The genomes of all living cells are under constant attack from both endogenous and exogenous agents that damage DNA. In order to maintain genetic integrity a variety of response pathways have evolved to recognize and eliminate DNA damage. Replication protein A (RPA), the eukaryotic single-stranded DNA (ssDNA) binding protein, is a required factor for all major DNA metabolisms. Although much work has been done to elucidate the nature of the interaction between RPA and ssDNA currently there is no structural information on how the full-length protein binds to ssDNA. This study presents a novel examination of the full nucleoprotein complex formed between RPA and ssDNA. We identified three previously unknown contacts between ssDNA and lysine residues in DNA binding domain C located in the p70 subunit. This represents the first single amino-acid resolution determination of how full-length RPA contacts ssDNA. The Ataxia-Telangiectasia Mutated and RAD3-Related (ATR) mediated DNA damage checkpoint and nucleotide excision repair (NER) pathway are primarily responsible for repair of UV-C-induced photolesions in DNA. However, it is unclear how these two pathways are coordinated. We found the ATR-dependent checkpoint induces a rapid nuclear accumulation of the required NER factor Xeroderma pigmentosum group A (XPA) in both a dose- and time-dependent fashion. Also, using surface topology mapping we have defined an α-helix motif on XPA required for XPA-ATR complex formation necessary for XPA phosphorylation. In addition, we have determined that XPA phosphorylation promotes repair of persistent DNA lesions, such as cyclobutane pyrimidine dimers. The basis for initial damage recognition in NER is structural distortion of duplex DNA; however, the effects of adduct structure and sequence on strand opening and recognition are unclear. Using the E. coli NER system we determined that the identity of the adduct dictates the size of the strand opening generated by the UvrA2B complex. In addition we found that the sequence immediately surrounding the damaged nucleotide affects damage recognition by influencing the amount of helical distortion induced by the adduct. These effects are a result of the equilibrium conformation the adduct adopts in addition to the amount of hydrogen bonding available to maintain the structure.

The H9N2 subtype of avian influenza A virus (aIAV) is circulating among birds worldwide, leading to severe economic losses. H9N2 cocirculation with other highly pathogenic aIAVs has the potential to contribute to the rise of new strains with pandemic potential. Therefore, rapid detection of H9 aIAVs infection is crucial to control virus spread. A qualitative reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of aIAV subtype H9N2 was developed. All results were compared to the gold standard (real-time reverse transcription polymerase chain reaction (RT-PCR)). The RT-RPA assay was designed to detect the hemagglutinin (HA) gene of H9N2 by testing three pairs of primers and a probe. A serial concentration between 106 and 100 EID50 (50% embryo infective dose)/mL was applied to calculate the analytical sensitivity. The H9 RT-RPA assay was highly sensitive as the lowest concentration point of a standard range at one EID50/mL was detected after 5 to 8 min. The H9N2 RT-RPA assay was highly specific as nucleic acid extracted from H9 negative samples and from other avian pathogens were not cross detected. The diagnostic sensitivity when testing clinical samples was 100% for RT-RPA and RT-PCR. In conclusion, H9N2 RT-RPA is a rapid sensitive and specific assay that easily operable in a portable device for field diagnosis of aIAV H9N2.

With the advancement of isothermal nucleic acid amplification techniques, detection of the pathogenic DNA in clinical samples at point-of-need is no longer a dream. The newly developed recombinase polymerase amplification (RPA) assay incorporated in a suitcase laboratory has shown promising diagnostic efficacy over real-time PCR in detection of leishmania DNA from clinical samples. For broader application of this point-of-need system, we undertook a current multi-country diagnostic evaluation study towards establishing this technique in different endemic settings which would be beneficial for the ongoing elimination programs for leishmaniasis. For this study purpose, clinical samples from confirmed visceral leishmaniasis (VL) and post-kala-azar dermal leishmaniasis (PKDL) patients were subjected to both real-time PCR and RPA assay in Bangladesh, India, and Nepal. Further skin samples from confirmed cutaneous leishmaniasis (CL) patients were also included from Sri Lanka. A total of 450 clinical samples from VL patients, 429 from PKDL patients, 47 from CL patients, and 322 from endemic healthy/healthy controls were under investigation to determine the diagnostic efficacy of RPA assay in comparison to real-time PCR. A comparative sensitivity of both methods was found where real-time PCR and RPA assay showed 96.86% (95% CI: 94.45–98.42) and 88.85% (95% CI: 85.08–91.96) sensitivity respectively in the diagnosis of VL cases. This new isothermal method also exhibited promising diagnostic sensitivity (93.50%) for PKDL cases, when a skin sample was used. Due to variation in the sequence of target amplicons, RPA assay showed comparatively lower sensitivity (55.32%) than that of real-time PCR in Sri Lanka for the diagnosis of CL cases. Except for India, the assay presented absolute specificity in the rest of the sites. Excellent concordance between the two molecular methods towards detection of leishmania DNA in clinical samples substantiates the application of RPA assay incorporated in a suitcase laboratory for point-of-need diagnosis of VL and PKDL in low resource endemic settings. However, further improvisation of the method is necessary for diagnosis of CL.

Trots att Sverige än så länge saknar en standard för hur intelligenta datorer får användas i offentlig sektor, så använder en allt större mängd myndigheter automatiserade beslutssystem i ärenden mot privatpersoner. Vetskapen om dessa system är låg hos den generella befolkningen, vilket riskerar göra det svårt för människor att ta till vara på sina intressen. I Trelleborgs kommun har man sedan 2017 använt automatiserad handläggning för att ta beslut i ärenden om ekonomiskt bistånd, vilket har gett upphov till kritiska granskningar av fallets rättsäkerhet och implikationer för handläggarrollen. Hur systemet påverkar den sökande individens förutsättningar och  demokratiska förvaltningsideal har emellertid varit ett underutvecklat ämnesområde. Följaktligen ämnar denna studie undersöka vilket utrymme demokratiska värden har vid automatiserat beslutsfattande i myndighetsärenden mot privatpersoner. Detta görs genom att jämföra implementeringen av automatiseringssystem i Trelleborgs kommun med en idealtyp för demokratiska värden i intelligent automatisering av förvaltningen. Analysresultaten visar på att flera demokratiska nyckelfunktioner saknas i Trelleborgsmodellen. Det bristfälliga utrymmet för demokratiska värden kan dock härledas i stor utsträckning till kommunens hantering av systemet snarare än begränsningar i systemet i sig.

No description available.

No description available.

The Random Phase Approximation and beyond Random Phase Approximation methods based on Adiabatic Connection Fluctuation Dissipation Theorem (ACFD) are tested for structural phase transitions of different groups of materials, including metal to metal, metal to semiconductor, semiconductor to semiconductor transitions. Also the performance assessment of semilocal density functionals with or without empirical long range dispersion corrections has been explored for the same cases. We have investigated the structural phase transitions of three broad group of materials, semi- conductor to metal transitions involving two symmetric structures, semiconductor to metal and wide bandgap semiconductor to semiconductor transitions involving at least one lower symmetric structure and lastly special cases comprising metal to metal transitions and transitions between energetically very close structural phases. The first group contains Si (diamond → β-tin), Ge (diamond → β-tin) and SiC (zinc blende → rocksalt), second group contains GaAs (zinc blende → cmcm) and SiO 2 (quartz → stishovite) and third group contains Pb (fcc → hcp), C(graphite → diamond) and BN (cubic → hexagonal) respectively. We have found that the difference in behavior of exchange and correlation in semilocal functionals and ACFD methods is striking. For the former, the exchange potential and energy often comprise the majority of the binding described by density functional approximations, and the addition of the correlation energy and potential often induce only a (relatively) small shift from the exchange- only results. For the ACFD, however, non self-consistent EXX typically underbinds by a considerable degree resulting in wildly inaccurate results. Thus the addition of correlation leads to very large shifts in the exchange-only results, in direct contrast to semilocal correlation. This difference in behavior is directly linked to the non-local nature of the EXX, and even though the exchange-only starting point is often nowhere close to experiment, the non-local correlation from the ACFD corrects this deficiency and yields the missing binding needed to produce accurate results. Thus we find the ACFD approach to be vital in the validation of semilocal results and recommend its use in materials where experimental results cannot be straightforwardly compared to other approximate electronic structure calculations. Utilizing the second-order approximation to Random Phase Approximation renormalized (RPAr) many-body perturbation theory for the interacting density-density response function, we have used a so-called higher-order terms (HOT) approximation for the correlation energy. In combination with the first-order RPAr correction, the HOT method faithfully captures the infinite- order correlation for a given exchange-correlation kernel, yielding errors of the total correlation energy on the order of 1% or less for most systems. For exchange-like kernels, our new method has the further benefit that the coupling-strength integration can be completely eliminated resulting in a modest reduction in computational cost compared to the traditional approach. When the correlation energy is accurately reproduced by the HOT approximation, structural properties and energy differences are also accurately reproduced, as confirmed by finding interlayer binding energies of several periodic solids and compared that to some molecular systems along with some phase transition parameters of SiC. Energy differences involving fragmentation have proved to be challenging for the HOT method, however, due to errors that do not cancel between a composite system and its constituent pieces which has been verified in our work as well. / Physics

La protéine auxiliaire Vpr du VIH-1 est exprimée tardivement au cours de la réplication virale. Toutefois, du fait de son encapsidation dans les particules virales, elle joue un rôle important dès les étapes initiales du cycle de réplication viral. Cette protéine de 96 acides aminés intervient en effet au cours de la rétrotranscription du génome viral puis de la translocation de l’ADN viral vers le noyau de la cellule hôte. Parallèlement, elle provoque un arrêt du cycle cellulaire et l’apoptose des lymphocytes T infectés. Alors qu’il a été établi que Vpr participait au contrôle de la fidélité de la rétrotranscription via le recrutement au sein des particules virales de l’uracile DNA glycosylase 2 (UNG2), enzyme impliquée dans les processus de réparation de l’ADN, certaines études ont ensuite remis en question l’impact positif de l’encapsidation de l’UNG2 sur la réplication virale. Les travaux présentés ici permettent de confirmer le rôle de l’UNG2 dans le contrôle du taux de mutations au sein de l’ADN synthétisé à partir de l'ARN viral par un mécanisme indépendant de son activité enzymatique, mais lié à des déterminants situés dans la partie N-terminale de la protéine engagée dans le recrutement de la sous-unité p32 du complexe RPA (Replication protein A) (RPA32). Nous avons montré, dans un premier temps, que la production de virus dans des cellules dont les niveaux d'expression de l'UNG2 et de RPA32 étaient diminués se traduisait par une réduction significative du pouvoir infectieux des particules virales et de la synthèse de l’ADN viral. Nous avons ensuite montré que la protéine Vpr est capable de former un complexe tri-moléculaire avec les protéines UNG2 et RPA32, et confirmé l’importance de ces deux protéines cellulaires pour permettre une réplication virale optimale aussi bien dans des lignées cellulaires T que dans les cellules primaires cibles du VIH-1. Même si les macrophages et les PBMCs (cellules mononucléaires du sang périphérique), cellules cibles du VIH-1, expriment des niveaux faibles d’UNG2 et de RPA32, ces protéines cellulaires semblent requises pour permettre une synthèse d'ADN virale suffisante à la réplication optimale du virus dans ces cellules primaires. L’ensemble de ces résultats suggère que le contrôle de la rétrotranscription par Vpr a lieu via le recrutement de deux protéines cellulaires UNG2 et RPA32 permettant la dissémination efficace du VIH-1 dans les cellules cibles primaires. / The HIV-1 auxiliary protein Vpr is expressed during the late steps of the viral replication. However, Vpr is incorporated into HIV-1 viral particles and plays a key role during the initial steps of the viral replication cycle. This 96 amino acids protein is involved in viral genome reverse transcription as well as in viral DNA translocation into the nucleus of the host cell. In parallel, Vpr provokes cell cycle arrest and apoptosis of infected T cells. Previously, it has been well established that Vpr participates in the control of the fidelity of the reverse transcription through the recruitment of the Uracil DNA Glycosylase 2 (UNG2) into the viral particles. UNG2 is an enzyme involved in different DNA repair pathway. However some studies have challenged the positive impact of UNG2 encapsidation for HIV-1 replication. Here, our studies confirm the important role of UNG2 for the control of the mutation rate in the newly synthesized viral DNA by a mechanism independent of its enzymatic activity but dependent to determinants located in the N-terminal domain that is involved in the recruitment of the p32 subunit of the RPA (Replication Protein A) complex (RPA32). First we showed that viruses produced in UNG2 or RPA32 depleted cells present a defect of infectivity and that the reverse transcription step is impaired during the course of infection of these viruses. Then we reported that the Vpr protein is able to form a trimolecular complex with UNG2 and RPA32 and we confirmed the importance of both UNG2 and RPA32 for optimal virus replication in a T cell line as well as in HIV-1 primary target cells. Even though macrophages and PBMCs (Peripheral Blood Mononuclear Cells), target cells of HIV-1, express low level of UNG2 and RPA32, these cellular proteins seem to be required for an efficient viral DNA synthesis leading to an optimal virus replication in primary cells. All these results suggest that Vpr controls the reverse transcription step through the recruitment of two cellular proteins UNG2 and RPA32 which allow the efficient dissemination of HIV-1 in the primary target cells.

La protéine auxiliaire Vpr du VIH-1 est exprimée tardivement au cours de la réplication virale. Toutefois, du fait de son encapsidation dans les particules virales, elle joue un rôle important dès les étapes initiales du cycle de réplication viral. Cette protéine de 96 acides aminés intervient en effet au cours de la rétrotranscription du génome viral puis de la translocation de l’ADN viral vers le noyau de la cellule hôte. Parallèlement, elle provoque un arrêt du cycle cellulaire et l’apoptose des lymphocytes T infectés. Alors qu’il a été établi que Vpr participait au contrôle de la fidélité de la rétrotranscription via le recrutement au sein des particules virales de l’uracile DNA glycosylase 2 (UNG2), enzyme impliquée dans les processus de réparation de l’ADN, certaines études ont ensuite remis en question l’impact positif de l’encapsidation de l’UNG2 sur la réplication virale. Les travaux présentés ici permettent de confirmer le rôle de l’UNG2 dans le contrôle du taux de mutations au sein de l’ADN synthétisé à partir de l'ARN viral par un mécanisme indépendant de son activité enzymatique, mais lié à des déterminants situés dans la partie N-terminale de la protéine engagée dans le recrutement de la sous-unité p32 du complexe RPA (Replication protein A) (RPA32). Nous avons montré, dans un premier temps, que la production de virus dans des cellules dont les niveaux d'expression de l'UNG2 et de RPA32 étaient diminués se traduisait par une réduction significative du pouvoir infectieux des particules virales et de la synthèse de l’ADN viral. Nous avons ensuite montré que la protéine Vpr est capable de former un complexe tri-moléculaire avec les protéines UNG2 et RPA32, et confirmé l’importance de ces deux protéines cellulaires pour permettre une réplication virale optimale aussi bien dans des lignées cellulaires T que dans les cellules primaires cibles du VIH-1. Même si les macrophages et les PBMCs (cellules mononucléaires du sang périphérique), cellules cibles du VIH-1, expriment des niveaux faibles d’UNG2 et de RPA32, ces protéines cellulaires semblent requises pour permettre une synthèse d'ADN virale suffisante à la réplication optimale du virus dans ces cellules primaires. L’ensemble de ces résultats suggère que le contrôle de la rétrotranscription par Vpr a lieu via le recrutement de deux protéines cellulaires UNG2 et RPA32 permettant la dissémination efficace du VIH-1 dans les cellules cibles primaires. / The HIV-1 auxiliary protein Vpr is expressed during the late steps of the viral replication. However, Vpr is incorporated into HIV-1 viral particles and plays a key role during the initial steps of the viral replication cycle. This 96 amino acids protein is involved in viral genome reverse transcription as well as in viral DNA translocation into the nucleus of the host cell. In parallel, Vpr provokes cell cycle arrest and apoptosis of infected T cells. Previously, it has been well established that Vpr participates in the control of the fidelity of the reverse transcription through the recruitment of the Uracil DNA Glycosylase 2 (UNG2) into the viral particles. UNG2 is an enzyme involved in different DNA repair pathway. However some studies have challenged the positive impact of UNG2 encapsidation for HIV-1 replication. Here, our studies confirm the important role of UNG2 for the control of the mutation rate in the newly synthesized viral DNA by a mechanism independent of its enzymatic activity but dependent to determinants located in the N-terminal domain that is involved in the recruitment of the p32 subunit of the RPA (Replication Protein A) complex (RPA32). First we showed that viruses produced in UNG2 or RPA32 depleted cells present a defect of infectivity and that the reverse transcription step is impaired during the course of infection of these viruses. Then we reported that the Vpr protein is able to form a trimolecular complex with UNG2 and RPA32 and we confirmed the importance of both UNG2 and RPA32 for optimal virus replication in a T cell line as well as in HIV-1 primary target cells. Even though macrophages and PBMCs (Peripheral Blood Mononuclear Cells), target cells of HIV-1, express low level of UNG2 and RPA32, these cellular proteins seem to be required for an efficient viral DNA synthesis leading to an optimal virus replication in primary cells. All these results suggest that Vpr controls the reverse transcription step through the recruitment of two cellular proteins UNG2 and RPA32 which allow the efficient dissemination of HIV-1 in the primary target cells.

Dans la modélisation de la matière dense, et partiellement ionisée, une question importante concerne le traitement des électrons libres. Vis-à-vis des électrons liés, la nature délocalisée et non discrète de ces électrons est responsable d’une différence de traitement, qui est souvent effectuée dans les modélisations des propriétés radiatives des plasmas. Cependant, afin d’éviter les incohérences dans le calcul des spectres d’absorption, tous les électrons devraient, en principe, être décrits dans un même formalisme.Nous utilisons deux modèles variationnels d’atome-moyen : un modèle semi-classique, et un modèle quantique, qui permettent cette égalité de traitement pour tous les électrons. Nous calculons la section-efficace de photo-extinction, en appliquant le cadre de la théorie de la réponse linéaire dynamique à chacun de ces modèles d’atome dans un plasma. Pour cette étude, nous développons et utilisons une approche auto-cohérente, de type random-phase-approximation (RPA), qui, en allant au-delà de la réponse des électrons indépendants, permet d’évaluer les effets collectifs, par l’introduction de la polarisation dynamique. Cette approche s’inscrit dans le formalisme de la théorie de la fonctionnelle de la densité dépendant du temps (TDDFT), appliquée au cas d’un système atomique immergé dans un plasma.Pour les deux modèles, semi-classique et quantique, nous dérivons, et vérifions dans nos calculs, une nouvelle règle de somme, qui permet d’évaluer le dipôle atomique à partir d’un volume fini dans le plasma. Cette règle de somme s’avère être un outil de premier ordre pour le calcul des propriétés radiatives des atomes dans les plasmas denses. / In modeling dense and partially ionized matter, the treatment of the free electrons remains an important issue. Compared to bound electrons, the delocalized and non-discrete nature of these electrons is responsible to treat them differently, which is usually adopted in the modelings of radiative properties of plasmas. However, in order to avoid inconsistencies in the calculation of absorption spectra, all the electrons should be described in the same formalism.We use two variational average-atom models: a semi-classical and a quantum model, which allow this common treatment for all the electrons. We calculate the photo-extinction cross-section, by applying the framework of the linear dynamical response theory to each of these models of an atom in a plasma. For this study, we develop and use a self-consistent approach, of random-phase-approximation (RPA) type, which, while going beyond the independent electron response, permits to evaluate the collective effects by the introduction of the dynamical polarization. This approach uses the formalism of the time dependent density functional theory (TDDFT), applied in the case of an atomic system immersed in a plasma.For both models, semi-classical and quantum, we derive and verify in our calculations, a new sum rule, which allows the evaluation of the atomic dipole from a finite volume in the plasma. This sum rule turns out to be a crucial device in the calculation of radiative properties of atoms in dense plasmas.