Trapalyzer: a computer program for quantitative analyses in fluorescent live-imaging studies of neutrophil extracellular trap formation

Neutrophil extracellular traps (NETs), pathogen-ensnaring structures formed by neutrophils by expelling their DNA into the environment, are believed to play an important role in immunity and autoimmune diseases. In recent years, a growing attention has been put into developing software tools to quantify NETs in fluorescent microscopy images. However, current solutions require large, manually-prepared training data sets, are difficult to use for users without background in computer science, or have limited capabilities. To overcome these problems, we developed Trapalyzer, a computer program for automatic quantification of NETs. Trapalyzer analyzes fluorescent microscopy images of samples double-stained with a cell-permeable and a cell-impermeable dye, such as the popular combination of Hoechst 33342 and SYTOX™ Green. The program is designed with emphasis on software ergonomy and accompanied with step-by-step tutorials to make its use easy and intuitive. The installation and configuration of the software takes less than half an hour for an untrained user. In addition to NETs, Trapalyzer detects, classifies and counts neutrophils at different stages of NET formation, allowing for gaining a greater insight into this process. It is the first tool that makes this possible without large training data sets. At the same time, it attains a precision of classification on par with state-of-the-art machine learning algorithms. As an example application, we show how to use Trapalyzer to study NET release in a neutrophil-bacteria co-culture. Here, after configuration, Trapalyzer processed 121 images and detected and classified 16 000 ROIs in approximately three minutes on a personal computer. The software and usage tutorials are available at https://github.com/Czaki/Trapalyzer

Locus-aware decomposition of gene trees with respect to polytomous species trees

Abstract Background Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values. Results We investigate the locus tree inference problem as a possible alternative that combines the advantages of both approaches. We present several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification. Conclusions Our approach allows for faster comparisons of gene and species trees and improves known algorithms for duplication inference in the presence of polytomies in the species trees. We have implemented our algorithms in a software tool available at https://github.com/mciach/LocusTreeInference

Multifunctional Nanoparticles Based on Iron Oxide and Gold-198 Designed for Magnetic Hyperthermia and Radionuclide Therapy as a Potential Tool for Combined HER2-Positive Cancer Treatment

Iron oxide nanoparticles are commonly used in many medical applications as they can be easily modified, have a high surface-to-volume ratio, and are biocompatible and biodegradable. This study was performed to synthesize nanoparticles designed for multimodal HER2-positive cancer treatment involving radionuclide therapy and magnetic hyperthermia. The magnetic core (Fe3O4) was coated with a gold-198 layer creating so-called core-shell nanoparticles. These were then further modified with a bifunctional PEG linker and monoclonal antibody to achieve the targeted therapy. Monoclonal antibody—trastuzumab was used to target specific breast and nipple HER2-positive cancer cells. The nanoparticles measured by transmission electron microscopy were as small as 9 nm. The bioconjugation of trastuzumab was confirmed by two separate methods: thermogravimetric analysis and iodine-131 labeling. Synthesized nanoparticles showed that they are good heat mediators in an alternating magnetic field and exhibit great specific binding and internalization capabilities towards the SKOV-3 (HER2 positive) cancer cell line. Radioactive nanoparticles also exhibit capabilities regarding spheroid degradation without and with the application of magnetic hyperthermia with a greater impact in the case of the latter. Designed radiobioconjugate shows great promise and has great potential for in vivo studies regarding magnetic hyperthermia and radionuclide combined therapy