Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation

Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods relying on pulsed metabolic labeling are popular to quantify turnover rates on a proteome-wide scale. Such data have traditionally been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture (pSILAC) for the study of protein phosphorylation. We demonstrate that metabolic labeling combined with PTM-specific enrichment does not measure effects of PTMs on protein stability. Rather, it reveals the relative order of PTM addition and removal along a protein's lifetime-a fundamentally different metric. This is due to interconversion of the measured proteoform species. Using this framework, we identify temporal phosphorylation sites on cell cycle-specific factors and protein complex assembly intermediates. Our results thus allow tying PTMs to the age of the modified proteins

Unrestricted symmetry-projected Hartree-Fock-Bogoliubov calculations for some PF-shell nuclei

Total binding energies and yrast energy spectra of three selected 1p0f–nuclei have been calculated using an unrestricted Hartree–Fock–Bogoliubov approach with symmetry–pro jec ti on before the variation. The full 1p0f–shell has been used as single–particle basis and the semi–empirical FPD6 interaction as effective Hamiltonian. The results are compared to those of truncated shell–model calculations performed with the OXBASH code. In the middle of the 1p0f–shell the variational method yields energy gains up to 4.5 MeV and thus proves to be far superior than the conventional truncation methods at least if in the latter only up to about 13000 configurations for each spin–isospin combination are admitted

Glycolytic flux-signaling controls mouse embryo mesoderm development

How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic PFKFB3 (cytoPFKFB3). Overexpression of cytoPFKFB3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPFKFB3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization

Linné : an object oriented language with parallelism

Godkänd; 1990; 20080410 (ysko)</p

Teknologian hyödyntämiseen liittyvä yksityisyydensuoja, tietoturva ja -suoja ikääntyneiden kotipalveluissa:kyselytutkimus johtajille

Tiivistelmä Tutkimuksen tarkoituksena on kuvata johtajien näkemyksiä teknologian hyödyntämiseen liittyvästä yksityisyydensuojasta, tietoturvasta ja -suojasta, niihin liittyvistä haasteista ja ratkaisuista sekä teknologisten ratkaisujen hankkimatta jättämiseen liittyvistä tekijöistä ikääntyneiden kotipalveluissa. Tutkimus on poikkileikkausasetelmassa tehty survey-tutkimus. Aineisto kerättiin syksyllä 2022 sähköisellä kyselyllä iäkkäiden kotipalvelujen johtajilta (n=68) viidestä sosiaali- ja terveydenhuollon kuntayhtymästä ja viidestätoista kunnasta tai kaupungista eri puolilta Suomea. Kyselylomake sisälsi neljä strukturoitua ja kaksi avointa kysymystä. Aineisto analysoitiin kuvailevilla tilastomenetelmillä ja induktiivisen sisällön analyysin periaatteilla. Tulosten mukaan teknologisten ratkaisujen käyttöönotossa huomioidaan Digi-HTA-arviointien asioita tietoturvasta ja -suojasta pääasiallisesti hyvin, mutta tässä tunnistettiin myös kehitettävää. Johtajien arvioiden mukaan teknologian hankintaprosesseissa huomioidaan tietosuojaan liittyvät tekijät hyvin, ja prosesseihin on luotu tietoturvaan liittyvät kriteerit. Teknologisten ratkaisujen hankkimatta jättämiseen arvioitiin vaikuttavan erityisesti se, että ratkaisut eivät vastanneet asiakkaiden tarpeisiin tai niiden ei nähty tehostavan toimintaa. Johtajien näkemykset teknologian hyödyntämiseen liittyvän yksityisyydensuojan ja tietoturvan ja -suojan haasteista liittyivät toimintaympäristöön, digitaalisiin ratkaisuihin, toimintatapoihin ja osaamiseen sekä organisaation käytäntöihin haasteiden ehkäisyssä. Näiden haasteiden ratkaisuiksi nähtiin viestintä ja vuorovaikutus, yksityisyydensuojaa, tietoturvaa ja -suojaa koskevien prosessien määrittäminen sekä toimintatapojen muuttaminen ja osaamisen kehittäminen. Yksityisyydensuojaan, tietoturvaan ja -suojaan liittyvien tekijöiden huomioiminen toteutuu ikääntyneiden kotipalveluissa pääasiallisesti hyvin, mutta toisaalta niihin liittyvät haasteet koetaan moninaisiksi. Tutkimuksessa tunnistettiin selkeä tarve koko henkilöstön laaja-alaiseen koulutukseen, konkreettisiin näyttöön perustuviin suosituksiin ja selkeisiin toimintaohjeisiin. Huomiota tulisi kiinnittää etenkin ikääntyneiden itsemääräämisoikeuden toteutumiseen ja tietoisen suostumuksen varmistamiseen.Abstract The purpose of this study was to describe managers’ perceptions of privacy protection, data security and protection in technology utilization, related challenges, and solutions, and factors related not acquiring technological solutions in home care services for the older people. This cross-sectional survey study was conducted by electronic survey in Autumn 2022. The data was collected from the managers of home care services (n=68) from five public social and healthcare joint municipal authorities and fifteen municipalities or cities located in different parts of Finland. The questionnaire included four structured and two open questions. The data was analyzed using descriptive statistical methods and the principles of inductive content analysis. According to results, the issues raised by the Digi-HTA evaluations regarding data security and protection are mainly adequately considered when implementing technological solutions, but areas for development were also identified. According to managers’ evaluations, factors related to data protection are adequately considered in the technology acquisition processes, and criteria related to data security have been created for the processes. Not acquiring technological solutions was estimated to be especially influenced by the fact that the solutions did not meet the clients’ needs or were not seen to make operations more efficient. The managers’ perceptions of the challenges of privacy protection and data security and protection in technology utilization, were related to the operating environment, digital solutions, procedures, competence, and the organization’ practices in the prevention of challenges. The solutions to these challenges were seen as communication and interaction, defining processes of privacy protection, data security and protection, changing procedures, and developing competence. Taking account of factors related to privacy protection, data security and protection is mainly adequately implemented in home care services, though the challenges associated with them are perceived as diversified. The research identified a clear need for comprehensive training of all personnel, concrete evidence-based recommendations, and clear instructions of procedures. Particularly, attention should be paid to realizing the older people’s right to self-determination and ensuring informed consent

Mycobacterium marinum Causes a Latent Infection that Can Be Reactivated by Gamma Irradiation in Adult Zebrafish

The mechanisms leading to latency and reactivation of human tuberculosis are still unclear, mainly due to the lack of standardized animal models for latent mycobacterial infection. In this longitudinal study of the progression of a mycobacterial disease in adult zebrafish, we show that an experimental intraperitoneal infection with a low dose (~35 bacteria) of Mycobacterium marinum, results in the development of a latent disease in most individuals. The infection is characterized by limited mortality (25%), stable bacterial loads 4 weeks following infection and constant numbers of highly organized granulomas in few target organs. The majority of bacteria are dormant during a latent mycobacterial infection in zebrafish, and can be activated by resuscitation promoting factor ex vivo. In 5–10% of tuberculosis cases in humans, the disease is reactivated usually as a consequence of immune suppression. In our model, we are able to show that reactivation can be efficiently induced in infected zebrafish by γ-irradiation that transiently depletes granulo/monocyte and lymphocyte pools, as determined by flow cytometry. This immunosuppression causes reactivation of the dormant mycobacterial population and a rapid outgrowth of bacteria, leading to 88% mortality in four weeks. In this study, the adult zebrafish presents itself as a unique non-mammalian vertebrate model for studying the development of latency, regulation of mycobacterial dormancy, as well as reactivation of latent or subclinical tuberculosis. The possibilities for screening for host and pathogen factors affecting the disease progression, and identifying novel therapeutic agents and vaccine targets make this established model especially attractive.Public Library of Science open acces