Electrochemical method for isolation of chitinous 3D scaffolds from cultivated Aplysina aerophoba marine demosponge and its biomimetic application

Three-dimensional (3D) biopolymer-based scaffolds including chitinous matrices have been widely used for tissue engineering, regenerative medicine and other modern interdisciplinary fields including extreme biomimetics. In this study, we introduce a novel, electrochemically assisted method for 3D chitin scaffolds isolation from the cultivated marine demosponge Aplysina aerophoba which consists of three main steps: (1) decellularization, (2) decalcification and (3) main deproteinization along with desilicification and depigmentation. For the first time, the obtained electrochemically isolated 3D chitinous scaffolds have been further biomineralized ex vivo using hemolymph of Cornu aspersum edible snail aimed to generate calcium carbonates-based layered biomimetic scaffolds. The analysis of prior to, during and post-electrochemical isolation samples as well as samples treated with molluscan hemolymph was conducted employing analytical techniques such as SEM, XRD, ATR–FTIR and Raman spectroscopy. Finally, the use of described method for chitin isolation combined with biomineralization ex vivo resulted in the formation of crystalline (calcite) calcium carbonate-based deposits on the surface of chitinous scaffolds, which could serve as promising biomaterials for the wide range of biomedical, environmental and biomimetic applications. © 2020, The Author(s).Politechnika PoznaÅ ska, PUT: 0911/SBAD/0380/2019Deutsche Forschungsgemeinschaft, DFG: HE 394/3Deutscher Akademischer Austauschdienst, DAADRussian Science Foundation, RSF: 18-13-00220PPN/BEK/2018/1/0007103/32/SBAD/0906Sächsisches Staatsministerium für Wissenschaft und Kunst, SMWK: 02010311This work was performed with the financial support of Poznan University of Technology, Poland (Grant No. 0911/SBAD/0380/2019), as well as by the Ministry of Science and Higher Education (Poland) as financial subsidy to PUT No. 03/32/SBAD/0906. Krzysztof Nowacki was supported by the Erasmus Plus program (2019). Also, this study was partially supported by the DFG Project HE 394/3 and SMWK Project No. 02010311 (Germany). Marcin Wysokowski is financially supported by the Polish National Agency for Academic Exchange (PPN/BEK/2018/1/00071). Tomasz Machałowski is supported by DAAD (Personal Ref. No. 91734605). Yuliya Khrunyk is supported by the Russian Science Foundation (Grant No. 18-13-00220)

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.

Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer protein levels from other omics measurements, we leveraged crowdsourcing via the NCI-CPTAC DREAM proteogenomic challenge. We asked for methods to predict protein and phosphorylation levels from genomic and transcriptomic data in cancer patients. The best performance was achieved by an ensemble of models, including as predictors transcript level of the corresponding genes, interaction between genes, conservation across tumor types, and phosphosite proximity for phosphorylation prediction. Proteins from metabolic pathways and complexes were the best and worst predicted, respectively. The performance of even the best-performing model was modest, suggesting that many proteins are strongly regulated through translational control and degradation. Our results set a reference for the limitations of computational inference in proteogenomics. A record of this paper's transparent peer review process is included in the Supplemental Information

Mammal responses to global changes in human activity vary by trophic group and landscape

Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human–wildlife interactions along gradients of human influence.Peer reviewe

The V471A polymorphism in autophagy-related gene ATG7 modifies age at onset specifically in Italian Huntington disease patients

The cause of Huntington disease (HD) is a polyglutamine repeat expansion of more than 36 units in the huntingtin protein, which is inversely correlated with the age at onset of the disease. However, additional genetic factors are believed to modify the course and the age at onset of HD. Recently, we identified the V471A polymorphism in the autophagy-related gene ATG7, a key component of the autophagy pathway that plays an important role in HD pathogenesis, to be associated with the age at onset in a large group of European Huntington disease patients. To confirm this association in a second independent patient cohort, we analysed the ATG7 V471A polymorphism in additional 1,464 European HD patients of the “REGISTRY” cohort from the European Huntington Disease Network (EHDN). In the entire REGISTRY cohort we could not confirm a modifying effect of the ATG7 V471A polymorphism. However, analysing a modifying effect of ATG7 in these REGISTRY patients and in patients of our previous HD cohort according to their ethnic origin, we identified a significant effect of the ATG7 V471A polymorphism on the HD age at onset only in the Italian population (327 patients). In these Italian patients, the polymorphism is associated with a 6-years earlier disease onset and thus seems to have an aggravating effect. We could specify the role of ATG7 as a genetic modifier for HD particularly in the Italian population. This result affirms the modifying influence of the autophagic pathway on the course of HD, but also suggests population-specific modifying mechanisms in HD pathogenesis

Travel length in the forecasting of potential road accessibility changes on case of two A2 motorway sections

Celem artykułu jest zaprezentowanie rezultatów badań nad dostępnością potencjałową na poziomie gminnym zrealizowanych w 2012r. w Instytucie Geografii i Przestrzennego Zagospodarowania PAN. Wskaźnik drogowej dostępności potencjałowej gmin uzyskano poprzez zsumowanie trzech komponentów: potencjału własnego, potencjału krajowego oraz potencjału zewnętrznego (międzynarodowego). Wskaźnik pozwala na wykonanie symulacji zmian dostępności w wyniku realizacji poszczególnych inwestycji infrastrukturalnych. W artykule symulację wykonano na przykładzie dwóch odcinków autostrady A2 – Łódź Północ-Warszawa oraz Świecko-Nowy Tomyśl. Zmiany drogowej dostępności potencjałowej gmin zostały pokazane na poziomie krajowym oraz międzynarodowym. Celem podróży dla wszystkich symulacji była liczba ludności w rejonach komunikacyjnych. Prognozowanie zmian dostępności ma na celu wskazanie priorytetów realizacji poszczególnych odcinków sieci w kontekście ich znaczenia dla zmian dostępności na różnych poziomach analizy. Szczególną rolę pełni również zakładana długość podróży, która różnicuje się poprzez dobór odpowiednich parametrów funkcji oporu przestrzeni. Dla wykorzystanej w referacie funkcji wykładniczej wykorzystano podział na podróże krótkie (β= 0,02) i długie (β = 0,005). W artykule wskazano, iż różnice w zmianach dostępności między krótkimi i długimi podróżami są najwyższe w kontekście międzynarodowym po otwarciu odcinka peryferyjnego położonego blisko tzw. europejskiego rdzenia (Świecko-Nowy Tomyśl). Jednocześnie odcinek ten nie ma dużego znaczenia dla zmian dostępności w ujęciu krajowym (niezależnie od długości podróży). Z kolei odcinek położony w centralnej Polsce skutkuje generalnie większymi zmianami dostępności na obszarze całego kraju. Jednak różnice między wariantami w zmianach dostępności nie są tak duże, jak przy odcinku peryferyjnym. Zastosowana w niniejszym artykule metoda badawcza w postaci tzw. dostępności potencjałowej daje ogromne możliwości ewaluacyjne zarówno w formie ewaluacji ex-post jak i ex-ante. Dzięki zastosowaniu modelu potencjału istnieje możliwość porównywania odcinków sieci drogowej pod kątem zmian dostępności w zależności od długości podróży, zasięgu przestrzennego badania, a także, co nie było tematem niniejszego artykułu, z punktu widzenia atrakcyjności celu podróży, a także typu i gałęzi transportu lub motywacji podróży.The purpose of this paper is to present the research results on potential accessibility at the community level. The potential road accessibility index of the communes was obtained by summing up the three following components: inner potential, national potential and external (international) potential. The index allows to perform a simulation of changes in accessibility resulting from particular infrastructure investments. Simulation was carried out basing on the case of two sections of the A2 motorway: Lodz North - Warsawa and Swiecko – Nowy Tomysl. The changes in potential road accessibility of the municipalities were shown at national and international levels. Forecasting the changes in accessibility aims at identifying the priorities for implementation of individual sections of the road network in terms of their relevance to changes in the accessibility at different levels of the analysis. A special role is assigned to the assumed journey duration, which is differentiated by selecting appropriate parameters of the spatial resistance function. For the exponential function used in the paper a division into short (β=0.02) and long (β = 0.005) travel was applied. A research method implemented in the article in the form of potential accessibility offers great evaluation possibilities for both ex-post and ex-ante assessment. With the application of the potential model it is possible to compare the road network sections in terms of changes in accessibility depending on trip length, spatial scope of the study, and what was not the subject of this article, from the destination attractiveness point of view as well as the type and mode of transport or travel motivation