviors of the cell population as a whole.

    Andere auteurs
    • Enrico Cundari
    • Rodolfo Negri
    • Marco Crescenzi
    • Lorenzo Farina
    • Alessandro Giuliani
    • Michele M Bianchi
    Publicatie weergeven
  • Optimization of recombinant fungal laccase production with strains of the yeast Kluyveromyces lactis from the pyruvate decarboxylase promoter

    FEMS yeast research (impact factor: 1.79)

    Laccases are multicopper oxidases of wide specificity that catalyze the oxidation of phenolic and related compounds using molecular oxygen as the electron acceptor. Here, we report the production of the Lcc1 laccase of the fungus Trametes trogii in strains of the yeast Kluyveromyces lactis, using the pyruvate decarboxylase promoter (KlPDC1) as an expression system. We assayed laccase production in various strains, with replicative and integrative transformants and with different cultivation…

    Laccases are multicopper oxidases of wide specificity that catalyze the oxidation of phenolic and related compounds using molecular oxygen as the electron acceptor. Here, we report the production of the Lcc1 laccase of the fungus Trametes trogii in strains of the yeast Kluyveromyces lactis, using the pyruvate decarboxylase promoter (KlPDC1) as an expression system. We assayed laccase production in various strains, with replicative and integrative transformants and with different cultivation parameters. A comparison with Lcc1 enzymes from other yeasts and from the original organism was also performed. The best production conditions were obtained with integrative transformants of an individual strain, whereas cultivation conditions were less stringent than the use of the regulated KlPDC1 promoter could anticipate. The secreted recombinant laccase showed better enzyme properties than the native enzyme or recombinant enzyme from other yeasts. We conclude that selected K. lactis strains, with opportune physiological properties and transcription regulation of the heterologous gene, could be optimal hosts for laccase isoenzyme production

    Andere auteurs
    • Danilo Ranieri
    • Maria Chiara Colao
    • Maurizio Ruzzi
    • Michele M Bianchi
    Publicatie weergeven

Patenten

  • Ureohydrolases as dominant selectable markers in yeast

    Toegekend EU WO 2015156675 A1

    The invention relates to a nucleic acid molecule encoding a novel selection marker. Said marker is a guanidinobutyrase from Kluyveromyces lactis, which, when expressed in Saccharomyces, allows the growth of the yeast in the presence of guanidinobutyrate as the sole nitrogen source. Said marker can be used in a method for producing a microorganism having an altered genome. The invention further relates to a set of constructs, comprising a first construct comprising a recognition site for an…

    The invention relates to a nucleic acid molecule encoding a novel selection marker. Said marker is a guanidinobutyrase from Kluyveromyces lactis, which, when expressed in Saccharomyces, allows the growth of the yeast in the presence of guanidinobutyrate as the sole nitrogen source. Said marker can be used in a method for producing a microorganism having an altered genome. The invention further relates to a set of constructs, comprising a first construct comprising a recognition site for an endonuclease, a first region of homology with a target gene of a microorganism, and a first part of a nucleotide sequence encoding the selection marker, and a second construct comprising a second part of the nucleotide sequence encoding the selection marker, a second region of homology with the target gene of the microorganism, and a copy of the endonuclease recognition site. The invention further relates to methods for altering a target gene in a microorganism, to methods for producing a microorganism, and to microorganisms that are produced by the methods of the invention

    Andere bedenkers
    Patent weergeven

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  • Dutch

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