Biology subjects

Vu, L. D.

Publications and source records attributed to Vu, L. D..

6 recordsLinked to original sources

bioRxiv2026

MurineCyto-Det: A High-Resolution Murine BALF Cytology Dataset for Leukocyte Segmentation and Detection

Automated analysis of murine bronchoalveolar lavage fluid (BALF) cytology is important for preclinical respiratory research, yet progress has been limited by the lack of publicly available, well-annotated mouse BALF image datasets. We present MurineCyto-Det, a high-resolution murine BALF cytology dataset comprising 333 image tiles of size 1024x1024 pixels, annotated across five cytological categories with both pixel-level segmentation masks and one-to-one matched bounding boxes. The dataset contains 14,551 annotated cell instances and supports two complementary analysis tasks: morphology-oriented cell segmentation and object-level cell detection. To establish reproducible benchmark baselines, we evaluated representative segmentation and detection models. The results demonstrate the practical utility of MurineCyto-Det while highlighting realistic challenges arising from class imbalance, small object size, irregular cell morphology, and ambiguous debris-like structures. MurineCyto-Det provides a standardized resource for developing, evaluating, and comparing automated methods for murine BALF cytology analysis. The dataset is publicly available at https://doi.org/10.5281/zenodo.17608677.

bioinformatics↗

bioRxiv2026

Fiber Formulation-Dependent Modulation of Gut Microbial Metabolism in Parkinsons Disease

Parkinsons disease (PD) is associated with altered gut-brain signaling, including microbial dysbiosis, intestinal inflammation, and reduced short-chain fatty acid (SCFA) production. Because dietary fibers are selectively fermented by intestinal microbes to generate SCFAs, fiber formulations tailored to the altered intestinal environment in PD offer a strategy to modulate microbial dysfunction. Here, we used the ex vivo Systemic Intestinal Fermentation Research (SIFR(R)) technology platform, which enables assessment of gut microbiome modulation and host-relevant readouts with demonstrated translational relevance, to assess how fiber substrates influence microbial composition and metabolism of fecal microbiota from individuals with PD (n = 6). Fecal samples were incubated for 24 h with single-fiber, multi-fiber, and food-based formulations. Fermentation outputs, including pH, gas, and SCFAs, were quantified, and select formulations were further characterized by profiling microbial community structure and metabolite output. Relative to a parallel untreated control and osmotic laxative comparator, multi-fiber formulations increased SCFA production ([~]2-fold, p = 0.001). These effects were accompanied by increased microbial biomass ([~]1.5-fold, p = 0.0007), enrichment of fiber-responsive taxa, and coordinated shifts in metabolites associated with gut-brain signaling. Collectively, these findings show that fiber blend complexity and formulation context shape microbial metabolic engagement, supporting formulation-dependent modulation of gut-derived metabolites linked to gut-brain signaling in PD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/718214v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@f84f37org.highwire.dtl.DTLVardef@18ad9borg.highwire.dtl.DTLVardef@2dd28eorg.highwire.dtl.DTLVardef@5a8da7_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Age-specific modulation of gut-brain axis metabolites by galacto-oligosaccharides and nutrient blends in early childhood

ObjectivesGut microbiome-derived metabolites, including short-chain fatty acids (SCFA) and tryptophan derivatives, are key mediators of the gut-brain axis. We examined how early-life nutritional interventions influence these metabolites during critical neurodevelopmental periods. MethodsUsing a standardized ex vivo fermentation system, we assessed the effects of galacto-oligosaccharides (GOS), nutrient blends (vitamins, minerals, amino acids), and their combinations on the gut microbiome of infants (2-4 months, n=6) and young children (2-3 years, n=6). ResultsBaseline microbiome composition differed by age: infants showed low -diversity and high interpersonal variability, while young children exhibited more adult-like profiles. Nutrient blends increased propionate/butyrate ratios and branched-chain fatty acids (BCFA) in young children, alongside B-vitamin and amino acid-derived metabolites, including neuroactive compounds (indole-3-carboxaldehyde, imidazoleacetic acid, pipecolinic acid). Combining nutrient blends with GOS produced synergistic effects on propionate (infants) and 2-hydroxyisocaproic acid (HICA, both groups). GOS-containing treatments strongly promoted Bifidobacteriaceae, driving production of acetate, HICA, N-acetylated amino acids, aromatic lactic acids, and acetylagmatine; in young children, also butyrate and {gamma}-aminobutyric acid (GABA). DiscussionGOS alone and combined with nutrient blends modulated microbiome-derived metabolites linked to the gut-brain axis. Synergistic effects on GABA, acetylagmatine, and HICA suggest roles in neurotransmission, neuroprotection, and immune-brain signaling. Despite shared bifidogenic effects, age-specific differences indicate developmental stage influences intervention outcomes. Further studies should explore neurodevelopmental benefits of these combinations and metabolites.

microbiology↗

bioRxiv2021

Auxin-triggered changes in the Arabidopsis root tip (phospho)proteome reveal novel root growth regulators

Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies revealed that, beyond transcriptional reprogramming, alternative auxin-controlled mechanisms regulate root growth. Here, we explored the impact of different auxin concentrations on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results together with previously published studies suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr31 phosphorylation site for growth regulation in the Arabidopsis root tip. ONE SENTENCE SUMMARYAn auxin-triggered Arabidopsis root tip (phospho)proteome reveals novel root growth regulators

plant biology↗

bioRxiv2018

Temperature-induced changes in wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term increase in temperature on the wheat leaf and spikelet phosphoproteome. The resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature, which will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which likely impacts protein activity.

plant biology↗

bioRxiv2018

The expa1-1 mutant reveals a new biophysical lateral root organogenesis checkpoint

In plants, post-embryonic formation of new organs helps shape the adult organism. This requires the tight regulation of when and where a new organ is formed, and a coordination of the underlying cell divisions. To build a root system, new lateral roots are continuously developing, and this process requires asymmetric cell division in adjacent pericycle cells. Characterization of an expansin a1 (expa1) mutant has revealed a novel checkpoint during lateral root formation. Specifically, a minimal pericycle width was found to be necessary and sufficient to trigger asymmetric pericycle cell divisions during auxin-driven lateral root formation. We conclude that a localized radial expansion of adjacent pericycle cells is required to position the asymmetric cell divisions and generate a core of small daughter cells, which is a prerequisite for lateral root organogenesis.\n\nSIGNFICANCE STATEMENTOrgan formation is an essential process in plants and animals, driven by cell division and cell identity establishment. Root branching, where lateral roots form along the primary root axis, increases the root system and aids capture of water and nutrients. We have discovered that tight control of cell width is necessary to co-ordinate asymmetric cell divisions in cells that give rise to a new lateral root organ. While biomechanical processes have been shown to play a role in plant organogenesis, including lateral root formation, our data give new mechanistic insights into the cell size checkpoint during lateral root initiation.

plant biology↗