Biology subjects

Groot, J.

Publications and source records attributed to Groot, J..

3 recordsLinked to original sources

bioRxiv2021

Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population

BackgroundOlder adults are more susceptible to respiratory pathogens, several of which have been associated with an altered respiratory microbiota. Influenza-like illness (ILI), a disease caused by respiratory pathogens including but not exclusively by influenza virus, is a major health concern in this population. However, there is little information on changes in the nasopharyngeal (NP) microbiota of older adults associated with respiratory infections identified by/ reported as ILI, as well as its dynamics during recovery. Here, we compared the NP microbiota in older adults who presented with ILI (n= 240) to the NP microbiota in older adults not reporting an ILI event (n= 157) during the 2014-2015 influenza season. To investigate the dynamics of the microbiota from the acute phase to the recovery phase of the infection, participants reporting an ILI event were sampled at onset of infection (<72 hours), at 14 days and at 7-9 weeks after infection (recovery sample). ResultsCross-sectional analysis of the microbiota at the different time-points showed no differences in alpha diversity between the groups. A small but significant effect of the ILI was observed on the microbiota community and structure when compared to controls and recovery samples. Furthermore, the NP microbiota exhibited inter-individual differences in dynamics from onset of ILI to recovery. Corynebacterium, one of the keystone species in the upper respiratory tract, was negatively associated with ILI and its abundance increased after recovery. Potential pathobionts such as Haemophilus, Porphyromonas and Gemella had higher abundances during acute-ILI. Stability and changes in the NP microbial community showed individual dynamics. Key core genera, Corynebacterium, Moraxella and Dolosigranulum exhibited higher inter-individual variability in acute-ILI, but showed comparable variability to controls after recovery. Participants in the ILI group with higher core microbiota abundances at the acute phase showed higher microbiota stability after recovery. ConclusionsOur findings demonstrate that acute-ILI is associated with small but significant alterations in the phylogenetic structure of the NP microbiota in older adults. The observed variation in the core microbiota suggests potential imbalances in the ecosystem, which could play a role in the recovery of the NP microbiota after an ILI event.

microbiology↗

bioRxiv2020

3 versus 7 Tesla Magnetic Resonance Imaging for parcellations of subcortical brain structures

7 Tesla (7T) magnetic resonance imaging holds great promise for improved visualization of the human brain for clinical purposes. To assess whether 7T is superior regarding localization procedures of small brain structures, we compared manual parcellations of the red nucleus, subthalamic nucleus, substantia nigra, globus pallidus interna and externa, created on a commonly used clinical anisotropic clinical 3T with an optimized isotropic (o)3T and standard 7T scan. While the clinical 3T MRI scan did not allow delineation of an anatomical plausible structure due to its limited spatial resolution, optimized 3T and 7T parcellations could be directly compared. We found that 7T outperformed the o3T MRI as reflected by higher Dice scores, which were used as a measurement of interrater agreement for manual parcellations on quantitative susceptibility maps. This increase in agreement was associated with higher contrast to noise ratios for smaller structures, but not for the larger globus pallidus segments. Additionally, control-analyses were performed to account for potential biases in manual parcellations by assessing semi-automatic parcellations. These results did not confirm increased Dice scores for 7T, although they revealed a higher consistency for structure volumes for 7T compared to optimized 3T, potentially indicative of more agreement with increased field strength. Together these results indicate the importance of the use of isotropic voxels with both 3T and 7T, and the potential for clinical applications.

neuroscience↗

bioRxiv2020

CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines

Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. High-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multilayer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to allow other omics data input and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research. The open-source tool is freely available at http://www.chomics.org.

bioinformatics↗