Design and synthesis of constrained dipeptide units for use as β-sheet promoters

The study of factors promoting beta-sheet formation has recently gained interest due to the suspected involvement of beta-sheets in brain degenerative diseases such as Alzheimer\u27s disease (AD), Creutzfeldt-Jacob disease (CJD) and bovine spongiform encephalopathy. Understanding beta-sheet formation and the factors that stabilize beta-sheet structure may serve as a basis for future drug design. The extended structure of a beta-sheet can be stabilized by constrained amino acid analogs that are pre-organized to adopt the extended conformation. In this dissertation using innovative synthetic organic chemistry methods, two dipeptide units are designed and synthesized that are constrained to form the extended conformation and mimic the hydrogen-bonding and side chain interactions that natural beta-sheets form along one edge of the individual peptide strands. DiPeptideUnit (DPU) 45 and Aza-DiPeptide unit (ADP) 46 are designed to have increasing levels of constraint in order to directly measure the relative beta-sheet forming propensity of the constrained dipeptides when incorporated into selected positions of a prototypical, semi-stable beta-hairpin peptide. An improved synthesis of DPU(Gly, Xxx) 45 from D-glutamic acid is reported. Previously described syntheses of lactam-constrained dipeptide amino acids involve lengthy and expensive procedures to obtain an aldehyde intermediate. The key to the synthesis of the DPU(Gly, Xxx) 45 is the convenient synthesis of an alpha-amino acid semialdehyde in high yields. When DPU(Gly, Leu) 47b is incorporated into an analogous peptide it stabilizes the beta-sheet secondary structure according to CD measurements and this stabilizing effect is higher when more DPU residues are incorporated. A very efficient way of synthesizing ADP(Gly, Phe) 46 is also reported. The key intermediate in this synthesis is a protected alpha-hydrazino ester derivative that is synthesized from alpha-amino esters using inexpensive reagents and in excellent overall yields. The key reaction step in the synthesis is the very effective coupling of a D-aspartic acid derivative with the N-alpha of the alpha-hydrazino ester by symmetrical anhydride method

When manipulations are harm[less]ful?

We say that a mechanism is harmless if no student can ever misreport his preferences so that he does not hurt but someone else. We consider a large class of rules which includes the Boston, the agent-proposing deferred acceptance, and the school-proposing deferred acceptance mechanisms (sDA). In this large class, the sDA happens to the unique harmless mechanism. We next provide two axiomatic characterizations of the sDA. First, the sDA is the unique stable, non-bossy, and independent of irrelevant student mechanism. The last axiom is a weak variant of consistency. As harmlessness implies non bossiness, the sDA is also the unique stable, harmless, and independent of irrelevant student mechanism

Volume changes during active shape fluctuations in cells

Cells modify their volume in response to changes in osmotic pressure but it is usually assumed that other active shape variations do not involve significant volume fluctuations. Here we report experiments demonstrating that water transport in and out of the cell is needed for the formation of blebs, commonly observed protrusions in the plasma membrane driven by cortex contraction. We develop and simulate a model of fluid mediated membrane-cortex deformations and show that a permeable membrane is necessary for bleb formation which is otherwise impaired. Taken together our experimental and theoretical results emphasize the subtle balance between hydrodynamics and elasticity in actively driven cell morphological changes.Comment: Phys. Rev. Lett. in press. 13 pages 4 figures, 9 supplementary figure

Accounting for localized deformation: a simple computation of true stress in micropillar compression experiments

Compression experiments are widely used to study the mechanical properties of materials at micro- and nanoscale. However, the conventional engineering stress measurement method used in these experiments neglects to account for the alterations in the material's shape during loading. This can lead to inaccurate stress values and potentially misleading conclusions about the material's mechanical behavior especially in the case of localized deformation. To address this issue, we present a method for calculating true stress in cases of localized plastic deformation commonly encountered in experimental settings: (i) a single band and (ii) two bands oriented in arbitrary directions with respect to the vertical axis of the pillar (either in the same or opposite directions). Our simple analytic formulas can be applied to homogeneous and isotropic materials and crystals, requiring only standard data (displacement-force curve, aspect ratio, shear band angle and elastic strain limit) obtained from experimental results and eliminating the need for finite element computations. Our approach provides a more precise interpretation of experimental results and can serve as a valuable and simple tool in material design and characterization.Comment: arXiv admin note: text overlap with arXiv:2012.1278

Semantic Web based Container Monitoring System for the Transportation Industry

Abstract: Goods are transported around the world in containers. Monitoring containers is a complex task. In this presentation, we will present a Container Monitoring System based on Semantic Web technologies. This system is currently being developed by Ege University, Bimar Information Technology Services and Capsenta for ARKAS Holding, one of Turkey's leading logistics and transportation companies. Our presentation consists of 1) introducing the challenges of monitoring containers in the transportation industry, 2) how existing technologies and solutions do not satisfy the needs, 3) why Semantic Web technologies can address the needs, 4) how we are using Semantic Web technologies including architectural design decisions and finally 5) describe lessons learned

Cdc45 Limits Replicon Usage from a Low Density of preRCs in Mammalian Cells

Little is known about mammalian preRC stoichiometry, the number of preRCs on chromosomes, and how this relates to replicon size and usage. We show here that, on average, each 100-kb of the mammalian genome contains a preRC composed of approximately one ORC hexamer, 4–5 MCM hexamers, and 2 Cdc6. Relative to these subunits, ∼0.35 total molecules of the pre-Initiation Complex factor Cdc45 are present. Thus, based on ORC availability, somatic cells contain ∼70,000 preRCs of this average total stoichiometry, although subunits may not be juxtaposed with each other. Except for ORC, the chromatin-bound complement of preRC subunits is even lower. Cdc45 is present at very low levels relative to the preRC subunits, but is highly stable, and the same limited number of stable Cdc45 molecules are present from the beginning of S-phase to its completion. Efforts to artificially increase Cdc45 levels through ectopic expression block cell growth. However, microinjection of excess purified Cdc45 into S-phase nuclei activates additional replication foci by three-fold, indicating that Cdc45 functions to activate dormant preRCs and is rate-limiting for somatic replicon usage. Paradoxically, although Cdc45 colocalizes in vivo with some MCM sites and is rate-limiting for DNA replication to occur, neither Cdc45 nor MCMs colocalize with active replication sites. Embryonic metazoan chromatin consists of small replicons that are used efficiently via an excess of preRC subunits. In contrast, somatic mammalian cells contain a low density of preRCs, each containing only a few MCMs that compete for limiting amounts of Cdc45. This provides a molecular explanation why, relative to embryonic replicon dynamics, somatic replicons are, on average, larger and origin efficiency tends to be lower. The stable, continuous, and rate-limiting nature of Cdc45 suggests that Cdc45 contributes to the staggering of replicon usage throughout S-phase, and that replicon activation requires reutilization of existing Cdc45 during S-phase

Relatório de estágio em farmácia comunitária

Relatório de estágio realizado no âmbito do Mestrado Integrado em Ciências Farmacêuticas, apresentado à Faculdade de Farmácia da Universidade de Coimbr