Biology subjects

van den Berg, T.

Publications and source records attributed to van den Berg, T..

4 recordsLinked to original sources

bioRxiv2024

A new framework for SubtiWiki, the database for the model organism Bacillus subtilis

Bacillus subtilis is a Gram-positive model bacterium and one of the most-studied and best understood organisms. The complex information resulting from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5) in an integrated and intuitive manner. To enhance the utility of SubtiWiki, we have added novel features such as a viewer to interrogate conserved genomic organization, a widget that shows mutant fitness data for all non-essential genes, and a widget showing protein structures, structure predictions and complex structures. Moreover, we have integrated metabolites as new entities. The new framework also includes a documented API, enabling programmatic access to data for computational tasks. Here we present the recent developments of SubtiWiki and the current state of the data for this organism. Key pointsO_LISubtiWiki is the most popular database for the model bacterium Bacillus subtilis. C_LIO_LITo facilitate the development of new research hypotheses, SubtiWiki has been enhanced by graphical information on conserved genomic organization, mutant fitness data, and a new protein structure viewer. C_LIO_LIMetabolites have been integrated as entities on their own with dedicated pages, interactive information on reactions and metabolite functions as well as their interactions. C_LI

bioinformatics↗

bioRxiv2022

Reverse engineering lateral root stable prebranch site formation; Complementary roles for auxin and auxin signalling

Priming is the process through which periodic elevations in auxin signalling prepattern future sites for lateral root formation, called prebranch sites. Thusfar is has remained a matter of debate to what extent elevations in auxin concentration and/or auxin signalling are critical for priming and prebranch site formation. Recently, we discovered a reflux-and-growth mechanism for priming generating periodic elevations in auxin concentration that subsequently dissipate. Here we reverse engineer a mechanism for prebranch site formation that translates these transient elevations into a persistent increase in auxin signalling, resolving the prior debate into a two-step process of auxin concentration mediated initial signal and auxin signalling capacity mediated memorization. A critical aspect of the prebranch site formation mechanism is its activation in response to time integrated rather than instantaneous auxin signalling. The proposed mechanism is demonstrated to be consistent with prebranch site auxin signalling dynamics, lateral inhibition and symmetry breaking mechanisms and perturbations in auxin homeostasis. Summary statementUsing computational modeling we reveal the likely complementary roles of auxin and auxin signalling in one of the earliest step in the formation of plant lateral roots, prebranch site formation.

developmental biology↗

bioRxiv2020

SIRPalpha on mouse B1 cells restricts lymphoid tissue migration and natural antibody production

The inhibitory immunoreceptor SIRP is expressed on myeloid and neuronal cells and interacts with the broadly expressed CD47. CD47-SIRP interactions form an innate immune checkpoint and its targeting has shown promising results in cancer patients. Here, we report expression of SIRP on B1 lymphocytes, a non-conventional subpopulation of murine B cells responsible for the production of natural antibodies. Mice defective in SIRP signaling (SIRP{Delta}CYT mice) displayed an enhanced CD11b/CD18 integrin-dependent B1 cell migration from the peritoneal cavity to the spleen, local B1 cell accumulation, and enhanced circulating natural antibody levels, which was further amplified upon immunization with T-independent type 2 antigen. As natural antibodies are atheroprotective we investigated the involvement of SIRP signaling in atherosclerosis development. Bone marrow (SIRP{Delta}CYT>LDLR-/-) chimaeric mice developed reduced atherosclerosis accompanied by increased natural antibody production. Collectively, our data identify SIRP as a unique B1 cell inhibitory receptor acting to control B1 cell migration, and imply SIRP as a potential therapeutic target in atherosclerosis.

immunology↗

bioRxiv2018

Lateral root priming synergystically arises from root growth and auxin transport dynamics

The root system is a major determinant of plant fitness. Its capacity to supply the plant with sufficient water and nutrients strongly depends on root system architecture, which arises from the repeated branching off of lateral roots. A critical first step in lateral root formation is priming, which prepatterns sites competent of forming a lateral root. Priming is characterized by temporal oscillations in auxin, auxin signalling and gene expression in the root meristem, which through growth become transformed into a spatially repetitive pattern of competent sites. Previous studies have demonstrated the importance of auxin synthesis, transport and perception for the amplitude of these oscillations and their chances of producing an actual competent site. Additionally, repeated lateral root cap apoptosis was demonstrated to be strongly correlated with repetitive lateral root priming. Intriguingly, no single mutation has been identified that fully abolishes lateral root formation, and thusfar the mechanism underlying oscillations has remained unknown. In this study, we investigated the impact of auxin reflux loop properties combined with root growth dynamics on priming, using a computational approach. To this end we developed a novel multi-scale root model incorporating a realistic root tip architecture and reflux loop properties as well as root growth dynamics. Excitingly, in this model, repetitive auxin elevations automatically emerge. First, we show that root tip architecture and reflux loop properties result in an auxin loading zone at the start of the elongation zone, with preferential auxin loading in narrow vasculature cells. Second, we demonstrate how meristematic root growth dynamics causes regular alternations in the sizes of cells arriving at the elongation zone, which subsequently become amplified during cell expansion. These cell size differences translate into differences in cellular auxin loading potential. Combined, these properties result in temporal and spatial fluctuations in auxin levels in vasculature and pericycle cells. Our model predicts that temporal priming frequency predominantly depends on cell cycle duration, while cell cycle duration together with meristem size control lateral root spacing.

plant biology↗