| 1. |
- Baraldi, Enrico, 1970-, et al.
(författare)
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Economic incentives for the development of new antibiotics : Report commissioned by the Public Health Agency of Sweden
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This report responds to a request by the Public Health Agency of Sweden (Folkhälsomyndigheten) concerning which incentives for antibiotics research and development (R&D) Sweden should take into consideration for potential public investments. Based on discussions and interviews with experts, feedback from stakeholders (i.e. potential recipients of Swedish incentives), company case studies and computer-based Monte Carlo simulations, this report provides a set of recommendations about the economic incentives that can be relevant for Sweden.The incentives identified for Sweden’s portfolio meet the following criteria: improving Sweden’s visibility in the antibiotics field, reinforcing Sweden’s national R&D infrastructure in this area, leveraging Sweden’s strengths and traditions, limiting the public expenditure per incentive, permitting rapid implementation and effects, providing highly needed support to the antibiotic pipeline in unique ways, and granting Sweden a key contribution and thus influence on the design and direction of each incentive.Based on these criteria, a Market Entry Reward (MER) was not considered a viable alternative for Sweden if implemented by Sweden alone, especially because of its demanding financial engagement (close to 1 B USD), which is necessary for this incentive to produce relevant effects on the antibiotics R&D pipeline. However, if Sweden were to decide to pilot an MER, it should focus on a fully delinked MER, which entirely substitutes market sales with lump sums paid on a yearly basis. An MER should moreover be financed primarily from the healthcare budget to avoid crowding out other incentives. A fully delinked MER would allow testing several features of this incentive model, such as the evaluation procedures to set the overall amount of the MER, the definition of the unit prizes to be paid by local healthcare facilities to the central government, and periodic reviews to reassess the amount of yearly lump-sum payments according to the confirmed therapeutic efficacy of the antibiotic.If Sweden were to collaborate with other countries, such as the G20 group or the 28 EU members, a reasonable amount for its share is 6 or 23 M USD, respectively, for a partially delinked MER and 9 or 34 M USD, respectively, for a fully delinked MER. There are, however, ways to combine push and pull incentives, which are quicker and more efficient than an MER, namely combinations of grants with milestone prizes, which are rewards paid to developers upon the successful completion of key R&D steps (e.g. Phase 1 clinical studies). In addition to producing better effects for the money spent, a combination of milestone prizes and grants also prevents large MERs from crowding out push investments as well as recipients such as small- and medium-sized firms (SMEs), who usually cannot wait for a reward that is delayed until the final approval of an antibiotic.The recommended portfolio of incentives for Sweden includes three incentives: grants, milestone prizes and Pipeline Coordinators, to be used in combination with each other as a way to cover the antibiotics R&D pipeline and achieve important synergies. The following features should be considered when implementing and funding the three selected incentives:1) Grants should be dedicated to early R&D projects (no later than Phase 2) and to reinforcing the national R&D infrastructure, with a longer-term perspective than the current 3-year timeframe. In this regard, Sweden should maintain and possibly increase its current yearly investments in antibiotics R&D grants of approximately 7 M USD/year (60 M SEK) over several years. These investments will pay off in the long run, both in terms of molecules that will enter the future R&D pipeline; and as a stock of competencies spread over an infrastructure of specialised R&D centres that can be leveragedfor future antibiotics research. These competences must be built up immediately and the seeds for future R&D projects need to be planted as soon as possible.2) Two types of milestone prizes should be in focus for Sweden: first, a prize awarding a sum between 10 and 20 M USD at the end of Clinical Phase 1 to highly innovative molecules addressing specific pathogens and, second, a prize for projects successfully completing preclinical steps. Establishing a prize at the end of Clinical Phase 1 is a much needed and unique initiative, with significant effects on the early R&D pipeline, granting also strong international visibility to Sweden. Sweden could also take major responsibility for such a milestone prize by covering a relatively large share. The other recommended milestone prize, awarded at the end of the preclinical steps, would help refill the clinical pipeline and would therefore have more of a long-term effect.3) Pipeline Coordinators, that is, organizations that take an active role in selecting and supporting a portfolio of antibiotics R&D projects in various ways, are the last recommended incentive. Selecting among currently existing Pipeline Coordinators rather than creating a new one, Sweden should fund two types of such organizations: R&D Collaborations, which create collaboration platforms to perform early development activities for the antibiotic projects they support, and Non-Profit Developers, who conduct their own antibiotic projects with the aim of bringing antibiotics to market but without pursuing profit goals. The first type of Pipeline Coordinator, R&D Collaborations, is relevant for a Swedish public investment because they are potentially the most efficient incentive in making R&D projects profitable. However, to fully exploit this potential, R&D Collaborations must be refined to become more flexible, reduce bureaucratic burden and avoid conflicts between participants.Non-Profit Developers provide the most extensive support to selected products by intervening across the entire antibiotic pipeline to ensure products reach the market. Moreover, this model strongly promotes both global availability and responsible use (stewardship). Therefore, Sweden may fund Non-Profit Developers through its international aid budget and in this way make important contributions to global health.Both types of Pipeline Coordinators also offer the advantage that they can help connect Swedish antibiotics R&D centres to international platforms, which reinforce the effects of infrastructure-related grants. Moreover, all forms of Pipeline Coordinators are incentive models that can be used as tools to manage the other two incentives (grants and milestone prizes). In this capacity, they can, for instance, evaluate grant applications and the antibiotic projects eligible for milestone prizes, which require a deep insight into the details of a drug development project.A fourth model, regulatory simplifications, which radically cut costs and times for Clinical Phase 3, can also be relevant for Sweden due to its contained costs, rapid implementation and effects and connection with Sweden’s expertise. However, this incentive requires further analysis to fully grasp its implications for regulators and patient safety before being recommended for implementation.The three incentives recommended by this report – grants, milestone prizes and Pipeline Coordinators – should be used in combination to exploit the synergies between them and their ability to push and pull molecules in different phases of the R&D pipeline. For instance, when grants and milestones are used together, the public investment per approved new antibiotic is lower than the combined spending if the two incentives were used in isolation. If it is not possible to introduce and use the three incentives simultaneously, the following priorities should be applied: first of all, grants need to be kept at current levels and possibly increased to fund both single antibiotic projects and competence development in the R&D infrastructure, while starting to invest in a Non-Profit Developer and a milestone prize at the end of Phase 1, followed by the development and funding of R&D Collaborations and, finally, a preclinical milestone prize.
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| 2. |
- Baraldi, Enrico, 1970-, et al.
(författare)
-
Ekonomiska incitamentsmodeller för utveckling av nya antibiotika : Rapport på uppdrag av Folkhälsomyndigheten
- 2018
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- På uppdrag av Folkhälsomyndigheten utreder vi i denna rapport en rad incitamentsmodeller för forskning och utveckling (FoU) av antibiotika som kan vara aktuella för en svensk offentlig investering. Baserat på diskussioner och intervjuer med experter, återkoppling från intressenter (d.v.s. potentiella mottagare av svenska incitament), företagsfallstudier och datorbaserade Monte Carlo-simuleringar lämnar rapporten rekommendationer kring de ekonomiska modeller som Sverige bör investera i. De incitamentsmodeller som valdes ut för den svenska portföljen uppfyller följande kriterier: de kan öka Sveriges visibilitet och förbättra den nationella FoU-infrastrukturen i antibiotikafältet, de bygger på Sveriges styrkor och tradition i detta fält, de innefattar begränsade investeringar, de kan införas och ge resultat relativt snabbt, de tillfredsställer på ett unikt sätt viktiga behov i antibiotikapipelinen, och de ger Sverige en möjlighet att spela en avgörande roll i själva skapandet och inriktningen av incitamentet. I enlighet med dessa kriterier, bedömdes att en ”Market Entry Reward” (MER) inte är genomförbar för Sverige ensamt. Det beror främst på att det krävs ett stort finansiellt åtagande (närmare 1 miljard USD) för att ett incitament som en MER ska kunna ge relevanta resultat på pipelinen. Om Sverige trots detta skulle välja att pilottesta en MER på egen hand, borde ett sådant försök fokusera på en s.k. ”totalt losskopplad” MER (Fully Delinked), vilket betyder att MER helt och hållet ersätter marknadsförsäljningen och istället ger fasta årliga utbetalningar till utvecklaren. En MER borde primärt finansieras via sjukvårdsbudgeten för att undvika undanträngningseffekter mot incitament i andra utgiftsområden. En totalt losskopplad MER skulle tillåta testning av flera olika aspekter såsom utvärderingsprocessen för att bestämma det totala värdet på en MER, internprissättning till sjukhus för att återfinansiera de statliga betalningarna, samt regelbundna mellanlägesrevideringar av årliga betalningar beroende på resistensläget. Om Sverige skulle samarbeta med andra länder, som exempelvis G20 eller EU:s medlemsländer, skulle en rimlig storlek på den svenska andelen vara 6 respektive 23 miljoner USD för en partiellt losskopplad MER, och 9 respektive 34 miljoner USD för en totalt losskopplad MER. Det finns dock andra sätt att kombinera push- och pull-incitament som är mer effektiva och snabbare än en MER, nämligen en rad kombinationer av ”grants” (forskningsanslag) och ”milestone prizes”, där det senare är belöningar som betalas ut till utvecklare när de framgångsrikt avslutar viktiga steg i sin FoU (t.ex. Fas 1 i kliniska studier). Förutom bättre effekter per investerat belopp, undviker en kombination av ”grants” och ”milestone prizes” dessutom att stora MER tränger undan push investeringar och mottagare såsom små- och medelstora företag (SMEs) som vanligtvis inte kan vänta på ett incitament ända tills det slutgiltiga godkännandet av ett antibiotikum. Den föreslagna incitamentportföljen för Sverige omfattar tre incitament: ”grants”, ”milestone prizes” och ”Pipeline Coordinators”. Dessa tre incitament skall användas tillsammans för att säkerställa att hela FoU-pipelinen för antibiotika stödjs och att viktiga synergier skapas. Följande aspekter borde tas i beaktning vid implementering och finansiering av de tre valda incitamenten: 1) ”Grants” borde riktas mot tidiga FoU-projekt (fram till Fas 2) och att förstärka den nationella FoUinfrastrukturen, med ett tidsperspektiv som ska vara längre än den nuvarande 3-åriga tidsramen. Det är viktigt att Sverige bibehåller och om möjligt höjer sina nuvarande årliga investeringar i ”grants” för FoU om antibiotika på cirka 60 miljoner SEK/år (7 M USD) och att dessa investeringar får fortsätta över många år i framtiden. Investeringarna kommer att ge långsiktiga effekter både i form av nya molekyler som kan fylla på den framtida FoU-pipelinen och genom fördjupade kompetenser, exempelvis i form av en nationell forskningsinfrastruktur bestående av specialiserade FoU-centra som kan utnyttjas i framtida antibiotikaforskning. Det bör understrykas att man inte kan fördröja dessa investeringar eftersom den här typen av kompetenser behöver byggas omedelbart och frön för framtida FoU-projekt behöver sås i detta nu. 2) Två typer av ”milestone prizes” borde implementeras av Sverige. Först och främst ett ”prize” som delar ut mellan 10 och 20 miljoner USD (bedömningar gjorda av de små företagen i fallstudien) vid slutet av klinisk Fas 1 som bör riktas mot höginnovativa molekyler mot specifika patogener. Därutöver bör ett ”prize” tilldelas projekt som framgångsrikt avslutar de prekliniska stegen. Att inrätta ett ”prize” vid slutet av klinisk Fas 1 skulle vara ett nödvändigt och unikt initiativ, som förutom starka effekter på den tidiga FoU-pipelinen dessutom skulle ge Sverige en stark internationell visibilitet. Genom att finansiera en större del av detta ”milestone prize” skulle Sverige ta ett stort ansvar för att aktivt skapa dessa mycket viktiga incitament. Det andra rekommenderade ”milestone prize”, som delas ut vid slutet av de prekliniska stegen, skulle bidra till att fylla på den kliniska pipelinen och skulle därmed ha mera långsiktiga effekter. 3) ”Pipeline Coordinators”, d.v.s. organisationer som på flera sätt tar en aktiv roll i att välja och stödja en portfölj av FoU-projekt om antibiotika, är det sista rekommenderade incitamentet. Snarare än att skapa en ny ”Pipeline Coordinator”, borde Sverige välja bland de som redan finns och finansiera följande två typer av sådana organisationer: ”R&D Collaborations”, som skapar samarbetsplattformar för att genomföra tidiga FoU aktiviteter för de projekten de stödjer, och ”Nonprofit Developers”, som genomför egna antibiotikaprojekt i syftet att föra nya antibiotika hela vägen till marknaden, dock utan vinstintressen. Den första typen av ”Pipeline Coordinator”, ”R&D Collaborations” är relevant för Sverige att investera i eftersom det handlar om den incitamentsmodell som potentiellt är mest effektiv i att skapa lönsamma FoU projekt. Men för att kunna utnyttja denna potential fullt ut behöver ”R&D Collaborations” vidareutvecklas för att bli mer flexibla samt minska byråkrati och konflikter mellan deltagarna. ”Non-profit Developers” är å andra sidan den modell som erbjuder det mest omfattande stödet till utvalda produkter genom att agera över hela antibiotikapipelinen för att se till att dessa produkter når marknadslansering. Dessutom, ger denna modell starkt stöd gällande global tillgång och ansvarsfull användning (”stewardship”). Därför, skulle Sverige kunna finansiera ”Non-profit Developers” via sin internationella biståndsbudget och därmed även ge ett viktigt bidrag till global hälsa. Båda typer av ”Pipeline Coordinators” har fördelen att de kan hjälpa att koppla svenska FoU-centra för antibiotika till internationella plattformar, vilket skulle förstärka effekterna av infrastrukturrelaterade ”grants”. Dessutom, är alla sorters ”Pipeline Coordinators” incitamentsmodeller som kan användas som verktyg för att styra övriga två incitament (”grants” och ”milestone prizes”). Tack vare denna förmåga, kan de utvärdera ansökningar till ”grants” och de antibiotikaprojekt som är berättigade till ”milestone prizes”, vilket kräver både djupa och detaljerade kunskaper i specifika antibiotikaprojekt. Utöver dessa tre incitamentsmodeller kan även en fjärde modell vara relevant: ”regulatory simplifications”. Denna modell innefattar regulatoriska förenklingar som radikalt sänker kostnader och tider för kliniska Fas 3-studier. Modellen kan vara relevant för Sverige tack vare att kostnaderna är begränsade, implementeringen och effekterna snabba samt att det finns en koppling till svensk expertis. Trots dessa fördelar, kräver detta incitament fortfarande vidare analyser för att fullt ut förstå dess implikationer för regelverket och patientsäkerhet innan den kan rekommenderas för implementering. De tre incitamenten som rekommenderas i denna rapport – ”grants”, ”milestone prizes” och ”Pipeline Coordinators” – bör användas tillsammans i särskilda kombinationer för att utnyttja synergierna mellan dem och deras förmåga att både trycka (”push”) och dra (”pull) molekylerna i olika faser i FoU-pipelinen. Dessa synergier innebär att när exempelvis ”grants” och ”milestone prizes” används samtidigt, blir den offentliga investeringen för varje nytt antibiotikum lägre än den sammanlagda investeringen om de två incitamenten används separat. Om det skulle vara omöjligt att införa och använda de tre incitamenten samtidigt, borde följande prioriteringsordning tillämpas: först och främst behöver nuvarande nivåer på ”grants” bibehållas och om möjligt höjas för att finansiera både enskilda projekt om FoU om antibiotika och för utveckling av kompetenser samt för FoU-infrastruktur, medan investeringar påbörjas i en ”Non-profit Developer” och i en ”milestone prize” vid slutet av Fas 1, följd av vidareutveckling och finansiering av ”R&D Collaborations” och slutligen av ett prekliniskt ”milestone prize”.
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| 3. |
- Callegari, Simone
(författare)
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Remodelling of the cellular environment in Epstein-Barr virus infection
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- For successful infection viruses modify the host cell environment by transcriptional, posttranscriptional or post-translational regulation of cellular signaling pathways. In the work described in this thesis bioinformatics analysis coupled with biochemical validations were used to dissect critical features of these viral strategies in the context of infection by Epstein–Barr virus (EBV), a human herpesvirus associated with lymphoid and epithelial cell tumors. The EBV nuclear antigen EBNA1 is the only viral protein ubiquitously expressed in all EBV infected cells and virus-associated neoplasms but its contribution to oncogenesis is not fully understood. EBNA1 binds to cellular chromatin via a bipartite Gly-Arg repeats (GRs) domain that resembles the AT-hook of the High Mobility Group-A (HMGA) architectural transcription factors. By microarray gene expression analysis of stable or inducible EBNA1 expressing cells, we found that EBNA1 orchestrates a broad and pleotropic rearrangement of cellular transcription, which resembles the one induced by architectural transcription factors and chromatin remodelers. Similar to HMGAs, EBNA1 is highly mobile in the nucleus and promotes large-scale chromatin de-condensation without recruitment of ATP-dependent remodelers, probably by displacing linker histone H1. The GR domain was sufficient for this effect. Furthermore, expression of the chromatin-binding GR domain was shown to regulate transcription. Thus, through its capacity to remodel the organization of cellular chromatin EBNA1 may reset the cellular transcriptional profile and prime the infected cells for malignant transformation. MicroRNAs (miRNAs) are powerful prost-transcriptional regulators of complex signaling networks. In order to assess the possible role of EBV-encoded miRNAs in the regulation of SUMO-dependent signaling cascades, a meta-predictor of miRNAs targets was developed and tested against a comprehensive database of the SUMO interactome that includes components of the SUMOconjugation machinery, their interacting partners and substrates, and other signal transducers and regulators of the system. This prediction strategy suggests that EBV miRNAs may target the expression of key SUMO-regulated cellular proteins involved in immune defense, DNA damage response, apoptosis, chromatin remodeling and TGF-beta signalling. Regulation of essential members of canonical TGF-beta/Smad signaling by EBV miRNAs was confirmed in EBV positive cells entering the productive virus cycle. Thus, EBV miRNAs are likely to regulate key aspects of viral replication and pathogenesis. Post-translational modifications by ubiquitin (Ub) and ubiquitin-like molecules (UbLs) regulate the stability and function of signal transducers and are often targeted by viruses in different phases of the infection. The large tegument protein of EBV, BPLF1, is an early viral product that plays a key role in virus assembly and maturation. The catalytic N-terminal domain of BPLF1 acts as a deneddylase that inactivates nuclear cullin-based Ub ligases (CRLs) to induce an S-phase-like environment that is required for efficient viral DNA replication. Structural bioinformatics methods were applied to predict the structure of BPLF1 and the site of interaction with cullins. A novel mechanism by which BPLF1 induces the proteasomal degradation of cullins by competing for binding of the CRL sequestering factor CAND1 was proposed and successfully validated. The work described in this thesis illustrates the power of gene expression analysis and bioinformatics tools for the characterization of different strategies adopted by viruses to remodel the host cellular environment in order to favor their own replication and transmission.
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| 4. |
- Ciabuschi, Francesco, 1973-, et al.
(författare)
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Supporting innovation against the threat of antibiotic resistance : Exploring the impact of public incentives on firm performance and entrepreneurial orientation
- 2020
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Ingår i: Journal of Business Research. - : Elsevier BV. - 0148-2963 .- 1873-7978. ; 112, s. 271-280
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Tidskriftsartikel (refereegranskat)abstract
- Although there is an urgent need to find new antibiotics to fight growing antibiotic resistance, the development of antibiotics is at its lowest level ever. This innovation drought in the antibiotics industry is a challenge for managers, policy makers, and public health authorities. Currently, several strategies to incentivize antibiotic innovation are being considered, but their effects are unknown. Using the theoretical lens of the entrepreneurial orientation framework and Monte Carlo-based simulations on state-of-the-art pharmaceutical industry data, this study found that several incentives can increase the innovativeness of firms in this industry. However, the results show that these effects vary between incentives, between large and small firms, and across different research and development stages. This study analyzed these findings in the light of the entrepreneurial orientation framework and presents implications for theory, policy makers, and managers.
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| 5. |
- Ciavardini, Alessandra, et al.
(författare)
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Ultra-Fast-VUV Photoemission Study of UV Excited 2-Nitrophenol
- 2019
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Ingår i: Journal of Physical Chemistry A. - : AMER CHEMICAL SOC. - 1089-5639 .- 1520-5215. ; 123:7, s. 1295-1302
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Tidskriftsartikel (refereegranskat)abstract
- The initial deactivation pathways of gaseous 2-nitrophenol excited at 268 nm were investigated by time-resolved photoelectron spectroscopy (TRPES) with femtosecond-VUV light, produced by a monochromatized high harmonic generation source. TRPES allowed us to obtain new, valuable experimental information about the ultrafast excited-state dynamics of 2-nitrophenol in the gas phase. In accord with recent ab initio on-the-fly nonadiabatic molecular dynamic simulations, our results validate the occurrence of an ultrafast intersystem crossing leading to an intermediate state that decays on a subpicosecond time scale with a branched mechanisms. Two decay pathways are experimentally observed. One probably involves proton transfer, leading to the most stable triplet aci-form of 2-nitrophenol; the second pathway may involve OH rotation. We propose that following intersystem crossing, an ultrafast fragmentation channel leading to OH or HONO loss could also be operative.
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| 6. |
- Coppotelli, Giuseppe, et al.
(författare)
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The Epstein-Barr virus nuclear antigen-1 reprograms transcription by mimicry of high mobility group A proteins
- 2013
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 41:5, s. 2950-2962
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Tidskriftsartikel (refereegranskat)abstract
- Viral proteins reprogram their host cells by hijacking regulatory components of protein networks. Here we describe a novel property of the Epstein-Barr virus (EBV) nuclear antigen-1 (EBNA1) that may underlie the capacity of the virus to promote a global remodeling of chromatin architecture and cellular transcription. We found that the expression of EBNA1 in transfected human and mouse cells is associated with decreased prevalence of heterochromatin foci, enhanced accessibility of cellular DNA to micrococcal nuclease digestion and decreased average length of nucleosome repeats, suggesting de-protection of the nucleosome linker regions. This is a direct effect of EBNA1 because targeting the viral protein to heterochromatin promotes large-scale chromatin decondensation with slow kinetics and independent of the recruitment of adenosine triphosphate-dependent chromatin remodelers. The remodeling function is mediated by a bipartite Gly-Arg rich domain of EBNA1 that resembles the AT-hook of High Mobility Group A (HMGA) architectural transcription factors. Similar to HMGAs, EBNA1 is highly mobile in interphase nuclei and promotes the mobility of linker histone H1, which counteracts chromatin condensation and alters the transcription of numerous cellular genes. Thus, by regulating chromatin compaction, EBNA1 may reset cellular transcription during infection and prime the infected cells for malignant transformation.
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| 7. |
- Guerra, Lina, et al.
(författare)
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Bacterial genotoxin triggers FEN1-dependent RhoA activation, cytoskeleton remodeling and cell survival
- 2011
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Ingår i: Journal of Cell Science. - : The Company of Biologists. - 0021-9533 .- 1477-9137. ; 124:16, s. 2735-2742
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Tidskriftsartikel (refereegranskat)abstract
- The DNA damage response triggered by bacterial cytolethal distending toxins (CDTs) is associated with activation of the actin-regulating protein RhoA and phosphorylation of the downstream-regulated mitogen-activated protein kinase (MAPK) p38, which promotes the survival of intoxicated (i.e. cells exposed to a bacterial toxin) cells. To identify the effectors of this CDT-induced survival response, we screened a library of 4492 Saccharomyces cerevisiae mutants that carry deletions in nonessential genes for reduced growth following inducible expression of CdtB. We identified 78 genes whose deletion confers hypersensitivity to toxin. Bioinformatics analysis revealed that DNA repair and endocytosis were the two most overrepresented signaling pathways. Among the human orthologs present in our data set, FEN1 and TSG101 regulate DNA repair and endocytosis, respectively, and also share common interacting partners with RhoA. We further demonstrate that FEN1, but not TSG101, regulates cell survival, MAPK p38 phosphorylation, RhoA activation and actin cytoskeleton reorganization in response to DNA damage. Our data reveal a previously unrecognized crosstalk between DNA damage and cytoskeleton dynamics in the regulation of cell survival, and might provide new insights on the role of chronic bacteria infection in carcinogenesis.
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| 8. |
- Gupta, Soham, et al.
(författare)
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Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome
- 2018
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Ingår i: PLoS Pathogens. - : PUBLIC LIBRARY SCIENCE. - 1553-7366 .- 1553-7374. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The N-terminal domains of the herpesvirus large tegument proteins encode a conserved cysteine protease with ubiquitin- and NEDD8-specific deconjugase activity. The proteins are expressed during the productive virus cycle and are incorporated into infectious virus particles, being delivered to the target cells upon primary infection. Members of this viral enzyme family were shown to regulate different aspects of the virus life cycle and the innate anti-viral response. However, only few substrates have been identified and the mechanisms of these effects remain largely unknown. In order to gain insights on the substrates and signaling pathways targeted by the viral enzymes, we have used co-immunoprecipitation and mass spectrometry to identify cellular proteins that interact with the Epstein-Barr virus encoded homologue BPLF1. Several members of the 14-3-3-family of scaffold proteins were found amongst the top hits of the BPLF1 interactome, suggesting that, through this interaction, BPLF1 may regulate a variety of cellular signaling pathways. Analysis of the shared protein-interaction network revealed that BPLF1 promotes the assembly of a trimolecular complex including, in addition to 14-3-3, the ubiquitin ligase TRIM25 that participates in the innate immune response via ubiquitination of cytosolic pattern recognition receptor, RIG-I. The involvement of BPLF1 in the regulation of this signaling pathway was confirmed by inhibition of the type-I IFN responses in cells transfected with a catalytically active BPLF1 N-terminal domain or expressing the endogenous protein upon reactivation of the productive virus cycle. We found that the active viral enzyme promotes the dimerization and autoubiquitination of TRIM25. Upon triggering of the IFN response, RIG-I is recruited to the complex but ubiquitination is severely impaired, which functionally inactivates the RIG-I signalosome. The capacity to bind to and functionally inactivate the RIG-I signalosome is shared by the homologues encoded by other human herpesviruses.
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| 9. |
- Illergård, Kristoffer, et al.
(författare)
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MPRAP : An accessibility predictor for a-helical transmem-brane proteins that performs well inside and outside the membrane
- 2010
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 11, s. 333-
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Tidskriftsartikel (refereegranskat)abstract
- Background: In water-soluble proteins it is energetically favorable to bury hydrophobic residues and to expose polar and charged residues. In contrast to water soluble proteins, transmembrane proteins face three distinct environments; a hydrophobic lipid environment inside the membrane, a hydrophilic water environment outside the membrane and an interface region rich in phospholipid head-groups. Therefore, it is energetically favorable for transmembrane proteins to expose different types of residues in the different regions. Results: Investigations of a set of structurally determined transmembrane proteins showed that the composition of solvent exposed residues differs significantly inside and outside the membrane. In contrast, residues buried within the interior of a protein show a much smaller difference. However, in all regions exposed residues are less conserved than buried residues. Further, we found that current state-of-the-art predictors for surface area are optimized for one of the regions and perform badly in the other regions. To circumvent this limitation we developed a new predictor, MPRAP, that performs well in all regions. In addition, MPRAP performs better on complete membrane proteins than a combination of specialized predictors and acceptably on water-soluble proteins. A web-server of MPRAP is available at http://mprap.cbr.su.se/ Conclusion: By including complete a-helical transmembrane proteins in the training MPRAP is able to predict surface accessibility accurately both inside and outside the membrane. This predictor can aid in the prediction of 3D-structure, and in the identification of erroneous protein structures.
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| 10. |
- Illergård, Kristoffer, et al.
(författare)
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MPRAP: An accessibility predictor for α-helical transmembrane proteins
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: During the folding of a protein some residues will become exposed to the environmentwhile others will become buried in the protein interior. For water soluble proteins it is en-ergetically favorable to bury hydrophobic residues and expose polar and charged residues tothe surrounding water. However, transmembrane proteins face three distinct environments; ahydrophobic lipid environment inside the membrane, a hydrophilic water environment outsidethe membrane and a interface region rich in phospholipid head-groups. Therefore, for ener-getic reasons the accessible surfaces of transmembrane proteins need to expose different typesof residues at different locations. Results: In a set of structurally determined transmembrane proteins it was found that solvent ex-posed residues are quite different inside compared to outside the membrane. In contrast,residues buried within the interior of the protein are much more similar. Further, we foundthat state-of-the-art predictors for surface area are optimized for one of the environments andtherefore perform badly in the other environment. To circumvent this problem we developeda new predictor, MPRAP, that performs well both inside and outside the membrane regions aswell as being better than a combination of specialized predictors. A web-server of MPRAP isavailable at http://mprap.cbr.su.se/ Conclusion: By including complete α-helical transmembrane proteins in the training we developed apredictor that accurately predicts accessibility both inside and outside the membrane. This pre-dictor can aid in predicting 3D-structure, predicting functional relevance of individual residuesand identification of erroneous protein structures.
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| 11. |
- Kumar Maroju, Praveen, et al.
(författare)
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Attosecond pulse shaping using a seeded free-electron laser
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578, s. 386-391
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Tidskriftsartikel (refereegranskat)abstract
- Attosecond pulses are central to the investigation of valence- and core-electron dynamics on their natural timescales. The reproducible generation and characterization of attosecond waveforms has been demonstrated so far only through the process of high-order harmonic generation. Several methods for shaping attosecond waveforms have been proposed, including the use of metallic filters, multilayer mirrors and manipulation of the driving field. However, none of these approaches allows the flexible manipulation of the temporal characteristics of the attosecond waveforms, and they suffer from the low conversion efficiency of the high-order harmonic generation process. Free-electron lasers, by contrast, deliver femtosecond, extreme-ultraviolet and X-ray pulses with energies ranging from tens of microjoules to a few millijoules. Recent experiments have shown that they can generate subfemtosecond spikes, but with temporal characteristics that change shot-to-shot. Here we report reproducible generation of high-energy (microjoule level) attosecond waveforms using a seeded free-electron laser. We demonstrate amplitude and phase manipulation of the harmonic components of an attosecond pulse train in combination with an approach for its temporal reconstruction. The results presented here open the way to performing attosecond time-resolved experiments with free-electron lasers.
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| 12. |
- Maroju, Praveen K., et al.
(författare)
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A Novel Attosecond Timing Tool for Free-Electron Laser Experiment
- 2020
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Ingår i: High Intensity Lasers and High Field Phenomena 2020. - 9781943580736
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Konferensbidrag (refereegranskat)abstract
- We demonstrate a novel timing tool for Free-Electron Lasers to determine the delay between an attosecond pulse train and infrared pulse with sub-optical-cycle resolu-. tion.
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| 13. |
- Okhravi, Christopher, et al.
(författare)
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Simulating Market Entry Rewards for Antibiotics Development
- 2018
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Ingår i: Journal of Law, Medicine & Ethics. - : SAGE PUBLICATIONS INC. - 1073-1105 .- 1748-720X. ; 46, s. 32-42
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Tidskriftsartikel (refereegranskat)abstract
- We design an agent based Monte Carlo model of antibiotics research and development (R&D) to explore the effects of the policy intervention known as Market Entry Reward (MER) on the likelihood that an antibiotic entering pre-clinical development reaches the market. By means of sensitivity analysis we explore the interaction between the MER and four key parameters: projected net revenues, R&D costs, venture capitalists discount rates, and large pharmaceutical organizations' financial thresholds. We show that improving revenues may be more efficient than reducing costs, and thus confirm that this pull-based policy intervention effectively stimulates antibiotics R&D.
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| 14. |
- Theuretzbacher, Ursula, et al.
(författare)
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Challenges and shortcomings of antibacterial discovery projects
- 2023
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Ingår i: Clinical Microbiology and Infection. - : Elsevier. - 1198-743X .- 1469-0691. ; 29:5, s. 610-615
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Tidskriftsartikel (refereegranskat)abstract
- ObjectivesAntibacterial drug discovery activities are essential for filling clinical pipelines with promising clinical candidates. Little information is available about the challenges and shortcomings of small companies and academic institutions in performing these important discovery tasks.MethodsWe performed a content analysis of 463 reviewer comments on 91 funding applications of antibacterial drug discovery projects submitted to two major global funders between 2016 and 2020 that had not proceeded further in the selection process. This quality assessment was complemented with the inputs (via e-mail) from a panel involving six antibiotic research and development (R&D) experts with long-standing expertise and experience in antibiotic drug discovery.ResultsCommon critical comments of reviewers are grouped into three main categories: scientific and technical shortcomings, unclear potential societal impact, and insufficient capability and expertise of the project team regarding the R&D process. Insufficient characterization of in vitro activity and/or testing of the hits/leads and insufficient antibacterial activity were the most common critical comments. Other areas of concern were insufficient or lack of differentiation from available drugs or projects with a long R&D history, and the research team's insufficient knowledge of a structured streamlined R&D process as reflected in severe gaps in the expertise of the R&D team. Little appreciation for the problem of the emergence of target-based resistance, especially in single-target approaches, and little awareness of toxicological issues, including approaches with historical liabilities were also commonly mentioned. The shortcomings identified through the analysis of funding applications are echoed by the results of the expert panel.DiscussionOur analysis identified an urgent need of strengthening the support for antibacterial drug discovery teams to help more projects reach such a quality to be eligible for global funders and private investors.
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| 15. |
- Wituschek, Andreas, et al.
(författare)
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Tracking attosecond electronic coherences using phase-manipulated extreme ultraviolet pulses
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- The recent development of ultrafast extreme ultraviolet (XUV) coherent light sources bears great potential for a better understanding of the structure and dynamics of matter. Promising routes are advanced coherent control and nonlinear spectroscopy schemes in the XUV energy range, yielding unprecedented spatial and temporal resolution. However, their implementation has been hampered by the experimental challenge of generating XUV pulse sequences with precisely controlled timing and phase properties. In particular, direct control and manipulation of the phase of individual pulses within an XUV pulse sequence opens exciting possibilities for coherent control and multidimensional spectroscopy, but has not been accomplished. Here, we overcome these constraints in a highly time-stabilized and phase-modulated XUV-pump, XUV-probe experiment, which directly probes the evolution and dephasing of an inner subshell electronic coherence. This approach, avoiding any XUV optics for direct pulse manipulation, opens up extensive applications of advanced nonlinear optics and spectroscopy at XUV wavelengths.
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