Biology subjects

Mattson, N.

Publications and source records attributed to Mattson, N..

5 recordsLinked to original sources

bioRxiv2025

Redefining Parkinson's Disease by Dysregulated Genetic Networks in Distinct Cell Types

Parkinsons disease (PD) is classically linked to dopaminergic neuron loss, but emerging evidence suggests broader cellular involvement. Here we show that PD risk variants converge on distinct molecular networks across specific brain cell types, enabling stratification of patients into six subgroups: dopaminergic, oligodendrocyte progenitor cells (O), excitatory (E), dopaminergic/excitatory, dopaminergic/oligodendrocyte and other. While all subgroups exhibit motor symptoms, the E-group individuals also display more severe non-motor symptoms, including dementia, hyposmia, and REM sleep behavior disorder. The O-group individuals exhibit reduced myelin integrity, as demonstrated by diffusion tensor imaging, implicating NRG6 (formerly C1orf56), a previously uncharacterized high-risk PD gene. We show that NRG6 encodes a conserved epidermal growth factor-like domain structurally and functionally analogous to neuregulin-1, which is critical for oligodendrocyte development and myelination. These findings redefine the cellular architecture of PD vulnerability and identify neuregulin-like signaling in oligodendrocytes as a potential contributor to non-motor symptoms.

neuroscience↗

bioRxiv2021

Design considerations for workflow management systems use in production genomics research and the clinic

BackgroundThe changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. ResultsThis work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, "which WfMS should be chosen for a given bioinformatics application regardless of analysis type?". ConclusionsThe choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance.

bioinformatics↗

bioRxiv2021

Effects of Hydrogen Peroxide on Organically Fertilized Hydroponic Lettuce (Lactuca sativa L.)

Hydroponic production typically uses conventional fertilizers and information is lacking on the use of organic hydroponic fertilizers. Development of biofilm is a common problem with organic hydroponics which can reduce dissolved oxygen availability to roots. One potential solution is the use of hydrogen peroxide, H2O2 which can reduce microbial populations and decomposes to form oxygen. However, information is lacking on the impact of hydrogen peroxide on hydroponic crops. The aim of this study was to determine the effects of H2O2 concentrations in deep water culture hydroponics by assessing how it affects plant size and yield in lettuce (Lactuca sativa L.) Rouxai. In this experiment, three different treatments consisting of a control without H2O2, and the application of 37.5 mg/L or 75 mg/L of hydrogen peroxide were added to aerated 4-L reservoirs that contained either organic (4-4-1) or inorganic nutrients (21-5-20), both applied at 150 mg{middle dot}L-1 N. Three replicates for each treatment and each fertilizer were prepared resulting in a total of eighteen mini hydroponic containers each with one head of lettuce. When added to conventional fertilizers, concentrations of 37.5 mg/L and 75 mg/L of H2O2 led to stunted growth or death lettuce plants. However, when 37.5 mg/L of H2O2 was applied to organic fertilizers, the lettuce yield nearly matched that of the conventionally fertilized control, demonstrating that the application of H2O2 has the potential to make organic hydroponic fertilization a more viable method in the future.

plant biology↗

bioRxiv2018

Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum)

Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoe-maker. This study aimed for determining the resistant populations via multiple phenotyping approaches and identifying potential resistance genes to the disease from genome-wide association studies in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in NY and PA) and artificial inoculations (detached leaf and leaf disk assays). There are ten out of the 66 populations showed the most resistant based on a combination of detached leaf, leaf disk, and mean from two locations. The GWAS from five subgroups from the association panel to different disease evaluation combinations yielded 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N accumulatively explaining phenotypic variance of BLUPs of detached leaf percent lesion via image analysis 26.52% at most and BLUPs of leaf disk percent lesion via image analysis 3.28% at least. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes including genes encoding for NBS-LRR, PPR, cell wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporters.

bioinformatics↗

bioRxiv2018

Programmed Variations of Cytokinesis Contribute to Morphogenesis in the C. elegans embryo

While cytokinesis has been intensely studied, how it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariant C. elegans embryo lineage and found several reproducibly altered parameters at different stages. During early divisions, furrow ingression asymmetry and midbody inheritance is consistent, suggesting specific regulation of these events. During morphogenesis, we find several unexpected alterations including migration of midbodies to the apical surface during epithelial polarization in different tissues. Aurora B kinase, which is essential for several aspects of cytokinesis, remains localized to the apical membrane after internalization of other midbody components. Inactivation of Aurora B causes cytokinesis failure, which disrupts polarization and tissue formation. Therefore, cytokinesis shows surprising diversity during development and is required during epithelial polarization to establish cellular architecture during morphogenesis.

cell biology↗