Ana Rakita

Bio: Ana Rakita is an academic researcher from Medical University of Vienna. The author has contributed to research in topics: Human skin & Wound healing. The author has an hindex of 2, co-authored 2 publications receiving 2646 citations.

Re-epithelialization and immune cell behaviour in an ex vivo human skin model.

Abstract: A large body of literature is available on wound healing in humans. Nonetheless, a standardized ex vivo wound model without disruption of the dermal compartment has not been put forward with compelling justification. Here, we present a novel wound model based on application of negative pressure and its effects for epidermal regeneration and immune cell behaviour. Importantly, the basement membrane remained intact after blister roof removal and keratinocytes were absent in the wounded area. Upon six days of culture, the wound was covered with one to three-cell thick K14+Ki67+ keratinocyte layers, indicating that proliferation and migration were involved in wound closure. After eight to twelve days, a multi-layered epidermis was formed expressing epidermal differentiation markers (K10, filaggrin, DSG-1, CDSN). Investigations about immune cell-specific manners revealed more T cells in the blister roof epidermis compared to normal epidermis. We identified several cell populations in blister roof epidermis and suction blister fluid that are absent in normal epidermis which correlated with their decrease in the dermis, indicating a dermal efflux upon negative pressure. Together, our model recapitulates the main features of epithelial wound regeneration, and can be applied for testing wound healing therapies and investigating underlying mechanisms.

Octenidine-based hydrogel shows anti-inflammatory and protease-inhibitory capacities in wounded human skin

Abstract: Octenidine dihydrochloride (OCT) is a widely used antiseptic molecule, promoting skin wound healing accompanied with improved scar quality after surgical procedures. However, the mechanisms by which OCT is contributing to tissue regeneration are not yet completely clear. In this study, we have used a superficial wound model by tape stripping of ex vivo human skin. Protein profiles of wounded skin biopsies treated with OCT-containing hydrogel and the released secretome were analyzed using liquid chromatography-mass spectrometry (LC-MS) and enzyme-linked immunosorbent assay (ELISA), respectively. Proteomics analysis of OCT-treated skin wounds revealed significant lower levels of key players in tissue remodeling as well as reepithelization after wounding such as pro-inflammatory cytokines (IL-8, IL-6) and matrix-metalloproteinases (MMP1, MMP2, MMP3, MMP9) when compared to controls. In addition, enzymatic activity of several released MMPs into culture supernatants was significantly lower in OCT-treated samples. Our data give insights on the mode of action based on which OCT positively influences wound healing and identified anti-inflammatory and protease-inhibitory activities of OCT.

Atmospheric transport is a major pathway of microplastics to remote regions

Abstract: In recent years, marine, freshwater and terrestrial pollution with microplastics has been discussed extensively, whereas atmospheric microplastic transport has been largely overlooked. Here, we present global simulations of atmospheric transport of microplastic particles produced by road traffic (TWPs – tire wear particles and BWPs – brake wear particles), a major source that can be quantified relatively well. We find a high transport efficiencies of these particles to remote regions. About 34% of the emitted coarse TWPs and 30% of the emitted coarse BWPs (100 kt yr−1 and 40 kt yr−1 respectively) were deposited in the World Ocean. These amounts are of similar magnitude as the total estimated direct and riverine transport of TWPs and fibres to the ocean (64 kt yr−1). We suggest that the Arctic may be a particularly sensitive receptor region, where the light-absorbing properties of TWPs and BWPs may also cause accelerated warming and melting of the cryosphere. Plastic pollution is a critical concern across diverse ecosystems, yet most research has focused on terrestrial and aquatic transport, neglecting other mechanisms. Here the authors show that atmospheric transport is a major pathway for road plastic pollution over remote regions.

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing.

Abstract: Cryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on global B-factor correction, suffer from limitations. For instance, they ignore the heterogeneity in the map local quality that reconstructions tend to exhibit. Aiming to overcome these problems, we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental maps and maps sharpened using their respective atomic models, DeepEMhancer has learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer was evaluated on a testing set of 20 different experimental maps, showing its ability to reduce noise levels and obtain more detailed versions of the experimental maps. Additionally, we illustrated the benefits of DeepEMhancer on the structure of the SARS-CoV-2 RNA polymerase.

Noisy intermediate-scale quantum algorithms

Abstract: Noisy quantum computers can in principle perform reliable quantum computations, but truly scalable systems require noise levels lower than are presently achieved. Still, moderate-complexity computations can be performed. This review discusses what is possible in this ``noisy intermediate scale'' quantum (NISQ) era. Topic areas include the simulation of many-body physics and chemistry, combinatorial optimization, and machine learning. It is evident that the NISQ era has produced new paradigms for programming that will be built upon as quantum computers are further perfected.

metaFlye: scalable long-read metagenome assembly using repeat graphs

Abstract: Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.

Recent advances on the removal of dyes from wastewater using various adsorbents: A critical review

Abstract: The rapid increase in toxic dye wastewater generated from various industries remains a severe public health issue and prime environmental protection concern, posing a major challenge to existing conventional water treatment systems. Consequently, various physicochemical and biological treatment processes have been studied, which exhibit varying removal abilities depending on their experimental constraints. Among them, adsorption is considered to be the most efficient due to its high removal efficiency, easy operation, cost-effectiveness, and recyclability of the adsorbents. Considering this, the present review article focused on presenting a comprehensive summary of the various types of adsorbents such as commercial activated carbon, metal oxide-based, carbon-based, metal–organic framework, and polymer-based adsorbents used in dye remediation of contaminated water. The effects of several critical factors such as initial dye concentration, solution pH, temperature, and adsorbent dose on the dye adsorption performance are also described. In addition, the adsorption mechanisms responsible for dye removal are explained based on electrostatic attraction, ion exchange, surface complexation, and π–π interactions. Finally, critiques, future perspectives, and a summary of the present article are given. Various adsorbents such as carbon-based materials, metal oxides, bio-adsorbents, and polymer-based materials, have been shown to be efficient for the removal of dye pollutants from wastewater. Thus, it is anticipated that dye removal by adsorption can provide a feasible solution for the treatment of dye-laden water.