The process of decoding is the most crucial determinant of the quality of protein synthesis. Ribosomal protein L9 was first implicated in decoding fidelity when a mutant version of L9 was found to increase the translation of a T4 phage gene. Later studies confirmed that the absence of L9 leads to increased translational bypassing, frameshifting, and stop codon readthrough. L9 is part of the large subunit of the prokaryotic ribosome and is located more than 90 Å from the site of decoding, making it difficult to envision how it might affect decoding and reading frame maintenance. Twenty years after the identification of L9's putative function, there is no mechanism for how a remotely located L9 improves translation fidelity. This mystery makes our picture of translation incomplete. Despite the high conservation of L9 in eubacteria, E.coli lacking L9 does not exhibit any obvious growth defects. Thus, the evolutionary advantage conferred by L9 in bacteria is masked under laboratory conditions. In order to uncover unique L9-dependent conditions, a library of E. coli mutants was screened to isolate those that rely on L9 for fitness. Interestingly, factors found to be synergistic with L9 had no known role in fidelity. Six independent mutants were isolated, each exhibiting a severe growth defect that is partially suppressed in the presence of L9. One class of L9-dependent mutations was present in an essential ribosome biogenesis factor, Der. Der's established function is in the maturation of the large ribosomal subunit. The identified mutations severely impaired the GTPase activity of Der. Interestingly, L9 did not directly compensate for the defective GTPase activity of mutant Der. The second class of L9-dependent mutations was present in EpmA and EpmB, factors required to post-translationally modify elongation factor, EF-P. EF-P's established function is in the translation of poly-proline containing proteins. EF-P deficient cells were nearly inviable in the absence of L9; however, L9 did not directly influence poly-proline translation. Therefore, in each case, L9 improved cell health without altering the activity of either Der or EF-P. Remarkably, the der mutants required only the N domain of L9, whereas the absence of active EF-P required full-length, wild-type L9 for growth complementation. Thus, each mutant class needed a different aspect of L9's unique architecture. In cells lacking either active EF-P or Der, there was a severe deficiency of 70S ribosomes and the indication of small subunit maturation defects, both of which worsened upon L9 depletion. These results strongly suggest that L9 plays a role in improving ribosome quality and abundance under certain conditions. Overall, the genetic screen lead to the discovery that bacteria need L9 when either of two important translation factors (Der or EF-P) is inactivated. This work has characterized the physiological requirement for L9 in each case and offers a new insight into L9's assigned role in translation fidelity.

No description available.

On constate un regain d’intérêt pour l’étude des potentiels de champs extracellulaires (EFP). Trois principaux rôles fonctionnels des oscillations enregistrées dans le système nerveux ont été proposés : i) le codage d’informations spécifiques ii) la modulation des états attentionnels du cerveau, mais aussi iii) la création d’assemblées dynamiques. Je me suis intéressé aux EFP enregistrés dans les régions du néocortex, de l’hippocampe et de la VTA dans deux cadres expérimentaux dits “contrôlés” - afin de déceler des “motifs” oscillatoires spécifiques dans les mécanismes de mémorisations d’une situation stressante d’une part et dans les prises de décision sous incertitude d’autre part. Nous avons dans un premier temps enregistré et analysé l’activité dans les circuits dopaminergiques de la VTA, le PFC et l’OFC dans un paradigme permettant d’analyser le comportement de souris dans un cadre de prise de décision sous incertitude. Nous avons pu montrer dans un premier temps, que les circuits PFC, OFC et la VTA montrent des séquences d’activations et de synchronisations spécifiques selon le choix de l’individu, en condition incertaine. Dans un second temps, je me suis intéressé à mesurer, chez l’animal éveillé, les effets que pouvait engendrer une situation stressante sur le PFC et l’HPC en fonction de l’âge. Nos résultats mettent en évidence que les principaux effets mesurables aux niveaux des spectres de puissances s’expliquent par l’apparition d’activités électriques de fortes amplitudes dans la gamme (7-12 Hz), dont l’apparition varie en fonction de l’âge et du contexte (repos, stress). / Currently, there is a renewed interest in studying extracellular field potentials (EFP). This signal and the oscillations associated with it are the basis of many studies on the mechanisms underlying cognitive processes in cortical networks. Three key functional roles of oscillations recorded in the nervous system have been proposed: i) encoding specific information ii) modulation of attentional states of the brain, but also iii) creating dynamic assemblies. Although the interest for EFP continues to grow, the interpretation of these signals are sparse. During my prject I focused on the interpretation of EFP patterns under stress and uncertainty and specifically studied neocortex, hippocampus (HPC) and the ventral tegmental area (VTA) signals in these two experimental settings.Firstly, we recorded and analyzed the activity in the dopaminergic circuits including the VTA, PFC (prefrontal cortex) and OFC (orbitofrontal cortex) in a probabilistic decision-making paradigm for mice. We demonstrated that the PFC, OFC and VTA circuit shows specific time-dependent activation sequences depending on the anticipated choice per trial. Secondly, I was interested to measure, in awake animals, the effects caused by a stressful situation at different ages on the PFC and HPC signals. Our results demonstrate major effects at the level of the power spectral analysis. We identified that particularly high amplitudes in the range (7-12 Hz) vary according age and context (rest, stress).

The Effective Fragment Potential (EFP) is a quantum-mechanical based model used to describe non-covalent interactions of small molecules or fragments. It can be used along with fully <i>ab initio</i> methods to study the electronic properties of complex systems, such as solvated chromophores or proteins. For this purpose, the system is divided into two regions: one modeled with quantum mechanics and the other with EFP. The interaction between the QM region and the effective fragments has popularly been described through electrostatics and polarization only. This thesis focuses on the development of the QM/EFP exchange-repulsion term, as well as the evaluation of the dispersion term and a charge-penetration correction. The goal of is to determine how these terms can increase the accuracy of QM/EFP calculations without an increase in their computational cost.

<p>Here we describe recent technical implementations and modifications to the libefp package as well as applications of those implementations. Applications of the EFP method to biologically relevant systems are provided on a benchmark EFP-SAPT-CCSD study on the SSI dataset along with suggested basis set recommendations and a study on the pairwise EFP total energy decomposition on Factor Xa. We also report the technical overview of two computational tools we believe will lower the human barrier to utilizing the EFP method - iSpiEFP and EFPdB.</p>

<div> <div> <div> <p>The Effective Fragment Potential (EFP) is a quantum-mechanical based model potential for accurate calculations of non-covalent interactions between molecules. It can be coupled with ab initio methods in so-called QM/EFP models to explore the electronic properties of extended molecular systems by providing rigorous description of surrounding environments. The current EFP formulation is, however, not well suited for large-scale simulations due to its inherent limitation of representing effective fragments as rigid structures. The process of utilizing EFP method for the molecular systems with flexible degrees of freedom entails multiple sets of parameter calculations requiring intensive computational resources. This work presents development of the EFP method for describing flexible molecular systems, so-called Flexible EFP. To validate the applicability of the Flexible EFP method, extensive benchmark studies on the amino acid interactions, binding energies, and electronic properties of flavin chromophore of the cryptochrome protein have been demonstrated. In addition to methodological developments, excitonic properties of the Fenna-Matthews-Olson (FMO) photosynthetic pigment-protein complex are explored. In biological systems where intermolecular interactions span a broad range from non-polar to polar and ionic forces, EFP is superior to the classical force fields. In the present study, we demonstrate excellent performance of the QM/EFP model for predicting excitonic interactions and spectral characteristics of the FMO wildtype complex. We characterize the key factors for accurate modeling of electronic properties of bacteriochlrophyll a (BChl a) photosynthetic pigments and suggest a robust computational protocol that can be applied for modeling other photosynthetic systems. Developed computational procedures were also successfully utilized to elucidate photostability and triplet dynamics in the FMO complex and spectroscopic effects of single-point mutagenesis in FMO. A combination of polarizable EFP molecular dynamics and QM/EFP vibrational frequency calculations were also applied to understanding and interpreting structures and Raman spectroscopy of tert-butyl alcohol solutions. </p> </div> </div> </div>

Abstract Every year the Swedish police handle 25,000 reports on missing people. A majority of those gone missing come back home, without the need of outside assistance. For some, help is critical, and many don’t even know that they are missing. These people are persons with dementia and a large percentage of them go missing in Sweden´s largest city, Stockholm. Searching for a person with dementia in a sprawling city creates its own set of obstacles and requires a certain skill from the police in order to execute assistance.   The result of the study is based on interviews with experienced police officers from the  Stockholm police force and their experience of searching for missing persons with dementia in an urban environment. The results of this study indicate that the Managing Search Operations, or “EFP-metoden” in Swedish, is a search method that works when the police search for a person with dementia in an urban environment. Why the method works can`t be explained and the reason is that there is lack of research and verified statistics in the research area of persons gone missing.  This indicates that there is a need of more research studies about people gone missing for the Swedish “EFP-metoden” to develop.    This study is done as a quality interview study and the study has been done to develop new information to the study of missing people who have dementia and to give suggestions to future research data in this field of study.

Cyanobacteria are an ancient lineage of gram-negative photosynthetic prokaryotes that play an important role in the nitrogen cycle in terrestrial and aquatic systems. Widespread cyanobacterial blooms have prompted numerous studies on the classification of this group, however defining species is problematic due to lack of clarity as to which characters best define the various taxonomic levels. The genera Anabaena, Aphanizomenon and Nostoc form one of the most controversial groups and are typically paraphyletic within phylogenetic trees and share similar morphological characters. This study’s purpose was to determine the taxonomic and phylogenetic relationships among isolates from these three genera using 16S rRNA and bacterial elongation factor P (efp) gene sequences as well as morphological analyses. These data confirmed the non-monophyly of Anabaena and Aphanizomenon and demonstrated that many of the isolates were intermixed among various clades in both gene phylogenies. In addition, the genus Nostoc was clearly not monophyletic and this finding differed from previous studies. The genetic divergence of the genus Nostoc was confirmed based on 16S rRNA gene sequence similarities (≥85.1%), and the isolates of Anabaena were genetically differentiated, contrary to previous studies (16S rRNA gene sequence similarities ≥89.4%). The morphological diversity was larger than the molecular diversity, since the statistical analysis ANOSIM showed that the isolates were morphologically well differentiated; however, the 16S rRNA gene sequence similarities showed some isolates as being related at the species level. Planktonic and benthic strains were not distinguished phylogenetically, although some well-supported clusters were noted. Cellular measurements (length and width of vegetative cells, end cells, heterocysts and akinetes) were noted to be the morphological characters that best supported the differentiation among isolates, more than qualitative characterization. Among the metric parameters, the length of akinetes resulted in better differentiation among isolates. The efp gene sequence analyses did not appear to be useful for the taxonomic differentiation at lower taxonomic levels, but gave well-supported clusters for Aphanizomenon that was supported by the morphological analyses. Both gene regions gave similar trees with the exception of the Aphanizomenon isolates which clustered together in phylogenetic trees based on the efp gene. This differed from the 16S rRNA gene in which this genus was paraphyletic with Anabaena species that were similar in morphology to Aphanizomenon. Hence, the application of multiple taxonomic criteria is required for the successful delineation of cyanobacterial species.

Cyanobacteria are an ancient lineage of gram-negative photosynthetic prokaryotes that play an important role in the nitrogen cycle in terrestrial and aquatic systems. Widespread cyanobacterial blooms have prompted numerous studies on the classification of this group, however defining species is problematic due to lack of clarity as to which characters best define the various taxonomic levels. The genera Anabaena, Aphanizomenon and Nostoc form one of the most controversial groups and are typically paraphyletic within phylogenetic trees and share similar morphological characters. This study’s purpose was to determine the taxonomic and phylogenetic relationships among isolates from these three genera using 16S rRNA and bacterial elongation factor P (efp) gene sequences as well as morphological analyses. These data confirmed the non-monophyly of Anabaena and Aphanizomenon and demonstrated that many of the isolates were intermixed among various clades in both gene phylogenies. In addition, the genus Nostoc was clearly not monophyletic and this finding differed from previous studies. The genetic divergence of the genus Nostoc was confirmed based on 16S rRNA gene sequence similarities (≥85.1%), and the isolates of Anabaena were genetically differentiated, contrary to previous studies (16S rRNA gene sequence similarities ≥89.4%). The morphological diversity was larger than the molecular diversity, since the statistical analysis ANOSIM showed that the isolates were morphologically well differentiated; however, the 16S rRNA gene sequence similarities showed some isolates as being related at the species level. Planktonic and benthic strains were not distinguished phylogenetically, although some well-supported clusters were noted. Cellular measurements (length and width of vegetative cells, end cells, heterocysts and akinetes) were noted to be the morphological characters that best supported the differentiation among isolates, more than qualitative characterization. Among the metric parameters, the length of akinetes resulted in better differentiation among isolates. The efp gene sequence analyses did not appear to be useful for the taxonomic differentiation at lower taxonomic levels, but gave well-supported clusters for Aphanizomenon that was supported by the morphological analyses. Both gene regions gave similar trees with the exception of the Aphanizomenon isolates which clustered together in phylogenetic trees based on the efp gene. This differed from the 16S rRNA gene in which this genus was paraphyletic with Anabaena species that were similar in morphology to Aphanizomenon. Hence, the application of multiple taxonomic criteria is required for the successful delineation of cyanobacterial species.

No description available.