Biology subjects

Neubauer, M.

Publications and source records attributed to Neubauer, M..

6 recordsLinked to original sources

bioRxiv2026

Viscoelastic recovery time of chondrocytes from monolayer and alginate cultures

This study uses a previously reported 3D-printed variable-height flow cell to investigate the viscoelastic properties of chondrocytes from 2D monolayer and 3D alginate cultures. It was hypothesized that chondrocytes could be distinguished by phenotype associated with their culture environment using viscoelastic recovery time, owing to variation in the pericellular matrix (PCM) produced by chondrocytes from different culture methods. The PCM surrounding the chondrocytes was imaged with confocal microscopy during applied deformation and subsequent recovery. The projected cell area was fitted with a Burgers mechanical model to extract the viscoelastic recovery time. No difference between bovine and primary OA cells from monolayer cultures was observed. However, a statistically significant difference in recovery time was observed between cells from monolayer and alginate cultures in both the bovine (31 s vs. 13 s) and primary OA (34 s vs. 13 s) groups. This work shows that viscoelastic recovery time is influenced by the culture method used for chondrocytes and further demonstrates the role of the PCM as a mechanical protector of chondrocytes.

cell biology↗

bioRxiv2025

EBSn, a robust synthetic reporter for monitoring ethylene responses in plants

Ethylene is a gaseous plant hormone that controls a wide array of physiologically relevant processes, including plant responses to biotic and abiotic stress, and induces ripening in climacteric fruits. To monitor ethylene in plants, analytical methods, phenotypic assays, gene expression analysis, and transcriptional or translational reporters are typically employed. In the model plant Arabidopsis, two ethylene-sensitive synthetic transcriptional reporters have been described, 5xEBS:GUS and 10x2EBS-S10:GUS. These reporters harbor a different type, arrangement, and number of homotypic cis-elements in their promoters and thus may recruit the ethylene master regulator EIN3 in the context of alternative transcriptional complexes. Accordingly, the patterns of GUS activity in these transgenic lines differ and neither of them encompasses all plant tissues even in the presence of saturating levels of exogenous ethylene. Herein, we set out to develop and test a more sensitive version of the ethylene-inducible promoter that we refer to as EBSnew (abbreviated as EBSn). EBSn leverages a tandem of ten non-identical, natural copies of a novel, dual, everted, 11bp-long EIN3-binding site, 2EBS(-1). We show that in Arabidopsis, EBSn outperforms its predecessors in terms of its ethylene sensitivity, having the capacity to monitor endogenous levels of ethylene and displaying more ubiquitous expression in response to the exogenous hormone. We demonstrate that the EBSn promoter is also functional in tomato, opening new avenues to manipulating ethylene-regulated processes, such as ripening and senescence, in crops.

plant biology↗

bioRxiv2024

Development of modular geminivirus-based vectors for high cargo expression and gene targeting in plants

Viral vectors can be useful tools for expressing recombinant proteins as well as delivering gene-editing machinery. Despite their utility, the development and subsequent optimization of these tools is often a difficult and tedious process. Thus, although considerable work has been done to create useful viral vectors for gene editing and protein expression, there is a lack of understanding of how best to design these vectors for specific applications. For instance, it is often unclear whether the inclusion of heterologous promoter sequences or different viral components will improve cargo expression or replicon accumulation. To address some of these hurdles, we designed a GoldenBraid (GB)-compatible viral vector system based on the geminivirus - Beet curly top virus (BCTV). This system allows for simple, modular cloning of a variety of reporter constructs. Making use of this modular cloning strategy, we compared a variety of alternative viral vector architectures. Interestingly, native BCTV promoters outperformed the constitutive 35S promoter, while the removal of the BCTV virion-sense genes promoted reporter expression. Intriguingly, these modifications had no effect on total replicon accumulation. These results show the utility of the new modular BCTV-based viral vectors for protein expression and gene targeting applications, as well as uncover design principles that may inform future geminivirus-based viral vector architectures. We anticipate that the availability of this new modular system will spark the broad adoption of replicon-based strategies in protein expression and gene editing experiments in plants.

synthetic biology↗

bioRxiv2023

Assembly of sequences of Northern China alligatorweed identifies processes and gene ontologies associated with invasiveness and provides genomic resources for population and gene regulation studies

Biological invasions remain a major global challenge. Alligatorweed (Alternanthera philoxeroides (Mart.) Griseb.), native to South America, has had profound negative effects on ecosystem function and economy in Australia, North America, and Asia. It is an invasive and primarily aquatic plant that, despite a documented lack of genetic diversity, is unusually adaptive - thriving in both aquatic and terrestrial environments. However, genetic resources for studying this invasive plant are limited. Here, we have assembled the transcriptome of alligatorweed using all publicly available cDNA sequences. The resulting assembly produced over 500K contigs with an average length of [~]700 bases and an N50 of >1000 bases and contains over 100K probable gene-coding sequences. Although this assembly is slightly smaller than the previously published assembly developed from just cold-treated shoot tips, the new assembly is slightly more complete with over 95% of the conserved plant genes being represented as full length transcripts, and only 2.3% of these conserved genes being unrepresented compared to 2.7% missing in the earlier assembly. Resources from the PANTHER database were used to annotate all transcripts containing long open reading frames. Comparisons to several plant species identified gene ontologies that were over- and under-represented in the alligatorweed transcriptome including cellular transport and cytoskeletal processes and cell signaling, which could explain the high growth rate and phenotypic plasticity that make alligatorweed particularly invasive. We also sequenced and assembled a genomic database for alligatorweed using only short read technologies. This assembly produced over ten million contigs with an average length of only 300 bases and an N50 of 451 bases. However, 88% of the transcripts were represented among the genomic contigs, indicating that these contigs could serve as a source for regulatory elements for genes previously shown to be differentially expressed under various conditions. Kmer analysis indicated that 22% of the alligatorweed genome was comprised of repetitive elements. A similarity search against the plant repetitive element database indicated that long terminal repeat containing elements including copia- and gypsy-like elements made up the bulk of the transposons present in the alligatorweed genome. Additionally, we assembled and annotated a full-length chloroplast and a partial mitochondrial genome. Combined, these resources provide a source of gene sequences that should be useful for more complete genomic assemblies and for investigating gene structure and function in this particularly adaptable and invasive species. The results will provide an excellent starting point for many different investigations into the biology and ecology of alligatorweed, strengthen our understanding of the invasiveness, biology and ecology of invasive plants, and will help develop a reasonable management strategy to reduce risk and costs of the impacts.

ecology↗

bioRxiv2020

The Arabidopsis N-terminal Acetyltransferase NAA50 Regulates Plant Growth and Defense

Stress signaling in plants is carefully regulated to ensure proper development and reproductive fitness. Overactive defense signaling can result in dwarfism as well as developmental defects. In addition to requiring a significant amount of energy, plant stress responses place a burden upon the cellular machinery, which can result in the accumulation of misfolded proteins and endoplasmic reticulum (ER) stress. Negative regulators of stress signaling, such as EDR1, ensure that stress responses are properly suspended when they are not needed. Here, we describe the role of an uncharacterized N-terminal acetyltransferase, NAA50, in the regulation of plant development and stress responses. Our results demonstrate that NAA50, an interactor of EDR1, plays an important role in regulating the tradeoff between plant growth and defense. Plants lacking NAA50 display severe developmental defects as well as induced stress responses. Reduction of NAA50 expression results in arrested stem and root growth and senescence. Furthermore, our results demonstrate that EDR1 and NAA50 are required for suppression of ER stress signaling. This work establishes that NAA50 is essential for plant development and the suppression of stress responses, likely through the regulation of ER stress. These experiments demonstrate a role for N-terminal acetylation in the suppression of ER stress, as well as the tradeoff between stress responses and development. One Sentence SummaryKnockout in Arabidopsis of the broadly conserved N-terminal acetyl transferase NAA50 induces ER stress, leading to severe dwarfism and induction of defense responses.

plant biology↗

bioRxiv2019

Arabidopsis ENHANCED DISEASE RESISTANCE1 Protein Kinase Regulates the Association of ENHANCED DISEASE SUSCEPTIBILITY1 and PHYTOALEXIN DEFICIENT4 to Inhibit Cell Death

ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) are sequence-related lipase-like proteins that function as a complex to regulate defense responses in Arabidopsis by both salicylic acid-dependent and independent pathways. Here we describe a gain-of-function mutation in PAD4 (S135F) that enhances resistance and cell death in response to infection by the powdery mildew pathogen Golovinomyces cichoracearum. The mutant PAD4 protein accumulates to wild-type levels in Arabidopsis cells, thus these phenotypes are unlikely to be due to PAD4 over accumulation. The phenotypes are similar to loss of function mutations in the protein kinase Enhanced Disease Resistance1 (EDR1), and previous work has shown that loss of PAD4 or EDS1 suppresses edr1-mediated phenotypes, placing these proteins downstream of EDR1. Here we show that EDR1 directly associates with EDS1 and PAD4 and inhibits their interaction in yeast and plant cells. We propose a model whereby EDR1 negatively regulates defense responses by interfering with the heteromeric association of EDS1 and PAD4. Our data indicate that the S135F mutation likely alters an EDS1-independent function of PAD4, potentially shedding light on a yet unknown PAD4 signaling function.

plant biology↗