Biology subjects

Kontra, L.

Publications and source records attributed to Kontra, L..

4 recordsLinked to original sources

bioRxiv2023

Infection-induced vascular inflammation in COVID-19 links focal microglial dysfunction with neuropathologies through IL-1/IL-6-related systemic inflammatory states

COVID-19 is associated with diverse neurological abnormalities, which predict poor outcome in patients. However, the mechanisms whereby infection-induced inflammation could affect complex neuropathologies in COVID-19 are unclear. We hypothesized that microglia, the resident immune cells of brain, are centrally involved in this process. To study this, we developed an autopsy platform allowing the integration of molecular anatomy-, protein- and mRNA data sets in post-mortem mirror blocks of brain and peripheral organ samples from COVID-19 cases. Nanoscale microscopy, single-cell RNA sequencing and analysis of inflammatory and metabolic signatures revealed distinct mechanisms of microglial dysfunction associated with cerebral SARS-CoV-2 infection. We observed focal loss of microglial P2Y12R at sites of virus-associated vascular inflammation together with dysregulated microglia-vascular-astrocyte interactions, Cx3Cr1-fractalkine axis deficits and mitochondrial failure in severely affected medullary autonomic nuclei and other brain areas. Microglial dysfunction occurs at sites of excessive synapse- and myelin phagocytosis and loss of glutamatergic terminals. While central and systemic viral load is strongly linked in individual patients, the regionally heterogenous microglial reactivity in the brain correlated with the extent of central and systemic inflammation related to IL-1 / IL-6 via virus-sensing pattern recognition receptors (PRRs) and inflammasome activation pathways. Thus, SARS-CoV-2-induced central and systemic inflammation might lead to a primarily glio-vascular failure in the brain, which could be a common contributor to diverse COVID-19-related neuropathologies.

immunology↗

bioRxiv2023

Improving anxiety research: novel approach to reveal trait anxiety through summary measures of multiple states

The reliability and validity of preclinical anxiety testing is essential for translating animal research into clinical use. However, the commonly used anxiety tests lack inter-test correlations and face challenges with repeatability. While translational animal research should be able to capture stable individual anxiety traits, the current approach employs a single type of test at a single time that only measures transient states of animals, heavily influenced by experimental conditions. Here, we propose a validated, optimized test battery capable of reliably capturing trait anxiety in rats and mice of both sexes. Instead of developing novel tests, we combined widely used tests (elevated plus-maze, open field and light-dark test) to provide instantly applicable adjustments for better predictive validity. We repeated these tests three times to capture behaviour across multiple challenges, which we combined to generate summary measures (SuMs). Our approach resolved between-test correlation issues and provided better predictions for subsequent outcomes under anxiogenic conditions or fear conditioning. SuMs were also able to reveal differences in anxiety in an etiological stress model. Finally, we tested our methods efficacy in discovering anxiety-related molecular pathways through RNA sequencing of the medial prefrontal cortex. Using SuMs, we identified four-times more molecular correlates of trait anxiety as compared to transient anxiety states, pointing out novel functional gene clusters. Furthermore, 16% of these molecular correlates of anxiety were replicated in amygdalar samples, as well. In summary, we provide a novel approach to capture trait anxiety in rodents, offering improved predictions for potential therapeutic targets for personalized medicine.

neuroscience↗

bioRxiv2022

Analysis of the abomasal transcriptome of LDA affected cattle

Left displacement of the abomasum (LDA) is a common condition in Holstein population mainly occur around the time of parturition. The entrapped abomasum located between the rumen and the abdominal wall caused by the abomasal hypomotility. The heritability of LDA estimated higher than for other bovine diseases but a number of management and nutritional conditions are also affecting the disease appearance. Genome studies revealed many significant genomic regions associated with LDA, although an RNA sequencing analysis of abomasum is missing from the literature. Within the framework of this research, we tried to patch up this area missing from the literature and to reveal the genetic causes and a complex interaction between the endocrine and neuromuscular pathways behind the symptoms of the disease with the help of transcriptomic analysis.

bioinformatics↗

bioRxiv2019

ChIPSummitDB: A ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them

ChIP-Seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein-protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3,727 human ChIP-Seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-Seq peak summits. ChIPSummitDB enables the analysis of ChIP-Seq data using multiple approaches. The 292 cistromes and corresponding ChIP-Seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-Seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly updated and extended with the newly available human and mouse ChIP-Seq data sets.

bioinformatics↗