Biology subjects

Schuster, C.

Publications and source records attributed to Schuster, C..

8 recordsLinked to original sources

bioRxiv2026

Geographic distribution of Adult Salmon Enteritis (ASE), Enterocytozoon schreckii, and Ceratonova shasta in Chinook Salmon Oncorhynchus tshawytscha (Walbaum, 1792) in Oregon and Washington state and expanded histopathologic description of ASE

Adult salmon enteritis (ASE) is a severe intestinal disease affecting spring Chinook Salmon (Oncorhynchus tshawytscha) in the Pacific Northwest. ASE is strongly associated with pre-spawn mortality (PSM), a critical concern for endangered populations and continued Chinook Salmon management. This study characterizes the geographic distribution of ASE across Oregon and Washington watersheds, examines its association with two common parasites (Ceratonova shasta and Enterocytozoon schreckii), and provides detailed histopathological characterization of the disease. We examined intestinal tissues from 259 adult spring Chinook Salmon collected from multiple hatcheries across the Columbia River Basin and Puget Sound between 2022 and 2025 using routine histopathology, specific histochemical stains, and immunohistochemistry. ASE was highly prevalent in all Columbia Basin populations, with chronic ulcerative and necrotizing enteritis, but was absent in Puget Sound populations. C. shasta prevalence was high in most Columbia Basin locations (10-100%), while E. schreckii prevalence was more variable (0-67%). Consistent histopathological findings of ASE included [≥] 10% mucosal ulceration, mixed inflammation expanding the lamina propria and extending into surrounding intestinal layers, and dissolution of the stratum granulosum. In chronic ASE lesions, we further characterized granulation tissue formation. Cold water holding of spawning adults appears to slow disease progression and reduce PSM without preventing ASE development. These findings demonstrate that ASE is a geographically restricted disease of the Columbia Basin that may have associations with diverse environmental exposures including water temperature and pathogens.

pathology↗

bioRxiv2026

HIDE-Deconv: A hierarchical deconvolution framework for multiscale characterization of cellular remodeling

Most deconvolution methods estimate cellular composition at a single level of cellular resolution despite biological processes often manifesting within fine-grained cellular subpopulations. We present HIDE-Deconv, a hierarchical deconvolution framework that jointly optimizes cellular compositions across multiple levels of a cell-type hierarchy while maintaining consistency between resolutions. In benchmark experiments, HIDE-Deconv achieved the highest overall predictive performance among evaluated methods. Analyses of lung adenocarcinoma, sepsis, COVID-19 and systemic lupus erythematosus revealed biologically relevant cellular remodeling that remained concealed at broader levels of cellular resolution. HIDE-Deconv is available as an open-source framework at https://github.com/dvoelkl/HIDE-deconv.

bioinformatics↗

bioRxiv2024

Comprehensive annotations of alternative splicing, lncRNAs, and circRNAs in seven species of flowering plants

The successful occupation of terrestrial habitats by early plants was catalyzed by the adaptive evolution of new organs able to supply water and compensate for the gravitational impact under changing land conditions. Because plants are sessile, it has been proposed that the capacity of plants to innovate specialized organs is driven by a complex interplay between developmental gene expression and regulatory RNAs such as lncRNAs and circRNAs, evolving through sequence polymorphisms, genomic rearrangements, and expression divergence. Despite the importance of alternative and noncoding transcripts for enabling plant life, their accurate quantification causes major challenges as many of them are expressed at low levels and tissue-specific. Here, we describe the re-annotation of seven land plant genomes based on deep, organ-specific, ribo-depleted developmental RNA-Seq data. Using this comparative resource, we uncover 5,000 new lncRNAs and 2,000 new circular RNAs that are promising candidates for further functional investigation. Our annotation will become a reference catalog for studies on plant organ evolution and for uncovering tissue-specific patterns of transcript emergence.

plant biology↗

bioRxiv2024

Rapid evolution of gene expression patterns in flowering plants

Phenotypic differences between species are largely driven by changes in both protein-coding sequence and gene expression 1. The evolutionary history of angiosperms (flowering plants) is characterised by a highly accelerated rate of diversification, which Darwin referred to as an "abominable mystery" 2. Here we show, by analysing the transcriptomes from eight organs across seven species, that angiosperm protein-coding gene expression patterns evolve rapidly: within 45 million years, expression levels of orthologous genes diverged so strongly that they are more similar between different organs within a species than between what are considered homologous organs from different species. This finding differs from previous observations in mammals, which demonstrated that organ-dependent gene expression levels are largely conserved 3, 4, 5. Among the angiosperm organs, meristems and leaves show the highest degree of expression conservation, whereas stamen and pollen transcriptomes diverge rapidly. Examining changes in the expression level of functionally related genes, we found low rates for those involved in key cellular, metabolic and developmental processes. In contrast, particularly high rates were observed for genes that are involved in the response to endogenous and external stimuli, presumably reflecting an adaptive response of flowering plants to ever-changing environments. Our work reveals that the evolution of gene expression progresses at different rates in angiosperms and mammals, and provides a comprehensive resource to perform cross-kingdom comparative studies of transcriptome evolution.

plant biology↗

bioRxiv2021

Circadian regulation of SARS-CoV-2 infection in lung epithelial cells

The COVID-19 pandemic, caused by SARS-CoV-2 coronavirus, is a global health issue with unprecedented challenges for public health. SARS-CoV-2 primarily infects cells of the respiratory tract, via Spike glycoprotein binding angiotensin-converting enzyme (ACE2). Circadian rhythms coordinate an organisms response to its environment and can regulate host susceptibility to virus infection. We demonstrate a circadian regulation of ACE2 in lung epithelial cells and show that silencing BMAL1 or treatment with a synthetic REV-ERB agonist SR9009 reduces ACE2 expression and inhibits SARS-CoV-2 entry. Treating infected cells with SR9009 limits viral replication and secretion of infectious particles, showing that post-entry steps in the viral life cycle are influenced by the circadian system. Transcriptome analysis revealed that Bmal1 silencing induced a wide spectrum of interferon stimulated genes in Calu-3 lung epithelial cells, providing a mechanism for the circadian pathway to dampen SARS-CoV-2 infection. Our study suggests new approaches to understand and improve therapeutic targeting of SARS-CoV-2.

microbiology↗

bioRxiv2019

Intraperitoneal injection of sodium pentobarbital is associated with pain in rats.

An effective and pain-free killing method is required to achieve the goal of euthanasia, a \"good death\". Overdose of sodium pentobarbital (PB) by intraperitoneal (IP) injection is a widely accepted technique, but questions remain regarding pain associated with administration. As PB rapidly causes sedation and loss of consciousness, most studies have relied on indirect evidence of pain. The objective of this study was to assess pain associated with IP PB using an appropriate vehicle control.\n\nAdult male and female Sprague Dawley (SD) and female Wistar rats (N = 112) were block randomised by sex and strain to receive one of four treatments: 1) 800 mg/kg PB (pH 11); 2) 800 mg/kg PB with 4 mg/kg lidocaine (PB+lido); 3) saline or 4) vehicle controls (pH 11 or 12.5). Behavior (Rat Grimace Scale [RGS], writhing, back arching) was evaluated at baseline, before loss of righting reflex (PB and PB+lido groups), 80s, 151s and 10 min post-injection (PI; saline and vehicle control groups).\n\nIn the vehicle control groups, the RGS scores were increased at 151s PI (SD: p = 0.0008, 95%CI -0.731 to -0.202) from baseline, as was relative frequency of writhing (SD: p < 0.00001; Wistar; p = 0.0004). RGS scores remained elevated 10 mins PI (SD: p = 0.0070, 95%CI -0.768 to -0.118; Wistar: p = 0.0236, 95%CI -0.907 to -0.0742) but the relative frequency of writhing did not (p > 0.05). The RGS scores and the relative frequency of writhing remained low in the PB, PB+lido and saline groups (p > 0.05). Back arching increased from baseline in the PB+lido group before loss of righting reflex and in the vehicle control group (SD rats) at 151s PI (p < 0.05).\n\nThese results show that IP PB results in signs associated with pain. The sedative effects of PB limit behavioral assessment.

physiology↗

bioRxiv2017

Nitrate modulates stem cell dynamics by regulating WUSCHEL expression through cytokinins

The shoot apical meristem (SAM) is responsible for the generation of all of the aerial parts of plants1. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment2. Using quantitative microscopy, grafting experiments and genetic perturbations, we connect the plant environment to the SAM, by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors3 mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of WUSCHEL, a key regulator of stem cell homeostasis4. In time-lapse experiments, we further show that this mechanism allows meristems to adapt to rapid changes in nitrate concentration, and thereby modulate their rate of organ production to the availability of mineral nutrients within a few days. Our work sheds new light on the role of the stem cell regulatory network, by showing that it does not only maintain meristem homeostasis but also allows plants to adapt to rapid changes in the environment.

plant biology↗

bioRxiv2017

Peripherally-induced regulatory T cells contribute to the control of autoimmune diabetes

Type 1 diabetes (T1D) results from the autoimmune destruction of pancreatic beta cells and is partly caused by deficiencies in the Foxp3+ regulatory T cell (Treg) compartment. Conversely, therapies that increase Treg function can prevent autoimmune diabetes in animal models. The majority of Tregs develop in the thymus (tTregs), but a proportion of Foxp3+ Tregs is generated in the periphery (pTregs) from Foxp3-CD4+ T cell precursors. Whether pTregs play a distinct role in T1D has not yet been explored. We report here that pTregs are a key modifier of disease in the nonobesed diabetic (NOD) mouse model for T1D. We generated NOD mice deficient for the Foxp3 enhancer CNS1 involved in pTreg induction. We show that CNS1 knockout decreased the frequency of pTregs and increased the risk of diabetes. Our results show that pTregs fulfill an important non-redundant function in the prevention of beta cell autoimmunity that causes T1D.

immunology↗