Biology subjects

Chu, R.

Publications and source records attributed to Chu, R..

11 recordsLinked to original sources

bioRxiv2026

Phytoplankton Dynamics and Urbanization Gradients Reshape Dissolved Organic Matter and Microbial Networks across a Freshwater Estuary

Freshwater estuaries process contaminants, cycle nutrients, and support biodiversity. However, watershed development degrades water quality, alters organic matter (OM) composition, and reshapes microbial and phytoplankton communities. Understanding how anthropogenic land use shapes estuarine ecosystem function remains a key challenge. We evaluated relationships among benthic and pelagic biogeochemistry, algal, and microbial communities across six sites along an urbanization gradient, combining FTICRMS characterization of water and sediment OM, with 16S and 18S rRNA gene amplicon sequencing of bacterial/archaeal and algal assemblages, alongside measurements of nutrients, ions, turbidity, temperature, phytoplankton biovolume, and land use. Pelagic OM and microbial variation tracked seasonal gradients and transient phytoplankton dynamics modulated by urban inputs, whereas sediments responded directly to urbanization: urban sediments were N-rich with protein, and amino-sugar-like OM, while rural sediments carried aromatic, terrestrial, plant-derived signatures. Both compartments showed non-linear responses, with microbial, algal, and OM abundances shifting abruptly across urbanization thresholds. Strong associations between sediment microbial dissimilarity and phytoplankton biovolume indicate benthic-pelagic coupling, whereby urban nutrients putatively stimulate phytoplankton growth and subsequent OM deposition restructures benthic assemblages. Thus, pelagic communities capture transient urban effects mediated by phytoplankton, whereas benthic communities integrate chronic impacts, highlighting the value of compartment-specific monitoring in estuarine ecosystems.

ecology↗

bioRxiv2026

Multiomics dissection of the CO2-dependent fast growth of Picochlorum celeri

With a sub-3-micrometer cell and a 27-Mbp diploid genome, the small but mighty Picochlorum celeri doubles within three hours and exceeds 30 g m-2 d-1 outdoors with CO2 supplied. In climate-simulating photobioreactors, productivity declined from 39 g m-2 d-1 under 2.25% CO2 to near zero in air and resumed within hours of CO2 restoration with photosystem II photochemistry largely retained. We profiled the transcriptome, proteome, phosphoproteome, ubiquitinome, acetylome, metabolome and lipidome, including the first site-resolved green-algal ubiquitinome. In air, the Rubisco large subunit tripled to 7.6% of protein while its two small-subunit isoforms, 70% identical, exchanged near-reciprocally, a novel CO2-dependent switch that we propose retunes Rubisco to low CO2. Photorespiratory enzymes increased in abundance whereas proteins involved in external nitrogen assimilation decreased, consistent with increased reliance on internal nitrogen recycling as carbon fixation became limiting. Transcript and protein responses were nearly uncoupled, with cytosolic ribosomal proteins declining despite increased transcripts and plastid ribosomal proteins spared. Phosphorylation was extensively remodeled, as were the lysine modifications ubiquitination, acetylation and CO2-dependent carbamylation, where a CO2-competition assay identified 86 bicarbonate-protected lysines, including RbcL K252. CO2 limitation therefore imposes a reversible growth arrest that reduces cytosolic translational investment while preserving photosynthetic capacity for rapid recovery.

plant biology↗

bioRxiv2026

Microbial communities in tropical soils are highly resilient to fluctuating redox conditions

Many wet tropical soils alternate frequently between fully oxygenated and anaerobic conditions, constraining the terminal electron acceptors available for microbial metabolism, and the mineral-organic matter interactions that regulate many aspects of soil carbon (C) cycling. However, it is still unclear how fluctuating soil redox conditions influence the microbial community composition and if microbially mediated C flux is sensitive to extended oxic or anoxic periods like those observed during drought and flooding respectively. Using a 44-day redox manipulation of tropical soils that experience daily-to-weekly oxygen (O2) fluctuations in the field, we measured how different redox regimes shape soil biogeochemistry and microbial and metabolite composition. Replicate microcosms were exposed to four treatments (static oxic, static anoxic, high frequency fluctuation (4 day oxic/4 day anoxic), or low frequency fluctuation (8 day oxic/4 day anoxic)) regimes, and harvested for microbial, metabolite, carbon dioxide (CO2) flux, and biogeochemical assays at multiple timepoints. Oxic and fluctuating redox conditions caused the microbial community to shift in a manner correlated with soil iron content and directly orthogonal to communities from anoxic soils. The identity of both iron oxidizers and iron reducers was distinct in static anoxic soils but was resilient to redox fluctuation and prolonged O2 exposure. The total amount of CO2 respired was similar across all four redox regimes. Water-extractable organic matter composition was distinct across redox treatments, with anoxic soils accumulating higher levels of carbohydrate-, proteins-, amino sugar-, and lignin-like compounds consistent with reduced enzymatic decomposition and release of mineral-associated organic matter via iron reduction, while oxic soils showed elevated lipid- and unsaturated hydrocarbon-like compounds indicative of greater microbial biomass turnover. The microbial community adapted to dynamic redox conditions and the results substantiate cycling of distinct C compounds under varying redox conditions resulting from varying bioavailability (driven by mineral-OM dynamics) and/or shifted microbial metabolism.

microbiology↗

bioRxiv2026

COUNTERING AGE-ASSOCIATED ALTERATIONS IN OLIGODENDROCYTE-DERIVED EXTRACELLULAR MATRIX REJUVENATES COGNITION

Efforts to rejuvenate age-related cognitive decline have predominantly targeted neurons, often overlooking non-neuronal cell types in the aging brain. Here, we show that countering alterations in oligodendrocyte-derived extracellular matrix (ECM) in the aging hippocampus restores cognition. We identify broad age-associated transcriptional and proteomic changes in oligodendrocytes, including dysregulation of the matrisome, with marked upregulation of ECM components and associated regulators with age. Among these, we detect an increase in Hyaluronan and proteoglycan link protein 2 (HAPLN2), an oligodendrocyte-derived core matrisome protein that locates specifically at the nodes of Ranvier, in the hippocampus of aged mice and older humans. Hapln2 overexpression in oligodendrocytes of young mice recapitulated age-related memory impairments. Conversely, abrogating the age-related increase in Hapln2 induced synaptic plasticity-related hippocampal transcriptional signatures and improved memory in aged mice. Together, these data define oligodendrocyte-derived ECM remodeling as a hallmark of brain aging that can be targeted to rescue cognitive decline.

neuroscience↗

bioRxiv2025

ODC1 restricts meningeal B cell age-associated-like phenotype and function in multiple sclerosis: a human and experimental study

Meningeal inflammation, as a clinical feature of multiple sclerosis (MS), is associated with worse clinical disease outcomes. In both relapsing and secondary progressive MS and the experimental autoimmune encephalomyelitis (EAE) MS model, the meninges have been found to contain ectopic lymphoid follicles enriched with B cells. The metabolic requirement of meningeal B cell function in MS or EAE is not well elucidated. Using 7-Tesla MRI brain scans of MS patients and leptomeningeal enhancement (LME) as a marker, we found a correlation between meningeal inflammation and metabolites of the arginine/polyamine pathway, a finding recapitulated in the EAE model. Ornithine Decarboxylase (ODC1), the rate limiting enzyme for polyamine biosynthesis, as well as polyamine metabolism was diminished in the dura meningeal B cells from mice with MOG35-55 induced EAE mice as compared to naive controls. Pharmacological inhibition of ODC1 restricted meningeal T cells but promoted meningeal B cell proliferation. B cell-specific deletion of ODC1 resulted in expansion of B cells with age-associated B cell-like phenotype (CD11c+CD21/35-CD23-IgD-) and exacerbated disease in the MOG1-125 EAE model. Together, these findings demonstrate a divergent role of polyamines in regulating B and T cell responses in the meninges during autoimmunity. Significance StatementThis study identified the polyamine pathway to be associated with meningeal inflammation in multiple sclerosis, a clinical phenotype associated with worse disease outcomes and without targeted therapy. Using a mouse experimental model, we found that ODC1, the rate limiting enzyme of the polyamine biosynthesis pathway, was suppressed in meningeal B cells, restricted the development of age-associated B cells in the meninges and limited disease severity. This study elucidated a metabolic pathway regulating meningeal B cell function, informing its therapeutic applications in autoimmune diseases.

immunology↗

bioRxiv2024

Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca

Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, as its emergence may depend on simple regulatory changes to deeply conserved metabolic pathways. Modern CAM research relies heavily on interpretation of transcriptomic data, though regulation occurs at multiple levels following transcription. Additionally, while most research to date has focused on a handful of genes and metabolites in the core CAM pathway, the co-option of conserved regulatory and functional genes is bound to have wide ranging effects on other aspects of primary metabolism. In this study, we integrate transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C3 species, Y. filamentosa. We observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. We also find evidence of shifts in gene expression and metabolite accumulation outside of the central CAM pathway suggesting that the shift to CAM has cascading effects across primary metabolism, especially nitrogen metabolism. Our findings provide insights into the metabolic shifts associated with CAM evolution and highlight the complexity of its regulation at multiple biological levels.

evolutionary biology↗

bioRxiv2023

Robust collection and processing for label-free single voxel proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures important tissue heterogeneity, which make it impossible for proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single tissue voxel and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single tissue voxel dissected by LCM into the PCR tube cap and MS-compatible surfactant-assisted one-pot voxel processing in the collection cap. This convenient method allows reproducible label-free quantification of [~]900 and [~]4,600 proteins for single voxel from fresh frozen human spleen tissue at 20 m x 20 m x 10 m (close to single cells) and 200 m x 200 m x 10 m ([~]100 cells), respectively. 100s-1000s of protein signatures with differential expression levels were identified to be spatially resolved between spleen red and white pulp regions depending on the voxel size. Region-specific signaling pathways were enriched from single voxel proteomics data. Antibody-based CODEX imaging was used to validate label-free MS quantitation for single voxel analysis. The wcSOP-MS method paves the way for routine robust single voxel proteomics and spatial proteomics.

molecular biology↗

bioRxiv2022

Inter-scanner brain MRI volumetric biases persist even in a harmonized multi-subject study of multiple sclerosis

Background/PurposeMulticenter study designs involving a variety of MRI scanners have become increasingly common. However, these present the issue of biases in image-based measures due to scanner or site differences. To assess these biases, we imaged 11 volunteers with multiple sclerosis (MS) with scan and rescan data at 4 sites. Materials and MethodsImages were acquired on Siemens or Philips scanners at 3-tesla. Automated white matter lesion detection and whole brain, gray and white matter, and thalamic volumetry were performed, as well as expert manual delineations of T1 and T2 (FLAIR) lesions. Random effect and permutation-based nonparametric modeling was performed to assess differences in estimated volumes within and across sites. ResultsRandom effect modeling demonstrated model assumption violations for most comparisons of interest. Non-parametric modeling indicated that site explained > 50% of the variation for most estimated volumes. This expanded to > 75% when data from both Siemens and Philips scanners were included. Permutation tests revealed significant differences between average inter- and intra-scanner differences in most estimated brain volumes (P < .05). The automatic activation of spine coil elements during some acquisitions resulted in a shading artifact in these images. Permutation tests revealed significant differences between thalamic volume measurements from acquisitions with and without this artifact. ConclusionDifferences in brain volumetry persisted across MR scanners despite protocol harmonization. These differences were not well explained by variance component modeling; however, statistical innovations for mitigating inter-scanner differences show promise in reducing biases in multi-center studies of MS.

neuroscience↗

bioRxiv2020

Iron Chelator-Mediated Anoxic Biotransformation of Lignin by Novel sp., Tolumonas lignolytica BRL6-1

Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of delignification, with a growing interest in the use of microbes. Here we investigate the physiology and lignin biotransformation mechanisms of the novel facultative anaerobic bacterium, Tolumonas lignolytica BRL6-1, under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 had a higher biomass and shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2 fold-change of 2 or greater were related to Fe(II) transport in early exponential phase. Ferrozine assays of the supernatant (<10 kDa fraction) confirmed that Fe(III) was bound to lignin and reduced to Fe(II) only in the presence of BRL6-1, suggesting redox activity by the cells. LC-MS/MS analysis of the secretome showed an extra band at 20 kDa in lignin-amended conditions. Protein sequencing of this band identified a protein of unknown function with homology to enzymes in the radical SAM superfamily. Expression of this protein in lignin-amended conditions suggests its role in radical formation. From our findings, we suggest that BRL6-1 is using a protein in the radical SAM superfamily to interact with the Fe(III) bound to lignin and reducing it to Fe(II) for cellular use, increasing BRL6-1 yield under lignin-amended conditions. This interaction potentially generates organic free radicals and causes a radical cascade which could modify and depolymerize lignin. Further research should clarify the extent to which this mechanism is similar to previously described aerobic chelator-mediated Fenton chemistry or radical producing lignolytic enzymes, such as lignin peroxidases, but under anoxic conditions.

microbiology↗

bioRxiv2020

Carbon limitation leads to thermodynamic regulation of aerobic metabolism

Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in global biogeochemical cycles, yet aquatic OM cycling remains poorly understood. Here, we present the first work to explicitly test OM thermodynamics as a key regulator of aerobic respiration, challenging long-held beliefs that organic carbon and oxygen concentrations are the primary determinants of respiration rates. We pair controlled microcosm experiments with ultrahigh-resolution OM characterization to demonstrate a clear relationship between OM thermodynamic favorability and aerobic respiration under carbon limitation. We also demonstrate a shift in the regulation of aerobic respiration from OM thermodynamics to nitrogen content when carbon is in excess, highlighting a central role for OM thermodynamics in aquatic biogeochemical cycling particularly in carbon-limited ecosystems. Our work therefore illuminates a structural gap in aquatic biogeochemical models and presents a new paradigm in which OM thermodynamics and nitrogen content interactively govern aerobic respiration.

ecology↗

bioRxiv2018

Sensory Over-Responsivity: Parent Report, Direct Assessment Measures, and Neural Architecture

BackgroundSensory processing differences are common across neurodevelopmental disorders. Thus, reliable measures are needed to understand biologic underpinnings of these differences. This study aims to define a scoring methodology specific to tactile (TOR) and auditory (AOR) over-responsivity. Second, using MRI Diffusion Tensor Imaging, we seek to determine whether children with AOR show measurable differences in their white matter integrity.\n\nMethodsThis study includes children with AOR and TOR from a mixed neurodevelopmental disorders cohort including autism and sensory processing dysfunction (n= 176) as well as neurotypical children (n= 128). We established cut-off scores for over-responsivity using the parent report: Short Sensory Profile (SSP), and the direct assessment: Sensory Processing-Three Dimensions:Assessment (SP-3D:A). Group comparisons, based on AOR phenotype, were then conducted comparing the white matter fractional anisotropy in 23 regions of interest.\n\nResultsUsing the direct assessment, 31% of the children with neurodevelopmental disorders had AOR and 27% had TOR. The Inter-test-agreement between SSP and SP-3D:A for AOR was 65% and TOR was 50%. Children with AOR had three white matter tracts showing decreased fractional anisotropy relative to children without AOR.\n\nConclusionsThis study identified cut scores for AOR and TOR using the SSP parent report and SP-3D:A observation. A combination of questionnaire and direct observation measures should be used in clinical and research settings. The SSP parent report and SP-3D:A direct observation ratings overlapped moderately for sensory related behaviors. Based on these initial structural neuroimaging results, we suggest a putative neural network may contribute to AOR.

neuroscience↗