Biology subjects

Bao, M.

Publications and source records attributed to Bao, M..

At least 19 recordsLinked to original sources

bioRxiv2026

GM-CSF regulates ILC states and myeloid cell signaling during ulceration in Crohns disease

Macrophage (M-), granulocyte (G-), and granulocyte-macrophage (GM-) colony-stimulating factors (CSFs) regulate myeloid cell function, yet their relative roles during inflammation remain poorly defined. To uncover how CSFs shape spatial immune niches in Crohns disease, we performed Xenium single-cell spatial transcriptomics on ileal tissues, revealing cell-type-specific expression and source-target interactions for each CSF. GM-CSF, unlike M-CSF or G-CSF, was locally enriched in ulcerated regions where lymphocytes adjacent to macrophage aggregates signaled through STAT5 phosphorylation. To study functional consequences, we developed a csf2rb-/- zebrafish model of intestinal injury. Using this model, we found that loss of GM-CSF signaling exacerbated epithelial damage and inflammation, whereas recombinant human GM-CSF limited injury by restraining ILC1 expansion, sustaining ILC3 maintenance, and promoting IL-22 production. Cross-species single-cell analysis revealed conserved ILC gene modules and GM-CSF-dependent transcriptional networks linking lymphoid and myeloid populations. These findings establish GM-CSF as a critical spatial regulator of myeloid- lymphoid crosstalk and intestinal immune homeostasis in Crohns disease.

immunology↗

bioRxiv2025

DNA Framework Nanoreactor for Programmable Membrane Fusion

Membrane fusion is a fundamental yet transient process that has long resisted direct structural and kinetic dissection. Here we introduce a DNA framework vesicle (DFV) nanoreactor that transforms this elusive biological phenomenon into a programmable, visualizable, and quantifiable process-a nanoreaction confined in space yet extended in time. By embedding lipid membranes and SNARE proteins within precisely defined DNA apertures, DFVs convert stochastic vesicle collisions into geometry-controlled fusion events with tunable kinetics. Cryo-electron microscopy resolves a complete sequence of six intermediates, revealing how nanoscale confinement reshapes the energetic landscape of bilayer merger. Quantitative fluorescence and nano-flow cytometry further establish a direct link between spatial design and fusion probability. Extending this concept to living cells, DFVs enable controllable membrane fusion and augmentation on VAMP2-expressing membranes, achieving direct cytosolic delivery of functional siRNA via fusion-driven transfer rather than endocytosis. This framework bridges structural precision and functional mimicry, offering a unified platform to reconstruct, quantify, and harness membrane fusion as a programmable process for synthetic biology and nanomedicine.

bioengineering↗

bioRxiv2025

Genetics in the ocean's twilight zone: Population structure of the Mueller's pearlside across its distribution range

The large estimates of mesopelagic fish biomass have fuelled harvesting interests in the relatively untouched oceans twilight zone. The Muellers pearlside, one of the most abundant species inhabiting the north Atlantic mesopelagic layer, is a candidate to such fisheries despite its enormous ecological importance and the insufficient knowledge about its population genetic structure. To shed light on the latter, 863 individuals sampled across the North Atlantic and Mediterranean were genotyped using 170 genome-wide SNPs. Analyses revealed habitat-driven differentiation in three units: Mediterranean Sea, oceanic samples, and Norwegian fjords. These groups were not completely isolated to each other as a cline of Mediterranean admixture was detected in the Eastern Atlantic facade up to 47{degrees}N in an otherwise genetically homogeneous oceanic cluster. Temperature seemed to modulate the differentiation patterns, and in the Mediterranean added to the complicated topography of the Greek Seas to shape genetic structure. In the Norwegian coastline, sills did not hamper genetic exchange among fjords ranging 200 km apart, probably due to the position of the species in the water column together with its swimming capacity. This genetic information should be combined with demographic properties to outline the management of this species prior to any eventual fishery attempt.

genetics↗

bioRxiv2024

In vivo regulation of an endogenously-tagged protein by a light-regulated kinase

Post-translational modifications (PTMs) are indispensable modulators of protein activity. Most cellular behaviours, from cell division to cytoskeletal organization, are controlled by PTMs, their miss-regulation being associated with a plethora of human diseases. Traditionally, the role of PTMs has been studied employing biochemical techniques. However, these approaches fall short when studying PTM dynamics in vivo. In recent years, functionalized protein binders have allowed the post-translational modification of endogenous proteins by bringing an enzymatic domain in close proximity to the protein they recognize. To date, most of these methods lack the temporal control necessary to understand the complex effects triggered by PTMs. In this study, we have developed a method to phosphorylate endogenous Myosin in a light-inducible manner. The method relies both on nanobody-targeting and light-inducible activation in order to achieve both tight specificity and temporal control. We demonstrate that this technology is able to disrupt cytoskeletal dynamics during Drosophila embryonic development. Together, our results highlight the potential of combining optogenetics and protein binders for the study of the proteome in multicellular systems.

developmental biology↗

bioRxiv2024

Spatial Transcriptomics of IPMN Reveals Divergent Indolent and Malignant Lineages

PurposeIntraductal papillary mucinous neoplasms (IPMN) occur in 5-10% of the population, but only a small minority progress to pancreatic ductal adenocarcinoma (PDAC). The lack of accurate predictors of high-risk disease leads both to unnecessary operations for indolent neoplasms as well as missed diagnoses of PDAC. Digital spatial RNA profiling (DSP-RNA) provides an opportunity to define and associate transcriptomic states with cancer risk. Experimental DesignWhole-transcriptome DSP-RNA profiling was performed on 10 IPMN specimens encompassing the spectrum of dysplastic changes from normal duct to cancer. Ductal epithelial regions within each tissue were annotated as normal duct (NL), low-grade dysplasia (LGD), high-grade dysplasia (HGD), or invasive carcinoma (INV). Gene expression count data was generated by Illumina sequencing and analyzed with R/Bioconductor. ResultsDimension reduction analysis exposed three clusters reflecting IPMN transcriptomic states denoted "normal-like" (cNL), "low-risk" (cLR) and "high-risk" (cHR). In addition to specific marker genes, the three states exhibited significant enrichment for the exocrine, classical, and basal-like programs in PDAC. Specifically, exocrine function diminished in cHR, classical activation distinguished neoplasia from cNL, and basal-like genes were specifically upregulated in cHR. Intriguingly, markers of cHR were detected in NL and LGD regions from specimens with PDAC but not low-grade IPMN. ConclusionsDSP-RNA of IPMN revealed low-risk (indolent) and high-risk (malignant) expression programs that correlated with the activity of exocrine and basal-like PDAC signatures, respectively, and distinguished pathologically low-grade from malignant specimens. These findings contextualize IPMN pathogenesis and have the potential to transform existing risk stratification models. Statement of translational relevanceCurrent consensus guidelines for management of intraductal papillary mucinous neoplasms (IPMN) of the pancreas utilize clinical and radiographic criteria for risk stratification. Unfortunately, the estimated positive predictive value of these criteria for IPMN-associated pancreatic ductal adenocarcinoma (PDAC) is under 50%, indicating that over half of pancreatectomies are performed for benign disease. Moreover, nearly 15% of patients who were deemed "low risk" by the same criteria harbored PDAC. Surgical resection of IPMN has maximal benefit when performed prior to the development of PDAC, as evidence of carcinoma has been associated with a high rate of recurrence and poor overall survival. Thus, the development of molecular diagnostics that improve the accuracy of IPMN risk classification would have immediate relevance for patient care, both in terms of better selecting patients for potentially curative operations, as well as sparing patients with low-risk lesions from invasive procedures.

cancer biology↗

bioRxiv2024

Directed assembly of single-stranded DNA fragments for data storage via enzyme-free catalytic splint ligation

Oligonucleotides or gene fragments can be ligated in a specified order to create longer DNA assemblies. We present a method where DNA symbols, or oligos designed to encode information for data storage, are joined to linker sequences at either end. These linkers dictate the assembly order of the symbols; the order of the symbols can be changed by changing the sequences of the linkers attached to them. Utilizing a ligating DNAzyme as a catalytic splint, we achieve room-temperature, enzyme-free assembly, offering a cost-effective alternative to traditional enzyme-based ligation methods. We demonstrate this technique by assembling three different five-symbol constructs, with the order of the symbols determined by their linking ends. This linker directed assembly technique allows data-encoding symbols to be assembled in any desired order. Furthermore, the DNAzyme-based assembly method is versatile and can be applied to various DNA assembly applications, particularly where cost-effectiveness and efficient room-temperature ligation are required.

synthetic biology↗

bioRxiv2024

Proteomic responses of oat (Avena sativa L.) to drought stress

Drought is a major abiotic factor limiting the growth and development of the oat industry, and understanding its drought tolerance mechanisms is vital to oat production. In this study, we measured the phenotypic and physiological indices of drought-resistant (Grain King [G]) and water-sensitive (XiYue [X]) oat varieties and performed comparative proteomic analysis under drought stress and normal water supply (soil water content of 75% {+/-} 5% of field water holding capacity) conditions. The results indicated that plant height, aboveground biomass, and underground biomass of variety X were 7.9%, 9.5%, and 14.6% lower than those under normal water supply, respectively, and the difference in plant height was significant (p < 0.05), whereas the decrease in all these indicators of variety G was small. Drought stress significantly increased malondialdehyde (MDA) content, soluble sugar (SS) content, superoxide dismutase (SOD) activity, and peroxidase (POD) activity of variety G by 48.6%, 68.5%, 81.3%, and 101.7%, respectively (p < 0.05). Variety X also showed increases up to various extents, but the increases were smaller than those of variety G. Additionally, 151 and 792 differentially expressed proteins (DEPs) identified in varieties G and X, respectively. Weighted Gene Co-expression Network Analysis(WGCNA), Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genome(KEGG) analyses demonstrated that the DEPs who were highly correlated with POD and SOD activity and SS content in variety G, were majorly involved in energy metabolism, protein translation, RNA processing, amino acid metabolism, and protein folding, whereas those with high correlation with the above three physiological indicators in variety X were primarily involved in RNA processing, protein stabilization, plant photosynthesis, intracellular signal transduction, and protein folding. Overall, the study elucidated the drought resistance mechanisms of different types of oats at the protein level

molecular biology↗

bioRxiv2023

Causal Role of the Frontal Eye Field in Attention-induced Ocular Dominance Plasticity

Previous research has found that prolonged eye-based attention can bias ocular dominance. If one eye long-termly views a regular movie meanwhile the opposite eye views a backward movie of the same episode, perceptual ocular dominance will shift towards the eye previously viewing the backward movie. Yet it remains unclear whether the role of eye-based attention in this phenomenon is causal or not. To address this issue, the present study relied on both the functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) techniques. We found robust activation of the frontal eye field (FEF) and intraparietal sulcus (IPS) when participants were watching the dichoptic movie while focusing their attention on the regular movie. Interestingly, we found a robust effect of attention-induced ocular dominance shift when the cortical function of vertex or IPS was transiently inhibited by continuous theta burst stimulation (cTBS), yet the effect was significantly attenuated to a negligible extent when cTBS was delivered to FEF. A control experiment verified that the attenuation of ocular dominance shift after inhibitory stimulation of FEF was not due to any impact of the cTBS on the binocular rivalry measurement of ocular dominance. These findings suggest that the fronto-parietal attentional network is involved in controlling eye-based attention in the "dichoptic-backward-movie" adaptation paradigm, and in this network, FEF plays a crucial causal role in generating the attention-induced ocular dominance shift.

neuroscience↗

bioRxiv2023

Neuroprotective Mechanism of Ribisin A on H 2 O 2 -induced PC12 cell injury model

Ribisin A has been shown to have neurotrophic activity. The aim of this study was to evaluate the neuroprotective effect of Ribisin A on injured PC12 cells and elucidate its mechanism. In this project, PC12 cells were induced by H2O2 to establish an injury model. After treatment with Ribisin A, the neuroprotective mechanism of Ribisin A was investigated by methyl tetrazolium (MTT) assay, Enzyme-linked immunosorbent assay (ELISA), flow cytometric analysis, fluorescent probe analysis, and western blot. We found that Ribisin A decreased the rate of lactate dehydrogenase (LDH) release, increased cellular superoxide dismutase (SOD) activity, decreased the levels of tumor necrosis factor- (TNF-), interleukin-6 (IL-6), Ca2+ expression and reactive oxygen species (ROS). Moreover, Ribisin A significantly increased mitochondrial membrane potential (MMP) and inhibited apoptosis of PC12 cells. Meanwhile, Ribisin A activated the phosphorylation of ERK1/2 and its downstream molecule CREB by upregulating the expression of Trk A and Trk B, the upstream molecules of the ERK signaling pathway. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/559840v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@ff9604org.highwire.dtl.DTLVardef@1d1ee75org.highwire.dtl.DTLVardef@17e4441org.highwire.dtl.DTLVardef@b347c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2023

Micropillar enhanced FRET-CRISPR biosensor for nucleic acid detection

CRISPR technology has gained widespread adoption for pathogen detection due to its exceptional sensitivity and specificity. Although recent studies have investigated the potential of high-aspect-ratio microstructures in enhancing biochemical applications, their application in CRISPR-based detection has been relatively rare. In this study, we developed a FRET-based biosensor in combination with high-aspect-ratio microstructures and Cas12a-mediated trans-cleavage for detecting HPV 16 DNA fragments. Remarkably, our results show that micropillars with higher density exhibit superior molecular binding capabilities, leading to a tenfold increase in detection sensitivity. Furthermore, we investigated the effectiveness of two surface chemical treatment methods for enhancing the developed FRET assay. A simple and effective approach was also developed to mitigate bubble generation in microfluidic devices, a crucial issue in biochemical reactions within such devices. Overall, this work introduces a novel approach using micropillars for CRISPR-based viral detection and provides valuable insights into optimizing biochemical reactions within microfluidic devices.

bioengineering↗

bioRxiv2023

A longitudinal resource for population neuroscience of school-age children and adolescents in China

During the past decade, cognitive neuroscience has been calling for population diversity to address the challenge of validity and generalizability, ushering in a new era of population neuroscience. The developing Chinese Color Nest Project (devCCNP, 2013-2022), a ten-year pilot stage of the lifespan CCNP (2013-2032), is an ongoing project focusing on brain-mind development. The project aims to create and share a large-scale, longitudinal and multimodal dataset of typically developing children and adolescents (ages 6.0-17.9 at enrolment) in the Chinese population. The devCCNP houses not only phenotypes measured by demographic, biophysical, psychological and behavioural, cognitive, affective, and ocular-tracking assessments but also neurotypes measured with magnetic resonance imaging (MRI) of brain morphometry, resting-state function, naturalistic viewing function and diffusion structure. This Data Descriptor introduces the first data release of devCCNP including a total of 864 visits from 479 participants. Herein, we provided details of the experimental design, sampling strategies, and technical validation of the devCCNP resource. We demonstrate and discuss the potential of a multicohort longitudinal design to depict normative brain growth curves from the perspective of developmental population neuroscience. The devCCNP resource is shared as part of the "Chinese Data-sharing Warehouse for In-vivo Imaging Brain" in the Chinese Color Nest Project (CCNP) - Lifespan Brain-Mind Development Data Community (https://www.scidb.cn/en/c/ccnp) at the Science Data Bank. Design TypesO_LIAccelerated longitudinal design C_LIO_LIBrain-mind development C_LIO_LIPopulation imaging C_LIO_LIBrain chart C_LIO_LIRepeated measure C_LI MeasurementsO_LIPsychological behaviours C_LIO_LIBiophysical and physical measures C_LIO_LIIntelligence quotient measure C_LIO_LINeuroimaging C_LI Sample Characteristic - OrganismO_LIHomo sapiens C_LI Sample Characteristic - EnvironmentO_LISchool- and community-based sample C_LI Sample Characteristic - LocationO_LIChongqing and Beijing, China C_LI DurationO_LI10 years (2013-2022) C_LI

neuroscience↗

bioRxiv2022

Tocilizumab treatment leads to early resolution of myeloid dysfunction and lymphopenia in patients hospitalized with COVID-19

High interleukin (IL)-6 levels are associated with more severe clinical manifestations in patients hospitalized with COVID-19, but the complex role of IL-6 in antiviral and inflammatory processes has made it difficult to decipher its involvement in the disease. IL-6 receptor blockade by tocilizumab (anti-IL6R; Actemra) is used globally for the treatment of severe COVID-19, yet a molecular understanding of the therapeutic benefit remains unclear. We characterized the immune profile and identified cellular and molecular pathways directly modified by tocilizumab in peripheral blood samples collected from patients enrolled in the COVACTA study, a phase 3, randomized, double-blind, placebo-controlled trial that assessed the efficacy and safety of tocilizumab in hospitalized patients with severe COVID-19 pneumonia. We identified factors predicting disease severity and clinical outcomes, including markers of inflammation, lymphopenia, myeloid dysregulation, and organ injury. Proteomic analysis confirmed a pharmacodynamic effect for tocilizumab in addition to identifying novel pharmacodynamic biomarkers. Transcriptomic analysis revealed that tocilizumab treatment leads to faster resolution of lymphopenia and myeloid dysregulation associated with severe COVID-19, indicating greater anti-inflammatory activity relative to standard of care and potentially leading to faster recovery in patients hospitalized with COVID-19. One sentence summaryInterleukin-6 receptor blockade with tocilizumab accelerated resolution of myeloid dysfunction and lymphopenia in patients hospitalized with COVID-19

immunology↗

bioRxiv2022

The Effects of CdSe/ZnS Quantum Dots on the Photosynthesis Rate of the Chlorella Vulgaris Beads

Photosynthesizing microalgae produce more than 50% of oxygen in the atmosphere and are crucial for the survival of many living systems such as coral reefs. To address the declining of coral reefs, artificial reefs have been introduced to encapsulate the aglae cells in a polymer matrix but the effects of nanoscale pollutants on these engineered systems have not been fully understood. In this work, quantum dots with a size smaller than 10 nm are being used to elucidate the photosynthesis performance of the sodium alginate beads encapsulated with Chlorella vulgaris (C. vulgaris). The fluorescent quantum dots can move into the alginate matrix and the fluorescence intensity in the algae beads is correlated with the quantum dot concentration. We further show that the photosynthesis of the algae beads are sensitive to the quantum dot concentration and are also time sensitive. In the first 48 min of quantum dot exposure, both carbon dioxide absorption and oxygen production are low, suggesting limited photosynthesis. After the initial incubation, the photosynthesis rate quickly increases even though more inhibition is still observed with higher concentration of the quantum dots.

bioengineering↗

bioRxiv2022

On-Demand Fully-Enclosed Superhydrophobic-Optofluidic Device Enabled by High Precision Microstereolithography

Superhydrophobic surface-based optofluidics have been introduced to biosensors and unconventional optics with unique advantages such as low light loss and power consumption. However, most of these platforms were made with planar-like micro- and nano-structures, which may cause bonding issues and resulting in significant waveguide loss. Here, we introduce a fully-enclosed superhydrophobic-based optofluidics system, enabled by a one-step high precision microstereolithography procedure. Various micro-structured cladding designs with a feature size down to 100 m were studied and a "T-type" overhang design exhibits the lowest optical loss, regardless of the excitation wavelength. Surprisingly, the optical loss of superhydrophobic-based optofluidics is not solely decided by the solid area fraction at the solid/water/air interface, but also the cross-section shape and the effective cladding layer composition. We show that this fully-enclosed optofluidic system can be used for CRISPR-labeled quantum dot quantification, intended for in vitro and in vivo CRISPR therapeutics.

bioengineering↗

bioRxiv2022

Differential modifications of the C-terminal tails of α-tubulin isoforms and their in vivo importance for kinesin function in Drosophila

Microtubules (MTs) are built from -/{beta}-tubulin dimers and used as tracks by kinesin and dynein motors to transport a variety of cargos, such as mRNAs, proteins, and organelles, within the cell. Tubulins are subjected to several post-translational modifications (PTMs). Glutamylation is one of them, and it is responsible for adding one or more glutamic acid residues as branched peptide chains to the C-terminal tails of both - and {beta}-tubulin. However, very little is known about the specific modifications found on the different tubulin isotypes in vivo and the role of these PTMs in MT transport and other cellular processes in vivo. In this study, we found that in Drosophila ovaries, glutamylation of -tubulin isotypes occurred clearly on the C-terminal ends of Tub84B and Tub84D (Tub84B/D). In contrast, the ovarian -tubulin, Tub67C, is not glutamylated. The C-terminal ends of Tub84B/D are glutamylated at several glutamyl side chains in various combinations. Drosophila TTLL5 is required for the mono- and poly-glutamylation of ovarian Tub84B/D and with this for the proper localization of glutamylated microtubules. Similarly, proper Kinesin-1 distribution in the germline also depends on TTLL5 as well as the refining of Staufen localization and the normal fast ooplasmic streaming with its directional movement, two processes known to depend on Kinesin-1 activities. In the nervous system, the pausing of anterograde axonal transport of mitochondria is affected by an enzymatically dead mutant of TTLL5. Our results demonstrate in vivo roles of TTLL5 in differential glutamylation of -tubulins and point to the in vivo importance of -tubulin glutamylation for Kinesin-1-dependent processes. SummaryO_LI-tubulin glutamylation was established in the C-terminal domain of Drosophila Tub84B and Tub84D (Tub84B/D). Multiple glutamyl residues were pinpointed in this domain. The female germline -tubulin, Tub67C, is, however, not glutamylated. C_LIO_LITTLL5 is required for mono- and poly-glutamylation of Tub84B/D. C_LIO_LITTLL5 is required for the proper Kinesin heavy chain (Khc) distribution in the germline, and the kinesin-based refinement of Staufen localization and ooplasmic streaming during late oogenesis. C_LIO_LITTLL5 is needed for the pausing of anterograde trafficking of mitochondria in axons. C_LI

cell biology↗

bioRxiv2022

Alnustone inhibits Streptococcus pneumoniae virulence by targeting pneumolysin and sortase A

Streptococcus pneumoniae (S. pneumoniae) is a significant Gram-positive opportunistic pathogen responsible for a variety of lethal infections. This bacterium accounts for more deaths from diseases than any other single pathogen worldwide. Distinctively, these symptoms arise despite effective antibiotic therapy. This study unveiled a novel mechanism of resistance to S. pneumoniae infection by targeting pneumolysin (PLY) and sortase A (Srt A), the key virulence factors of S. pneumoniae. Through protein phenotype assays, we found alnustone to be a potent drug that inhibits both PLY and Srt A. Using a PLY-mediated hemolysis assay, we found that albumin can effectively reduce Srt A peptidase activity by blocking PLY oligomerization, thereby directly inhibiting PLY-expressing cytolysis. Co-incubation of S. pneumoniae D39 Srt A with small-molecule inhibitors reduces cell wall-bound Nan A (pneumococcal-anchored surface protein Srt A), inhibits biofilm formation, and significantly reduces biomass. But more interestingly, the protective effect of invasive pneumococcal disease (IPD) on murine streptococcus pneumoniae was further demonstrated. Our study proposes a detailed bacteriostatic mechanism of pneumococcal and highlights the major translational potential of targeting circulating PLY and Srt A to protect against pneumococcal infections. Our results suggest that the antiviral strategy of directly targeting PLY and Srt A with alnustone is a promising treatment option for Streptococcus pneumoniae and that alnustone can be used as an effective inhibitor of PLY and Srt A.

microbiology↗

bioRxiv2022

Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation

Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, involvement of histone methylation in regulating petal senescence is still largely unknown. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during the ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). The H3K4me3 levels are positively associated with the expression of transcription factor DcWRKY75, ethylene biosynthetic genes DcACS1 and DcACO1, and senescence associated genes (SAGs) DcSAG12 and DcSAG29. Further, we identified that carnation DcATX1 (ARABIDOPSIS HOMOLOG OF TRITHORAX1) encodes a histone lysine methyltransferase which can methylate H3K4. Knockdown of DcATX1 delays ethylene induced petal senescence in carnation, which is associated with the downregulated expression of DcWRKY75, DcACO1 and DcSAG12. While overexpression of DcATX1 exhibits the opposite effects. DcATX1 promotes the transcription of DcWRKY75, DcACO1 and DcSAG12 by targeting to their promoters to elevate the H3K4me3 levels. Overall, our results demonstrate that DcATX1 is a H3K4 methyltransferase that promotes the expression of DcWRKY75, DcACO1 and DcSAG12 by regulating H3K4me3 levels, thereby accelerating ethylene induced petal senescence in carnation. This study further indicates that epigenetic regulation is important for plant senescence process. One sentence summaryA histone methyltransferase promotes ethylene induced petal senescence in cut flower

plant biology↗

bioRxiv2020

High contrast probe cleavage detection on porous silicon biosensors via quantum dot labeled DNA probes

Using porous silicon (PSi) interferometer sensors, we show the first experimental implementation of the high contrast probe cleavage detection (HCPCD) mechanism. HCPCD makes use of dramatic optical signal amplification caused by cleavage of high-contrast nanoparticle labels on probes instead of the capture of low-index biological molecules. An approximately 2 nm reflectance peak shift was detected after cleavage of DNA-quantum dot probes from the PSi surface via exposure to a 12.5 nM DNase enzyme solution for 2 hrs. This signal change is 20 times greater than the resolution of the spectrometer used for the interferometric measurements, and the interferometric measurements agree with the interferometric response predicted by simulations and fluorescence measurements. These proof of principle experiments show a clear path to real-time, highly sensitive and inexpensive point-of-care readout for a broad range of biological diagnostic assays that generate signal via nucleic acid cleavage.

bioengineering↗