Clathrin-dependent and independent endocytic pathways in tobacco protoplasts revealed by labelling with charged nanogold

Positively charged nanogold was used as a probe to trace the internalization of plasma membrane (PM) domains carrying negatively charged residues at an ultrastructural level. The probe revealed distinct endocytic pathways within tobacco protoplasts and allowed the morphology of the organelles involved in endocytosis to be characterized in great detail. Putative early endosomes with a tubulo-vesicular structure, similar to that observed in animal cells, are described and a new compartment, characterized by interconnected vesicles, was identified as a late endosome using the Arabidopsis anti-syntaxin family Syp-21 antibody. Endocytosis dissection using Brefeldin A (BFA), pulse chase, temperature- and energy-dependent experiments combined with quantitative analysis of nanogold particles in different compartments, suggested that recycling to the PM predominated with respect to degradation. Further experiments using ikarugamycin (IKA), an inhibitor of clathrin-dependent endocytosis, and negatively charged nanogold confirmed that distinct endocytic pathways coexist in tobacco protoplast

Synthesis of zwitterionic-functionalized conjugated nanoparticles for targeted drug delivery applications

Polymeric Nanoparticles (NPs) represent a promising pharmacological tool, since their structure can be modified to obtain: i) encapsulation and controlled release of a wide range of active compounds, ranging from small molecules to siRNA or oligonucleotides; ii) selective cell targeting, thus allowing precise drug delivery to the desired site of action. A powerful strategy to achieve selectivity of uptake in specific cell types is to conjugate the nanoparticles to a ligand specific for receptors expressed by the target cell type. This offers the advantage of a potentially improved drug efficacy with limited side effects and toxicity. Polymeric nanoparticles in a range of 20–100 nm have a high potential for in vivo applications, due to their ability to circulate in the blood for a long period of time. In fact, this size range allows to avoid renal and lymphatic clearance, to prevent opsonization and at the same time improves the internalization by cells. In this work we address the synthesis by reversible addition-fragmentation chain transfer (RAFT) of biodegradable, zwitterionic-based nanoparticles. This Zwitterionic nanoparticles act as super non-fouling surfaces that prevent protein adsorption from complex biological media. The nanoparticles were functionalized with different numbers of selective ligands through click chemistry; different dimensions were synthetized changing the length of the hydrophobic part. In vitro studies were performed to evaluate the uptake of functionalized nanoparticles

Correction to: Metachromatic leukodystrophy with late adult-onset: diagnostic clues and differences from other genetic leukoencephalopathies with dementia

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Effect of lithiation on micro-scale fracture toughness of LixMn2O4 cathode

An optimized nanoindentation pillar splitting technique is used for the fracture toughness measurement of spinel LixMn2O4 cathode material under different states of charge (SoC), along with the high-speed nanoindentation results for nanomechanical property mapping. High-speed nanoindentation enables for a robust and efficient evaluation of elastic modulus and hardness as a function of the SoC on strongly heterogeneous materials. The fracture toughness decreases linearly upon de-lithiation, with an overall reduction of 53% from 0% to 100% SoC. Decrease in fracture toughness is associated with the volume change, increase of defect density and stresses related to diffusion of lithium upon de-lithiation

gene relevance based on multiple evidences in complex networks

Abstract Motivation Multi-omics approaches offer the opportunity to reconstruct a more complete picture of the molecular events associated with human diseases, but pose challenges in data analysis. Network-based methods for the analysis of multi-omics leverage the complex web of macromolecular interactions occurring within cells to extract significant patterns of molecular alterations. Existing network-based approaches typically address specific combinations of omics and are limited in terms of the number of layers that can be jointly analysed. In this study, we investigate the application of network diffusion to quantify gene relevance on the basis of multiple evidences (layers). Results We introduce a gene score (mND) that quantifies the relevance of a gene in a biological process taking into account the network proximity of the gene and its first neighbours to other altered genes. We show that mND has a better performance over existing methods in finding altered genes in network proximity in one or more layers. We also report good performances in recovering known cancer genes. The pipeline described in this article is broadly applicable, because it can handle different types of inputs: in addition to multi-omics datasets, datasets that are stratified in many classes (e.g., cell clusters emerging from single cell analyses) or a combination of the two scenarios. Availability and implementation The R package 'mND' is available at URL: https://www.itb.cnr.it/mnd. Supplementary information Supplementary data are available at Bioinformatics online

Removing duplicate reads using graphics processing units

Background: During library construction polymerase chain reaction is used to enrich the DNA before sequencing. Typically, this process generates duplicate read sequences. Removal of these artifacts is mandatory, as they can affect the correct interpretation of data in several analyses. Ideally, duplicate reads should be characterized by identical nucleotide sequences. However, due to sequencing errors, duplicates may also be nearly-identical. Removing nearly-identical duplicates can result in a notable computational effort. To deal with this challenge, we recently proposed a GPU method aimed at removing identical and nearly-identical duplicates generated with an Illumina platform. The method implements an approach based on prefix-suffix comparison. Read sequences with identical prefix are considered potential duplicates. Then, their suffixes are compared to identify and remove those that are actually duplicated. Although the method can be efficiently used to remove duplicates, there are some limitations that need to be overcome. In particular, it cannot to detect potential duplicates in the event that prefixes are longer than 27 bases, and it does not provide support for paired-end read libraries. Moreover, large clusters of potential duplicates are split into smaller with the aim to guarantees a reasonable computing time. This heuristic may affect the accuracy of the analysis. Results: In this work we propose GPU-DupRemoval, a new implementation of our method able to (i) cluster reads without constraints on the maximum length of the prefixes, (ii) support both single- and paired-end read libraries, and (iii) analyze large clusters of potential duplicates. Conclusions: Due to the massive parallelization obtained by exploiting graphics cards, GPU-DupRemoval removes duplicate reads faster than other cutting-edge solutions, while outperforming most of them in terms of amount of duplicates reads

Attenuation and localization of waves in taut cables with suspended masses

This work analyzes structural waves that propagate freely along taut cables, characterized by a discrete array of scatter elements. The outcomes underline the role played by the periodic distribution of such elements, whose presence alters the response of the system when subjected to propagating waves. Namely, when the domain is perfectly periodic, band gaps are found in the spectrum of the problem. It is also shown that the introduction of a defect of periodicity can lead to the appearance of eigenvalues inside band gaps, corresponding to a motion localized around the defect

A 3D Geological Model as a Base for the Development of a Conceptual Groundwater Scheme in the Area of the Colosseum (Rome, Italy)

Geological models are very useful tools for developing conceptual schemes owing to their capacity to optimize the management of stratigraphic information. This is particularly true in areas where archaeological heritage is exposed to hydrogeological hazards; 3D models can constitute the first step toward the construction of numerical models created to understand processes and plan mitigation actions to improve visitor safety and preserve archaeological heritage. This paper illustrates the results of a 3D hydrostratigraphic model of the site of the Colosseum in the Central Archaeological Area of Rome. In recent years, this area has experienced numerous floods caused by intense meteorological events. A new borehole survey provided the opportunity to update previous maps and cross sections and build a local scale 3D model. The resulting conceptual model was used to identify primary gaps in existing knowledge about the groundwater system and to optimize the planning of a piezometer monitoring network. Further studies can then focus on the development of groundwater numerical models to verify hypotheses regarding inflow-outflow dynamics and facilitate the optimization of water management