OPEN Repository
Welcome to OPEN - the Repository of Open Scientific Publications, run by the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, previously operating as the CeON Repository. The Repository enables Polish researchers from all fields to openly share their articles, books, conference materials, reports, doctoral theses, and other scientific texts.
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23414 archived items
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Recent Submissions
Item
Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing & Superresolution Microscopy
(Wiley Online Library, 2021-05-03) Kamińska, Izabela; Bohlen, Johann; Yaadav, Renukka; Schüler, Patrick; Raab, Mario; Schröder, Tim; Zähringer, Jonas; Zielonka, Karolina; Krause, Stefan; Tinnefeld, Philip; Institute of Physical Chemistry, Polish Academy of Sciences; Department of Chemistry and Center for NanoScience Ludwig-Maximilians-Universität München, Germany
Graphene is considered a game-changing material, especially for its mechanical and electrical properties. This work exploits that graphene is almost transparent but quenches fluorescence in a range up to ≈40 nm. Graphene as a broadband and unbleachable energy-transfer acceptor without labeling, is used to precisely determine the height of molecules with respect to graphene, to visualize the dynamics of DNA nanostructures, and to determine the orientation of Förster-type resonance energy transfer (FRET) pairs. Using DNA origami nanopositioners, biosensing, single-molecule tracking, and DNA PAINT super-resolution with <3 nm z-resolution are demonstrated. The range of examples shows the potential of graphene-on-glass coverslips as a versatile platform for single-molecule biophysics, biosensing, and super-resolution microscopy.
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Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy
(ACS Publications, 2021-04-09) Krause, Stefan; Ploetz, Evelyn; Bohlen, Johann; Schüler, Patrick; Yaadav, Renukka; Selbach, Florian; Steiner, Florian; Kamińska, Izabela; Tinnefeld, Philip; Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Germany; Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
Graphene exhibits outstanding fluorescence quenching properties that can become useful for biophysics and biosensing applications, but it remains challenging to harness these advantages due to the complex transfer procedure of chemical vapor deposition-grown graphene to glass coverslips and the low yield of usable samples. Here, we screen 10 graphene-on-glass preparation methods and present an optimized protocol. To obtain the required quality for single-molecule and super-resolution imaging on graphene, we introduce a graphene screening method that avoids consuming the investigated sample. We apply DNA origami nanostructures to place fluorescent probes at a defined distance on top of graphene-on-glass coverslips. Subsequent fluorescence lifetime imaging directly reports on the graphene quality, as deviations from the expected fluorescence lifetime indicate imperfections. We compare the DNA origami probes with conventional techniques for graphene characterization, including light microscopy, atomic force microscopy, and Raman spectroscopy. For the latter, we observe a discrepancy between the graphene quality implied by Raman spectra in comparison to the quality probed by fluorescence lifetime quenching measured at the same position. We attribute this discrepancy to the difference in the effective area that is probed by Raman spectroscopy and fluorescence quenching. Moreover, we demonstrate the applicability of already screened and positively evaluated graphene for studying single-molecule conformational dynamics on a second DNA origami structure. Our results constitute the basis for graphene-based biophysics and super-resolution microscopy.
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Can standardisation of the unit costs of wood extraction be applied in the financial system of the State Forests?
(Committee on Forestry Sciences and Wood Technology of the Polish Academy of Sciences and the Forest Research Institute in Sękocin Stary, 2021-09-19) Kocel, Janusz; Jodłowski, Krzysztof; Forest Research Institute, Department of Forest Resources Management, Sękocin Stary, Poland
The paper presents a method for grouping forest districts that are characterised by similar natural and forest conditions and the results of standardisation of wood extraction costs for forest districts and regional directorates of the State Forests. The adopted standard costs referred to the costs which determine the reasonable level of costs necessary to perform a specific management task in the given natural, forest and economic conditions of forest districts. Forest districts were grouped based on the forest habitat types and the land diversity index (Wtri), which were determined with statistical methods to be the factors that shape wood extraction costs. In order to determine the standard unit costs of wood extraction, source materials for the year 2017 have been used, which had been obtained from the State Forests Information System for all forest districts in the country. The method of standardising wood extraction unit costs on the basis of forest district groups with similar natural and forest conditions was reduced in 2017 to the designation of eight uniform forest district groups in terms of forest habitat type structure and Wtri index. Standard unit costs of wood extraction, determined on the basis of the methodology presented in the paper, should be used in the State Forests’ financial system.
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The damage caused by wind in middle-aged Scots pine stands on permanent thinning experimental plots
(Committee on Forestry Sciences and Wood Technology of the Polish Academy of Sciences and the Forest Research Institute in Sękocin Stary, 2021-09-19) Zachara, Tadeusz; Gil, Wojciech; Forest Research Institute, Department of Silviculture and Genetics of Forest Trees, Sękocin Stary, Poland
In July 2002, the very strong hurricane appeared in northern Poland, which caused destruction of forest cover of area more than 10,000 ha. The permanent thinning research plot in a 53-year-old pine stand located in Myszyniec forest district (150 km north of Warsaw) was lying on the edge of damaged area. The following treatments were tested on this plot: 1) control plot (without thinning); 2) schematic cut in 20-year-old stand, selective thinning to 40 years, then thinning from below; 3) schematic cut in 20-year-old stand, then selective thinning; 4) selective thinning in young stand (20–40 years), then thinning from below and 5) selective thinning all the time. A significant part of this plot was completely destroyed and in the other part of the plot, some trees survived. A small part of the plot resisted the wind attack. An analysis of the amount of destroyed trees (measured by basal area) showed no differences between particular silvicultural treatments. The level of damage differed between particular parts of the plot. Another plot located in Ostrów Mazowiecka forest district (100 km NE of Warsaw) with the same thinning treatments was touched by heavy wind in July 2011 when the stand was 62 years old. Unlike the hurricane of 2002, this storm did not destroy the experimental plot which was located outside the zone of heaviest calamity. Therefore, damage on this plot had point and group character. Although on particular measurement units, share of broken or fallen trees did not exceed 10% of total basal area, it can be observed that the lowest level of damage was noticed on plots with selective thinning in young age and thinning from below in older stand.
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Successive processes at quarry waste dumps of various ages
(Committee on Forestry Sciences and Wood Technology of the Polish Academy of Sciences and the Forest Research Institute in Sękocin Stary, 2021-09-19) Smirnov, Aleksandr; Mutalibova, Gavakhirat; Leontyev, Vyacheslav; Lozano-Rivas, William; Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, Department of Agricultural Construction and Property Expertise, Moscow, Russian Federation; Kazan Federal University, Department of Biology and Chemistry, Elabuga, Russian Federation; Piloto of Colombia University, Department of Environmental Sciences, Bogotá, Colombia
This work is dedicated to the study of the succession processes in quarries of different ages in the territory of the Russian Federation and neighbouring countries, namely, Kazakhstan and Ukraine. In selected soil samples from the areas studied, certain physical and chemical properties, the quantitative composition of microbial communities and the diversity of floral species from the quarries were studied. The pH values for the Kuzbass area were found to decrease to 4.8, and in the area of the younger quarries – Inguletsky and Sokolovsky – higher pH values were recorded. The basal soil respiration rate of the Kuzbass quarry was approximately 0.2 mg CO2/g/h. The CO2 carbonate content ranged from 0.05% to 0.6%. The microbial biomass in Kuzbass soil was from 0.87 to 5.10 μg C/g soil, while its quantity in other quarries was 6 times lower, which is associated with the relatively young age of these sites. The study of the diversity of floral species in the Kuznetsk coalfield identified 120 species of upper plants belonging to 34 families. Among them, cereals, legumes and mosses, lichens and algae were predominant. In the territory of Inguletsky and Sokolovsky quarries, the diversity of plant species was much poorer. In this regard, further research will focus on increasing the rate of succession and maintaining ecosystem stability by increasing the share of microorganisms. Also, the study of the possibility to accelerate the restoration of younger flora in the discharges of age careers at the expense of the mycorrhizal communities formation is of high relevance.