Mass Spectrometry for the Elucidation of the Subtle Molecular Structure of Biodegradable Polymers and their Degradation Products

Contemporary reports by Polish authors on the application of mass spectrometric methods for the elucidation of the subtle molecular structure of biodegradable polymers and their degradation products will be presented. Special emphasis will be given to natural aliphatic (co)polyesters (PHA) and their synthetic analogues, formed through anionic ring-opening polymerization (ROP) of b-substituted b-lactones. Moreover, the application of MS techniques for the evaluation of the structure of biodegradable polymers obtained in ionic and coordination polymerization of cyclic ethers and esters as well as products of step-growth polymerization, in which bifunctional or multifunctional monomers react to form oligomers and eventually long chain polymers, will be discussed. Furthermore, the application of modern MS techniques for the assessment of polymer degradation products, frequently bearing characteristic end groups that can be revealed and differentiated by MS, will be discussed within the context of specific degradation pathways. Finally, recent Polish accomplishments in the area of mass spectrometry will be outlined.Project ID 2013/11/B/ST5/02222, 2012/07/B/ST5/00627, 3CE368P1 Project Funder National Science Centre (NCN) Poland, Central Europe Programme, University of Wolverhampto

Architektura gridu bazodanowego oparta o podejście peer-to-peer

W artykule autorzy przedstawiają zaimplementowane i zweryfikowane poprzez w pełni funkcjonalny prototyp, podejście do realizacji obiektowego gridu bazodanowego przy wykorzystaniu wirtualnej sieci peer-to-peer omawiając szczegółowo najważniejszy element mechanizmu jakim jest proces integracji rozproszonych obiektów. W artykule przeprowadzono gruntowną analizę rozwiązań będących fundamentalnym zbiorem wiedzy na temat integracji danych. Zaprezentowano trójwarstwowy model intagracyjny oparty o aktualizowalne obiektowe perspektywy oraz prototyp gridowej warstwy pośredniej wykorzystującej sieć wirtualną peer-to-peer.In the article authors present an approach for realisation of object-oriented database grid using virtual peer-to-peer networking. The approach has been verified by implementation of fully functional prototype. The article shows in details a process for integration of distributed objects which is provided by the core mechanism of the prototype. Authors also described three-layer integration model based on obiect-oriented updateable views and middleware prototype containing mentioned peer-to-peer solution. Moreover the article contains analysis of solutions being the fundamental knowledge about integration of data

Przezroczysta integracja zasobów relacyjnych do obiektowego wirtualnego repozytorium

Prezentowana w artykule idea polega na wirtualnej integracji rozproszonych heterogenicznych zasobów bazodanowych w scentralizowaną, jednorodną, spójną i pozbawioną fragmentacji oraz nadmiarowości całość tworzącą wirtualne repozytorium zapewniające pewne powszechne funkcjonalności i usługi, włączając w to infrastrukturę zaufania (bezpieczeństwo, prywatność, licencjonowanie, płatności, itp.), Web Services, rozproszone transakcje, zarządzanie procesami (workflow management), itd. Opisane poniżej metody integracji skupiają się właśnie na najpopularniejszych zasobach relacyjnych, do których zostaje umożliwiony w pełni przezroczysty dostęp poprzez niezwykle elastyczny obiektowy język zapytań. Opracowane specjalnie do tego celu mechanizmy optymalizacyjne stanowią kombinację dedykowanych technik obiektowych z niezwykle wydajnymi optymalizatorami relacyjnymi.The presented idea aims to virtually integrate distributed heterogeneous database resources into a centralised consistent and non-fragmented and non-redundant whole creating a virtual repository. The repository provides common functionalities and services, including trust infrastructure (like security, privacy, licensing, payments), Web Services, distributed transactions, workflow management, etc. The described integration methods focus on the most popular and commonly used relational resources. Such resources become fully transparently accessible with an extremely flexible object-oriented query language. The dedicated optimisation mechanisms are a combination of object-oriented techniąues and very efficient relational optimisers

The synthesis and structural characterization of graft copolymers composed of γ-PGA backbone and oligoesters pendant chains

© 2017 The Authors. Published by American Chemical Society. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1021/jasms.8b05393The novel copolymers composed of poly-γ-glutamic acid (γ-PGA) and oligoesters have been developed. The structures of the obtained copolymers including variety of end groups were determined at the molecular level with the aid of electrospray ionization multistage mass spectrometry (ESI-MSn). The fragmentation experiment performed for the selected sodium adducts of the copolymers confirmed that the developed methods lead to the formation of graft copolymers composed of poly-γ-glutamic acid (γ-PGA) backbone and oligoesters pendant chains. Moreover, it was established that fragmentation of selected sodium adducts of graft copolymers proceeded via random breakage of amide bonds along the backbone and ester bonds of the oligoesters pendant chains. Considering potential applications of the synthesized copolymers in the area of biomaterials, the hydrolytic degradation under laboratory conditions and in vitro cytotoxicity tests were performed. The ESI-MSn technique applied in this study has been proven to be a useful tool in structural studies of novel graft copolymers as well as their degradation products.This work was supported by the Polish National Science Centre (Decision No DEC-2013/11/N/ST5/01364

On distributed data processing in data grid architecture for a virtual repository

The article describes the problem of integration of distributed, heterogeneous and fragmented collections of data with application of the virtual repository and the data grid concept. The technology involves: wrappers enveloping external resources, a virtual network (based on the peer-topeer technology) responsible for integration of data into one global schema and a distributed index for speeding-up data retrieval. Authors present a method for obtaining data from heterogeneously structured external databases and then a procedure of integration the data to one, commonly available, global schema. The core of the described solution is based on the Stack-Based Query Language (SBQL) and virtual updatable SBQL views. The system transport and indexing layer is based on the P2P architecture

Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA

SMC5/6 is a highly conserved protein complex related to cohesin and condensin, which are the key components of higher-order chromatin structures. The SMC5/6 complex is essential for proliferation in yeast and is involved in replication fork stability and processing. However, the precise mechanism of action of SMC5/6 is not known. Here we present evidence that the NSE1/NSE3/NSE4 sub-complex of SMC5/6 binds to double-stranded DNA without any preference for DNA-replication/recombination intermediates. Mutations of key basic residues within the NSE1/NSE3/NSE4 DNA-binding surface reduce binding to DNA in vitro. Their introduction into the Schizosaccharomyces pombe genome results in cell death or hypersensitivity to DNA damaging agents. Chromatin immunoprecipitation analysis of the hypomorphic nse3 DNA-binding mutant shows a reduced association of fission yeast SMC5/6 with chromatin. Based on our results, we propose a model for loading of the SMC5/6 complex onto the chromatin

A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6

The SMC (Structural Maintenance of Chromosomes) complexes are composed of SMC dimers, kleisin and kleisin-interacting (HAWK or KITE) subunits. Mutual interactions of these subunits constitute the basal architecture of the SMC complexes. In addition, binding of ATP molecules to the SMC subunits and their hydrolysis drive dynamics of these complexes. Here, we developed new systems to follow the interactions between SMC5/6 subunits and the relative stability of the complex. First, we show that the N-terminal domain of the Nse4 kleisin molecule binds to the SMC6 neck and bridges it to the SMC5 head. Second, binding of the Nse1 and Nse3 KITE proteins to the Nse4 linker increased stability of the ATP-free SMC5/6 complex. In contrast, binding of ATP to SMC5/6 containing KITE subunits significantly decreased its stability. Elongation of the Nse4 linker partially suppressed instability of the ATP-bound complex, suggesting that the binding of the KITE proteins to the Nse4 linker constrains its limited size. Our data suggest that the KITE proteins may shape the Nse4 linker to fit the ATP-free complex optimally and to facilitate opening of the complex upon ATP binding. This mechanism suggests an important role of the KITE subunits in the dynamics of the SMC5/6 complexes

Bioactive oligomers from natural polyhydroxyalkanoates and their synthetic analogues

Contemporary reports on the bioactive oligomers derived from natural aliphatic (co)polyesters (PHA) and their synthetic analogues, formed through anionic ring-opening polymerization (ROP) of β-substituted β-lactones are presented. Synthetic routes for such oligomers, developed mostly by Polish authors, are discussed. The described approaches enable design of novel biodegradable and bioactive oligomers for diverse applications in medicine, cosmetic industry and agrochemistry. Abstrakt: Przedstawiono przegląd aktualnych wyników badań dotyczących bioaktywnych oligomerów otrzymywanych z naturalnych alifatycznych (ko)poliestrów (PHA) oraz ich syntetycznych analogów, uzyskanych na drodze anionowej polimeryzacji z otwarciem pierścienia (ROP) β-podstawionych β-laktonów. Omówiono ścieżki syntezy tych oligomerów opracowane głównie przez polskich badaczy. Zaprezentowane metody umożliwiają projektowanie nowych biodegradowalnych a zarazem bioaktywnych oligomerów dla różnorodnych zastosowań w medycynie, przemyśle kosmetyczny i agrochemii

Bacterial-derived Polymer Poly-y-Glutamic Acid (y-PGA)-based micro/nanoparticles as a delivery system for antimicrobials and other biomedical applications

Abstract: In the past decade, poly-γ-glutamic acid (γ-PGA)-based micro/nanoparticles have garnered remarkable attention as antimicrobial agents and for drug delivery, owing to their controlled and sustained-release properties, low toxicity, as well as biocompatibility with tissue and cells. γ-PGA is a naturally occurring biopolymer produced by several gram-positive bacteria that, due to its biodegradable, non-toxic and non-immunogenic properties, has been used successfully in the medical, food and wastewater industries. Moreover, its carboxylic group on the side chains can offer an attachment point to conjugate antimicrobial and various therapeutic agents, or to chemically modify the solubility of the biopolymer. The unique characteristics of γ-PGA have a promising future for medical and pharmaceutical applications. In the present review, the structure, properties and micro/nanoparticle preparation methods of γ-PGA and its derivatives are covered. Also, we have highlighted the impact of micro/nanoencapsulation or immobilisation of antimicrobial agents and various disease-related drugs on biodegradable γ-PGA micro/nanoparticles.Iraqi cultural attach

A New Type of Thermoalkalophilic Hydrolase of Paucimonas lemoignei with High Specificity for Amorphous Polyesters of Short Chain-length Hydroxyalkanoic Acids

A novel type of hydrolase was purified from culture fluid of Paucimonas (formerly Pseudomonas) lemoignei. Biochemical characterization revealed an unusual substrate specificity of the purified enzyme for amorphous poly((R)-3-hydroxyalkanoates) (PHA) such as native granules of natural poly((R)-3-hydroxybutyrate) (PHB) or poly((R)-3-hydroxyvalerate) (PHV), artificial cholate-coated granules of natural PHB or PHV, atactic poly((R,S)-3-hydroxybutyrate), and oligomers of (R)-3-hydroxybutyrate (3HB) with six or more 3HB units. The enzyme has the unique property to recognize the physical state of the polymeric substrate by discrimination between amorphous PHA (good substrate) and denatured, partially crystalline PHA (no substrate). The pentamers of 3HB or 3HV were identified as the main products of enzymatic hydrolysis of native PHB or PHV, respectively. No activity was found with any denatured PHA, oligomers of (R)-3HB with five or less 3HB units, poly(6-hydroxyhexanoate), substrates of lipases such as tributyrin or triolein, substrates for amidases/nitrilases, DNA, RNA, casein, N-alpha-benzoyl-l-arginine-4-nitranilide, or starch. The purified enzyme (M(r) 36,209) was remarkably stable and active at high temperature (60 degrees C), high pH (up to 12.0), low ionic strength (distilled water), and in solvents (e.g. n-propyl alcohol). The depolymerase contained no essential SH groups or essential disulfide bridges and was insensitive to high concentrations of ionic (SDS) and nonionic (Triton and Tween) detergents. Characterization of the cloned structural gene (phaZ7) and the DNA-deduced amino acid sequence revealed no homologies to any PHB depolymerase or any other sequence of data banks except for a short sequence related to the active site serine of serine hydrolases. A classification of the enzyme into a new family (family 9) of carboxyesterases (Arpigny, J. L., and Jaeger, K.-E. (1999) Biochem. J. 343, 177-183) is suggested