Biology subjects

Kovacs, J.

Publications and source records attributed to Kovacs, J..

5 recordsLinked to original sources

bioRxiv2025

Comparison of Pairwise Samples of Endotracheal Aspirate and Bronchoalveolar Lavage for Microbial Analysis in Critically ill Patients

IntroductionBronchoalveolar lavage (BAL) is considered as gold-standard for the characterization of the lung microbiome. The aim of this study was to elucidate the applicability of less-invasive sampling by endotracheal aspirate (ETA) compared with BAL for the analysis of respiratory microorganisms in critically ill patients who required mechanical ventilation. MethodsPairwise samples of ETA and BAL obtained from mechanically ventilated patients at our intensive care units were collected anonymously for testing the accuracy of ETA compared to BAL. Bacterial community structure was assessed by a metabarcoding approach based on 16S rRNA gene sequencing in ETA and BAL samples. ResultsIn total, 13 samples of each, BAL and ETA, were collected from 13 critically ill patients. No differences between BAL and ETA were found for alpha diversity based on species richness (p=0.77), Shannon diversity (p = 0.41), Simpson index (p = 0.85) and evenness (p = 0.98). Overall, BAL and ETA samples demonstrated strong taxonomic concordance at the levels of bacterial phyla and genera but differed distinctly at the amplicon sequence variants (ASV) level. ConclusionIn an unselected cohort of mechanically ventilated patients, BAL and ETA samples exhibited profound resemblance at higher taxonomic ranks, with increasing divergence observed at finer taxonomic resolutions. Our findings may facilitate guidance towards the reliability of non-invasive ETA as a valuable approach for clinical studies investigating the lung microbiome.

microbiology↗

bioRxiv2024

CD40 Expression by B cells is Required for Optimal Immunity to Murine Pneumocystis Infection

CD40-CD40L interactions are critical for controlling Pneumocystis infection. However, which CD40-expressing cell populations are important for this interaction have not been well-defined. We used a cohousing mouse model of Pneumocystis infection, combined with flow cytometry and qPCR, to examine the ability of different populations of cells from C57BL/6 mice to reconstitute immunity in CD40 knockout (KO) mice. Unfractionated splenocytes, as well as purified B cells, were able to control Pneumocystis infection, while B cell depleted splenocytes and unstimulated bone-marrow derived dendritic cells (BMDCs) were unable to control infection in CD40 KO mice. Pneumocystis antigen-pulsed BMDCs showed early, but limited, control of infection. Consistent with recent studies that have suggested a role for antigen presentation by B cells, using cells from immunized animals, B cells were able to present Pneumocystis antigens to induce proliferation of T cells. Thus, CD40 expression by B cells appears necessary for robust immunity to Pneumocystis.

microbiology↗

bioRxiv2022

Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification

Plants growing in proximity to other plants are exposed to a variety of metabolites that these neighbors release into the environment. Some species produce allelochemicals to inhibit growth of neighboring plants, which in turn have evolved ways to detoxify these compounds. In order to understand how the allelochemical-receiving target plants respond to chemically diverse compounds, we performed whole-genome transcriptome analysis of Arabidopsis thaliana exposed to either the benzoxazinoid derivative 2-amino-3H-phenoxazin-3-one (APO) or momilactone B. These two allelochemicals belong to two very different compound classes, benzoxazinoids and diterpenes, respectively, produced by different cereal crop species. Despite their distinct chemical nature, we observed similar molecular responses of A. thaliana to these allelochemicals. In particular, many of the same or closely related genes belonging to the three-phase detoxification pathway were upregulated in both treatments. Further, we observed an overlap between genes upregulated by allelochemicals and those involved in herbicide detoxification. Our findings highlight the overlap in the transcriptional response of a target plant to natural and synthetic phytotoxic compounds and illustrate how herbicide resistance could arise via pathways involved in plant-plant interaction.

plant biology↗

bioRxiv2019

Correction of missing-wedge artifacts in filamentous tomograms by template-based constrained deconvolution

Cryo-electron tomography maps often exhibit considerable noise and anisotropic resolution, due to the low-dose requirements and the missing wedge in Fourier space. These spurious features are visually unappealing and, more importantly, prevent an automated segmentation of geometric shapes, requiring a highly subjective, labor-intensive manual tracing. We developed a novel computational strategy for objectively denoising and correcting missing-wedge artifacts in the special but important case of repetitive basic shapes, such as filamentous structures. In this approach, we use the template and a non-negative "location map" to constrain the deconvolution scheme, allowing us to recover, to a considerable degree, the information lost in the missing wedge. We applied our method to data of actin-filament bundles of inner-ear stereocilia, which are critical in hearing transduction processes, and found a good overlap with the experimental map and with manual tracing. In addition, we demonstrate that our method can also be used for membrane detection.

biophysics↗

bioRxiv2019

A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1

Electron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long distances, there were gaps of significant size that were stochastically distributed throughout the actin core. Actin crosslinkers were distributed through the stereocilium, but did not occupy all possible binding sites. At stereocilia tips, protein density extended beyond actin filaments, especially on the side of the tip where a tip link should anchor. Along the shaft, repeating density was observed that corresponds to actin-to-membrane connectors. In the taper region, most actin filaments terminated near the plasma membrane. The remaining filaments twisted together to make a tighter bundle than was present in the shaft region; the spacing between them decreased from 13 nm to 9 nm. Our models illustrate detailed features of distinct structural domains that are present within the stereocilium.

neuroscience↗