Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations

A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force-peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e. by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids

QR kod jako uzupełnienie tradycyjnej monografii. Korzyści i konsekwencje

The article describes the possibility of using QR codes in traditional scientific monographs. By using this kind of tools authors have an opportunity to disseminate results of their work in a pose-text way. That way of publishing is attractive to authors – they gain additional opportunity to present their theses, as well as for readers, for whom such a message may be more attractive. The use of modern technologies in the process of publishing scientific monographs may also raise concerns. The consequences resulting from the tabloidization of the science sphere can be dangerous for the authority of the scientific community. The article presents an example of a monograph where authors decided to use QR codes as a complement to the traditional monograph. The publication included results of qualitative research conducted by anthropologists in Lithuania.W tekście opisano możliwość wykorzystania w tradycyjnych monografiach naukowych kodów QR. Dzięki zastosowaniu tego rodzaju narzędzi autorzy uzyskują okazję do upowszechniania wyników swojej pracy w sposób pozatekstowy. Taki rodzaj publikowania jest atrakcyjny zarówno dla autorów – zdobywają oni wizualne możliwości prezentowania, jak i dla czytelników, dla których taki przekaz może być bardziej atrakcyjny. Wykorzystanie nowoczesnych technologii w procesie publikowania monografii naukowych może jednak budzić obawy. Ewentualne konsekwencje wynikające z banalizacji i tabloidyzacji sfery naukowej są groźne dla autorytetu środowiska naukowego. W tekście został opisany konkretny przykład monografii, której autorzy zdecydowali się na wykorzystanie kodów QR jako uzupełnienia tradycyjnej monografii naukowej. Kody zostały dołączone do publikacji, w której znalazły się wyniki badań jakościowych przeprowadzonych przez antropologów kulturowych na Litwie

Action research in the Vilnius region

The author in his text dedicated to action research made in the Vilnius region, Lithuania (a project realized by undergraduate students, PhD students, and one of the employees of the Chair of Ethnology and Anthropology University of Wrocław and a Lithuanian partner), presents an approach of engaged anthropology, basing on the characteristics important for it: cooperation, dialogism, openness, voluntariness. The paper presents the main features of the methodology of action research and further – the objectives and results of the research. It describes the cooperation between the academic anthropologists and non-professionals, moreover – the reflections on fieldwork and the problems that researcher has to cope with

Topological Aspects of DNA Function and Protein Folding Topological features in stretching of proteins

Abstract In the present article, we highlight the diversity of mechanical clamps, some of them topological in nature, that have been found by making surveys of mechanostability of approximately 18 000 proteins within structure-based models. The existence of superstable proteins (with the characteristic unfolding force in the region of 1000 pN) is predicted

Current strategies of the brachial plexus palsy management

The importance of brachial plexus palsy treatment is associated with its significant severity, along with Brachial plexus palsies can be treated by means of many different surgical and non-surgical methods which allow regeneration of full efficiency of the affected limb. The choice of method depends on such factors as type and region of injury, patient’s age or clinical presentation of the injury. The purpose of this review is to present current strategies of treating brachial plexus palsies, depending on therapeutic needs of the particular patient. This is a review study based upon selective literature overview, with emphasis on works published within past 13 years. 6 separate methods of brachial plexus palsy were assessed, without distinction of the reason of palsy occurring. Some of the invasive methods include operative treatment performed directly on occupied nervous tissue, such as microneural plexus reconstruction and nerve transfers (lower subscapular nerve transfer and contralateral C7 nerve transfer) whilst the others revolve around restoration of function of affected neighboring structures by themselves, e.g. shoulder tendon transfers. Rehabilitation and botulinum toxin-based treatment are non-operative methods revolving around enhancement of the function of the affected upper limb. Main measure of effectiveness of the treatment is assessment of the range of motion of the affected limb (ROM). There is still not enough information available regarding long-term efficiency of microneural plexus reconstruction and botulinum toxin-based treatment. They require further investigation while other methods are used commonly