Biology subjects

Ruan, M.

Publications and source records attributed to Ruan, M..

7 recordsLinked to original sources

bioRxiv2026

Integrating mass spectrometry with Nanopore direct RNA sequencing for de novo modification profiling of bacteriophage MS2

RNA modifications contribute to the regulatory and structural complexity of RNA molecules, influencing key biological processes. Nanopore direct RNA sequencing (DRS) enables the detection of these modifications at single-molecule resolution without chemical conversion. Oxford Nanopore Technologies recently introduced RNA004 sequencing chemistry and the Dorado basecaller, which improves accuracy and enables the identification of eight RNA modifications. However, the reliability of these predictions requires careful validation using orthogonal approaches. Here, we profiled RNA modifications in the MS2 bacteriophage genome using both LC-MS/MS and Nanopore DRS. LC-MS/MS analysis revealed that {Psi} is the predominant modification, present at approximately one site per RNA molecule, while all other modifications were found at low levels (< 0.04 modifications per RNA). In contrast, Dorado-based modification calling not only confirmed {Psi} but also predicted multiple m6A, m5C, 2OMe, and inosine sites not supported by LC-MS/MS data. To refine modification calling, we used in vitro transcribed (IVT) RNA as a negative control and subtracted IVT-derived false positive rates from native RNA predictions. This adjustment reduced overcalling and improved confidence in site-specific predictions. These data demonstrate that while Dorado can detect RNA modifications de novo, its predictions require careful filtering and validation. Our studies of provide a rare benchmark dataset for assessing the ability of transcriptome-wide methods to accurately identify RNA modifications and estimate modification stoichiometry. These findings support the use of orthogonal approaches, including LC-MS/MS and IVT controls, alongside Nanopore sequencing to provide a more reliable and interpretable strategy for studying RNA modification patterns. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/729303v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@637a55org.highwire.dtl.DTLVardef@f48272org.highwire.dtl.DTLVardef@a0465aorg.highwire.dtl.DTLVardef@6af045_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Cytoplasmic localization of PUS7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance

Pseudouridine ({Psi}) is an abundant post-transcriptional modification found across all classes of RNA. It has been widely speculated that {Psi} inclusion in mRNAs might provide an avenue for cells to control gene expression post-transcriptionally. Here we demonstrate that one of the principal mRNA pseudouridylating enzymes, pseudouridine synthase 7 (PUS7), exhibits a stress-induced accumulation in the cytoplasm of yeast and human epithelial lung cells. Stress-induced and cytoplasmic localization of PUS7 promote {Psi}-incorporation into hundreds of mRNA targets. Furthermore, engineered PUS7 cytoplasmic localization increases cellular fitness under ROS and divalent metal ion stress. Consistent with this, transcripts modified upon PUS7 cytoplasmic localization are enriched within mRNAs encoding proteins involved in divalent metal metabolism and ROS stress pathways. In contrast, tRNA sites modified by PUS7 ({Psi}13 and {Psi}35 are unperturbed). Quantitative proteomics reveal a reshaping of the proteome upon PUS7 relocalization under stress, with proteins involved in metal and ROS homeostasis being particularly sensitive to PUS7 localization. Collectively, our data demonstrate that PUS7 localization alters mRNA pseudouridylation patterns to modulate protein production and enhance cellular fitness.

biochemistry↗

bioRxiv2024

Effects of Forefoot versus Rearfoot Landing on Biomechanical Risk Factors for Lower Limb Injuries and Performance During Stop-Jump Tasks

BackgroundLower limb injuries commonly occur during sudden deceleration movements. Instructing landing with forefoot or rearfoot is hard to answer, especially considering the injury prevention and keep the performance. Therefore, the purpose of this study is to evaluate the effect of the forefoot and rearfoot landing on the biomechanical risk of lower limb injury prevention and performance during the stop-jumping task. MethodTwenty-three male health subjects were recruited for this study. During a stop-jumping task, three-dimensional kinematic and kinetic, and performance data were collected under two conditions: forefoot landing at initial ground contact and rearfoot landing at initial ground contact. Statistical parametric mapping analysis was used to compare the differences between different landing strategies. ResultSignificant differences were found in ankle internal rotation angle and ankle joint moment at foot initial contact with ground between different landing strategies. Landing with forefoot has shorter stance time compared with landing with rearfoot. In the rearfoot strike, posterior ground reaction force (GRF) and GRF inclination angle were smaller than forefoot strike in 0-14% of the stance phase. ConclusionLanding with forefoot may decrease the risk of non-contact anterior cruciate ligament injuries and have an advancement in quick reaction time, as indicated by decreased stance time, but the risk of lateral ankle sprain may increase for the stop-jump task.

bioengineering↗

bioRxiv2024

Osteochondroprogenitor cells and neutrophils expressing p21 and senescence markers modulate fracture repair

Cells expressing features of senescence, including upregulation of p21 and p16, appear transiently following tissue injury, yet the properties of these cells or how they contrast with age-induced senescent cells remains unclear. Here, we used skeletal injury as a model and identified the rapid appearance following fracture of p21+ cells expressing senescence markers, mainly as osteochondroprogenitors (OCHs) and neutrophils. Targeted genetic clearance of p21+ cells suppressed senescence-associated signatures within the fracture callus and accelerated fracture healing. By contrast, p21+ cell clearance did not alter bone loss due to aging; conversely, p16+ cell clearance, known to alleviate skeletal aging, did not affect fracture healing. Following fracture, p21+ neutrophils were enriched in signaling pathways known to induce paracrine stromal senescence, while p21+ OCHs were highly enriched in senescence-associated secretory phenotype factors known to impair bone formation. Further analysis revealed an injury-specific stem cell-like OCH subset that was p21+ and highly inflammatory, with a similar inflammatory mesenchymal population (fibro-adipogenic progenitors) evident following muscle injury. Thus, intercommunicating senescent-like neutrophils and mesenchymal progenitor cells are key regulators of tissue repair in bone and potentially across tissues. Moreover, our findings establish contextual roles of p21+ vs p16+ senescent/senescent-like cells that may be leveraged for therapeutic opportunities.

physiology↗

bioRxiv2023

Free long chain fatty acid solitarily primes early postembryonic development in Caenorhabditis elegans under starvation

Postembryonic development of animals is long considered an internal predetermined program, while macronutrient is essential only because they provide biomatters and energy to support this process. However, in this study, by using a nematode Caenorhabditis elegans model, we surprisingly found that dietary supplementation of palmitic acid alone, but not other essential nutrients of abundance such as glucose or amino acid mixture, sufficiently initiated the early postembryonic development under complete macronutrient deprivation. Such a development was indicated by changes in morphology, cellular markers in multiple tissues, behaviors and the global transcription pattern. Mechanistically, palmitate doesnt function as a biomatter/energy provider, but as a ligand to activate the nuclear hormone receptor NHR-49/80 and generate an obscure peroxisome-derived secretive hormone in the intestine. Such a hormonal signal was received by chemosensory neurons in the head in regulating the insulin-like neuropeptide secretion and its downstream nuclear receptor to orchestrate the global development. Moreover, the nutrient-sensing hub mTORC1 played a negative role in this process. In conclusion, our data indicate that free fatty acid acts as a prime nutrient signal to launch the early development in C. elegans; and implicate that specific nutrient rather than the internal genetic program is the first impetus of postembryonic development.

developmental biology↗

bioRxiv2021

A lipid-mTORC1 nutrient-sensing pathway regulates animal development by peroxisome-derived hormones

Animals have developed many signaling mechanisms that alter cellular and developmental programs in response to changes in nutrients and their derived metabolites, many of which remain to be understood. We recently uncovered that glucosylceramides, a core sphingolipid, act as a critical nutrient signal for overall amino-acid level to promote development by activating the intestinal mTORC1 pathway. However, how the intestinal GlcCer-mTORC1 activity regulates development throughout the whole body is unknown. Through a large-scale genetic screen, we found that the peroxisomes are critical for antagonizing the GlcCer-mTORC1-mediated nutrient signal. Mechanistically, deficiency of glucosylceramide, inactivation of the downstream mTORC1 activity, or prolonged starvation relocated peroxisomes closer to the intestinal apical region to release peroxisomal-beta-oxidation derived hormones that targeting chemosensory neurons to arrest the animal development. Our data illustrated a new gut-brain axis for orchestrating nutrient-sensing dependent development in Caenorhabditis elegans, which may also explain why glucosylceramide and peroxisome become essential in metazoans.

cell biology↗

bioRxiv2020

Speed modulation of hippocampal theta frequency and power predicts water maze learning

Theta oscillations in the hippocampus have many behavioural correlates, with the magnitude and vigour of ongoing movement being the most salient. Many consider correlates of locomotion with hippocampal theta to be a confound in delineating theta contributions to cognitive processes. But, theory and empirical experiments suggest theta-movement relationships are important if spatial navigation is to support higher cognitive processes. In the current study, we tested if variations in speed modulation of hippocampal theta can predict spatial learning rates in the water maze. Using multi-step regression, we find the magnitude and robustness of hippocampal theta frequency versus speed scaling can predict water maze learning rates. Using generalised linear models, we also demonstrate that speed and water maze learning are the best predictors of hippocampal theta frequency and power. Theta oscillations recorded from the supramammillary area showed much weaker, or non-existent, relationships, which supports the idea that hippocampal theta has specific roles in speed representation and spatial learning. Our findings suggest movement-speed correlations with hippocampal theta frequency may be actively used in spatial learning.

neuroscience↗