Bochner's theorem in infinite dimensions

Generalized extension and applications of Bochner theorem in infinite dimension

A multipoint method of third order

Multipoint algorithm applied to nonlinear Chandrasekar integral equatio

Infinite dimensional multipoint methods and the solution of two point boundary value problems

Infinite dimensional multipoint methods and solution of two point boundary value problem

Costs of Inaction on Maternal Mortality: Qualitative Evidence of the Impacts of Maternal Deaths on Living Children in Tanzania.

Little is known about the interconnectedness of maternal deaths and impacts on children, beyond infants, or the mechanisms through which this interconnectedness is established. A study was conducted in rural Tanzania to provide qualitative insight regarding how maternal mortality affects index as well as other living children and to identify shared structural and social factors that foster high levels of maternal mortality and child vulnerabilities. Adult family members of women who died due to maternal causes (N = 45) and key stakeholders (N = 35) participated in in-depth interviews. Twelve focus group discussions were also conducted (N = 83) among community leaders in three rural regions of Tanzania. Findings highlight the widespread impact of a woman's death on her children's health, education, and economic status, and, by inference, the roles that women play within their families in rural Tanzanian communities. The full costs of failing to address preventable maternal mortality include intergenerational impacts on the nutritional status, health, and education of children, as well as the economic capacity of families. When setting priorities in a resource-poor, high maternal mortality country, such as Tanzania, the far-reaching effects that reducing maternal deaths can have on families and communities, as well as women's own lives, should be considered

NMR Structural Investigations of the U4 snRNA kink-turn and of a lariat-forming ribozyme

Three-dimensional fold of the U4 5’stem loop snRNA in its unbound form: The spliceosome, which catalyzes the splicing of eucaryotic pre-mRNAs, consists of five uridine-rich small nuclear ribonucleoprotein particles (U snRNPs) and numerous other factors. To activate the spliceosome and to enable the first step of splicing, the paired U4 and U6 snRNAs of the U4/U6 snRNP complex need to dissociate from each other. An initial step is the binding of the protein 15.5K to the 5’ stem loop of U4 snRNA (U4 5’ SL). Subsequently, further proteins are recruited, in particular protein hPrp31, which forms a ternary complex with the U4 5’ SL and 15.5K. Upon binding to the 15.5K protein, the U4 5’ SL folds into a characteristic structural motif, called the kink-turn (k-turn), in which the phosphodiester backbone presents a particular sharp turn. In this work the three-dimensional conformation of the free U4 5’ SL RNA in solution was investigated in order to elucidate whether the k-turn structural element is already present in the absence of protein binders. By using NMR spectroscopy, the structure of the unbound U4 5’ SL was solved at a precision of 0.6 Å. In the structure, the canonical as well as the non-canonical stem of the U4 5’ SL present a well-defined helix fold. The U4 5’ SL lacks the characteristic sharp turn of the k-turn motif reported for the protein bound form. Instead, the free U4 5’ SL presents a more opened, extended conformation. The two non-canonical G-A base-pairs found in the k-turn structure are already formed in the unbound RNA, but the three unpaired residues of the internal loop (AAU) are stacked differently with respect to the k-turn motif. In this work it was shown that the free U4 k-turn RNA is prevalently found in the extended conformation in solution. Thus, the consensus sequence of the k-turn does not per se code for the sharp bent in the RNA backbone. Instead, the structural k-turn element is highly disfavoured in solution and needs to be stabilized by protein binding, which favors the thesis of a protein-assisted mechanism for k-turn RNA folding. Structural investigations of a spliceosomal related lariat-forming ribozyme: In eukaryotic cells, pre-mRNAs are processed by the spliceosome in a way that internal non-coding regions (introns) are excised and the remaining segments (exons) are joined together. The active spliceosomal core consists of paired U2 and U6 snRNAs, which juxtapose the splice site residues of the pre-mRNA substrate. While the RNA-RNA interactions during splicing have been well-characterized in the past, the description of tertiary structure of the spliceosomal catalytic center remains a challenge due to the large size and dynamics of the complex. In our laboratory a model ribozyme is investigated, which undergoes a transesterfication reaction with striking similarity to the first step of splicing by forming a 2’-5’ lariat. The lariat formation has the same sequence specificity, including the phylogenetically highly conserved ACAGAGA box that is essential for catalytic activity in the spliceosome of higher eukaryotes. In this work, mutational studies were carried out to identify specific sites that can be either linked to folding of the ribozyme or to their function in the catalytic activity of the RNA molecule. With these studies it could be shown that the residues A29, G32, A33 and A35 are functionally the most important residues within the ACAGAGA-segment. Furthermore, a well defined helical moiety in the 5’ region of the ribozyme with an unusual high content of non-canonical base-pairs was revealed by combining information of the mutational studies with NMR derived distance constraints. Another aim of this work was to gain first insights into the three-dimensional fold of the ribozyme prior to catalysis. NMR investigation and analysis were performed, with several differentially 13C, 15N-labeled NMR samples, in order to retrieve numerous complementary NMR spectra for the resonance assignment of the ribozyme. However, although various labeling schemes were applied, the assignment remained ambiguous for some nucleotides, due to both spectral overlap and a conformational exchange process that was detected for half of the resonances. To overcome the spectral complexity, eight RNA mutants were constructed, which enabled a complete, unambiguous resonance assignment of all nucleotides of the lariat-forming ribozyme. This resonance assignment is a perquisite for the collection of structural restraints, mainly of NOE peak intensities. NOE signals reflect direct distances of neighboring atoms in a molecule and suggest a compact fold, presumably containing both a ribose zipper motif and a pseudoknot motif, for the lariat-forming ribozyme. All these data represent an excellent starting point to explore the complete three-dimensional structure of the lariat-forming ribozyme and will facilitate its understanding in terms of functionality

Computational Genome and Pathway Analysis of Halophilic Archaea

Halophilic archaea inhabit hypersaline environments and share common physiological features such as acidic protein machineries in order to adapt to high internal salt concentrations as well as electron transport chains for oxidative respiration. Surprisingly, nutritional demands were found to differ considerably amongst haloarchaeal species, though, and in this project several complete genomes of halophilic archaea were analysed to predict their metabolic capabilities. Comparative analysis of gene equipments showed that haloarchaea adopted several strategies to utilize abundant cell material available in brines such as the acquisition of catabolic enzymes, secretion of hydrolytic enzymes, and elimination of biosynthesis gene clusters. For example, metabolic genes of the well-studied Halobacterium salinarum were found to be consistent with the known degradation of glycerol and amino acids. Further, the complex requirement of H. salinarum for various amino acids and vitamins in comparison with other halophiles was explained by the lack of several genes and gene clusters, e.g. for the biosynthesis of methionine, lysine, and thiamine. Nitrogen metabolism varied also among halophilic archaea, and the haloalkaliphile Natronomonas pharaonis was predicted to apply several modes of N-assimilation to cope with severe ammonium deficiencies in its highly alkaline habitat. This species was experimentally shown to possess a functional respiratory chain, but comparative analysis with several archaea suggests a yet unknown complex III analogue in N. pharaonis. Respiratory chains of halophilic and other respiratory archaea were found to share similar genes for pre-quinone electron transfer steps but show great diversity in post-quinone electron transfer steps indicating adaptation to changing environmental conditions in extreme habitats. Finally, secretomes of halophilic and non-halophilic archaea were predicted proposing that haloarchaea secretion proteins are predominantly exported via the twin-arginine pathway and commonly exhibit a lipobox motif for N-terminal lipid anchoring. In N. pharaonis, lipoboxcontaining proteins were most frequent suggesting that lipid anchoring might prevent protein extraction under alkaline conditions. By contrast, non-halophilic archaea seem to prefer the general secretion pathway for protein translocation and to retain only few secretion proteins by N-terminal lipid anchors. Membrane attachment was preferentially observed for interacting components of ABC transporters and respiratory chains and might further occur via postulated C-terminal anchors in archaea. Within this project, the complete genome of the newly sequenced N. pharaonis was analysed with focus on curation of automatically generated data in order to retrieve reliable gene prediction and protein function assignment results as a basis for additional studies. Through the development of a post-processing routine and expert validation as well as by integration of proteomics data, a highly reliable gene set was created for N. pharaonis which was subsequently used to assess various microbial gene finders. This showed that all automatic gene tools predicted a rather correct gene set for the GC-rich N. pharaonis genome but produced insufficient results in respect to their start codon assignments. Available proteomics results for N. pharaonis and H. salinarum were further analysed for posttranslational modifications, and N-terminal peptides of haloarchaeal proteins were found to be commonly processed by N-terminal methionine cleavage and to some extent further modified by N-acetylation. For general function assignment of predicted N. pharaonis proteins and for enzyme assignment in H. salinarum, similarity-based searches, genecontext methods such as neighbourhood analysis but also manual curation were applied in order to reduce the number of hypothetical proteins and to avoid cross-species transfer of misassigned functions. This permitted to reliably reconstruct the metabolism of H. salinarum and N. pharaonis. Generated metabolic data were stored in a newly developed metabolic database that also integrates experimental data retrieved from the literature. The pathway data can be assessed as coloured KEGG maps and were combined with data resulting from transcriptomics and proteomics techniques. In future, expert-curated reaction entries of the created metabolic database will be a valuable source for the design of metabolic experiments and will deliver a reliable input for metabolic models of halophilic archaea

On decoupling of linear time delay systems by generalized output feedback

Special Issue on Time delay systemsInternational audienceWe consider the row-by-row decoupling problem for linear delay systems by output feedback. The characterization of the solvability of this problem is given in terms of some easily checkable structural conditions. The main contribution is, in particular, to use generalized output feedback laws which may incorporate derivatives of the delayed new reference