Biology subjects

Wu, L.

Publications and source records attributed to Wu, L..

At least 217 records · Page 12Linked to original sources

bioRxiv2022

Subtype-specific roles of ellipsoid body ring neurons in sleep regulation in Drosophila

The ellipsoid body (EB) is a major structure of the central complex of the Drosophila melanogaster brain. 22 subtypes of EB ring neurons have been identified based on anatomical and morphological characteristics with light-level microscopy and EM connectomics. A few studies have associated ring neurons with the regulation of sleep homeostasis and structure. However, cell type-specific and population interactions in the regulation of sleep remain unclear. Employing a unbiased thermogenetic screen of collected EB drivers, we found: 1) multiple ring neurons are involved in the modulation of amount of sleep and structure in a synergistic manner; 2) analysis of data for {Delta}P(doze)/ {Delta}P(wake) using a mixed Gaussian model detected 5 clusters of GAL4 drivers which had similar effects on sleep pressure and/or depth: lines driving arousal contained R4m neurons, whereas lines that increased sleep pressure had R3m cells; 3) a general linear model analysis correlating ring cell subtype and activity-dependent changes in sleep parameters across all the lines identified several cell types significantly associated with specific sleep effects: R3p for daytime sleep promotion, and R4m for nighttime wake-promoting; and 4) another subclass, R3d cells present in 5HT7-GAL4+ neurons and in GAL4 lines from our screen which exclusively affect sleep structure, were found to contribute to fragmentation of sleep during both day and night. Thus, multiple subtypes of ring neurons distinctively control sleep amount and/or structure, and the unique highly interconnected structure of the EB and its connections with other regions of brain suggest a local-network model worth future investigation. SIGNIFICANCE STATEMENTHow multiple brain regions, with many cell types, can coherently regulate sleep remains unclear, but identification of cell type-specific roles can generate opportunities for understanding the principles of integration and cooperation. The ellipsoid body (EB) of the fly brain exhibits a high level of connectivity and functional heterogeneity yet is able to tune multiple behaviours in real-time, including sleep. Leveraging the powerful genetic tools available in Drosophila and recent progress in the characterization of the morphology and connectivity of EB ring neurons, we identify several EB subtypes specifically associated with distinct aspects of sleep. Our findings will aid in revealing the rules of coding and integration in the brain.

neuroscience↗

bioRxiv2022

Regulation of Auditory Sensory Neuron Diversity by Runx1

Functional heterogeneity among sensory neurons is a cardinal property of the vertebrate auditory system, yet it is not known how this heterogeneity is established to ensure proper encoding of sound. Here, we show that the transcription factor Runx1 controls the composition of molecularly and physiologically diverse sensory neurons (Ia, Ib, Ic) in the murine cochlea, which collectively encode a wide range of sound intensities. Runx1 is enriched in Ib and Ic spiral ganglion neuron (SGN) precursors by late embryogenesis. Loss of Runx1 from embryonic SGNs (Runx1CKO) shifted the balance of subtype identities without affecting neuron number, with more SGNs taking on Ia identities at the expense of Ib/Ic identities, as shown by single cell RNA-sequencing. This conversion was more complete for genes linked to neuronal function than for those related to connectivity. Accordingly, although synaptic position did not change, synapses in the Ib/Ic location took on Ia-like properties. Suprathreshold responses to sound were enhanced in the auditory nerve of Runx1CKO mice, confirming an expansion of neurons behaving functionally like Ia SGNs. Fate-mapping experiments further showed that deletion of Runx1 shortly after birth also redirected Ib and Ic SGNs towards Ia identity, indicating that SGN subtype identities remain plastic postnatally. Altogether, these findings show that diverse neuronal identities essential for normal auditory stimulus coding arise in a hierarchical fashion that remains malleable during postnatal development.

neuroscience↗

bioRxiv2022

Transcriptome Response of Cannabis (Cannabis sativa L.) to the Pathogenic fungus Golovinomyces ambrosiae

Powdery mildew (PM), caused by the obligate biotrophic fungus Golovinomyces ambrosiae, is an economically important fungal disease of hemp - and marijuana-type cannabis. While the PM disease can be managed effectively by cultivating resistant hosts, there is no known PM-resistant genetic variant. This is the first report of transcript level responses of the hemp cultivar X59 to G. ambrosiae. Transcript level changes at 5-, 8-, and 11-days post-inoculation (DPI) of C. sativa were evaluated against uninoculated control. Our analysis revealed that 1,898 genes were significantly (q-value < 0.05) differentially expressed (DE) following the pathogen challenge. Among these, 910 and 988 genes were upregulated and downregulated, respectively as the infection progressed to 11 DPI. Genes related to salicylic acid (SA), (LOC115715124 and LOC115711424) and WRKY transcription factor (LOC115707546, LOC115715968, and LOC115707511) were highly upregulated. There were 45 DEGs that were homologous to PM-related genes, including chitin elicitor receptor kinase 1 (CERK 1), enhanced disease resistance 2, (EDR2), and powdery mildew resistance (PMR) genes. Moreover, the genes related to glycosyl hydrolases, particularly LOC115699396, LOC115708023, LOC115710105, and LOC115710100, were highly upregulated and potentially important in mediating pathogen responses. Collectively, this study has contributed to an enhanced understanding of the molecular mechanisms that are involved in cannabis and PM disease interaction and has identified several gene candidates that can be further investigated for their role in defence mechanisms.

plant biology↗

bioRxiv2022

Epitranscriptomic N6-methyladenosine profile of SARS-CoV-2-infected human lung epithelial cells

N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification that plays an important role in determining transcript fate. Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has caused the global pandemic of coronavirus disease 2019 (COVID-19) and the virus has been extensively studied. However, how m6A modification of host cell RNAs change during SARS-CoV-2 infection has not been reported. Here we define the epitranscriptomic m6A profile of SARS-CoV-2-infected human lung epithelial cells compared to uninfected controls. Biological pathway analyses revealed that differentially methylated transcripts were significantly associated with cancer-related pathways, protein processing in the endoplasmic reticulum, cell death and proliferation. Upstream regulators predicted to be associated with the proteins encoded by differentially methylated mRNAs include proteins involved in the type I interferon response, inflammation, and cytokine signaling. These data suggest that m6A modification of cellular RNA is an important mechanism of regulating host gene expression during SARS-CoV-2 infection of lung epithelial cells.

microbiology↗

bioRxiv2022

3D CentroidNet: Nuclei Centroid Detection With Vector Flow Voting

Automated microscope systems are increasingly used to collect large-scale 3D image volumes of biological tissues. Since cell boundaries are seldom delineated in these images, detection of nuclei is a critical step for identifying and analyzing individual cells. Due to the large intra-class variability in nuclei morphology and the difficulty of generating ground truth annotations, accurate nuclei detection remains a challenging task. We propose a 3D nuclei centroid detection method by estimating the "vector flow" volume where each voxel represents a 3D vector pointing to its nearest nuclei centroid in the corresponding microscopy volume. We then use a voting mechanism to estimate the 3D nuclei centroids from the "vector flow" volume. Our system is trained on synthetic microscopy volumes and tested on real microscopy volumes. The evaluation results indicate our method outperforms other methods both visually and quantitatively.

cell biology↗

bioRxiv2022

KAI2-KL signalling regulates root hair elongation under magnesium deficiency by activating auxin, ethylene, and nitric oxide biosynthesis and signalling genes.

Root hair elongation (RHL), which expands the absorptive surface area of the root, is a crucial adaptation in plants for survival under magnesium (Mg) deficient soil. Despite the significance of this trait, the molecular mechanism in Mg starvation regulating RHL is elusive. We demonstrated that karrikins regulate RHL under a limited supply of Mg via crosstalk with auxin, ethylene, and NO. We used KAI2-KL-signalling mutants, auxin, ethylene, and NO-related genes mutants Arabidopsis and pharmacological method to investigate the role of KAI2-KL-signalling, and its interaction with ethylene, auxin, and NO in the process of RHL in Mg deficient conditions. Mg deficiency could not enhance RHL in KAI2-KL-signalling mutants such as kai2 and max2 Arabidopsis. Interestingly, exogenous application of ethylene, nitric oxide, or auxin recovered RHL of kai2 and max2 Arabidopsis under Mg deficiency. In contrast, exogenous supplementation of KAR1 could not rescue RHL in auxin, ethylene, and NO-related mutants Arabidopsis. In conclusion, we suggest that karrikins signalling might regulate the RHL in response to low Mg by acting as an upstream signalling pathway of auxin, ethylene, and NO signalling.

plant biology↗

bioRxiv2022

Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment

We previously observed increased levels of adenosine-deaminase-acting-on-dsRNA (Adar)-dependent RNA editing during mesothelioma development in mice exposed to asbestos. The aim of this study was to characterize and assess the role of ADAR-dependent RNA editing in mesothelioma. Tumors and mesothelioma primary cultures have higher ADAR-mediated RNA editing compared to mesothelial cells. Unsupervised clustering of editing in different genomic regions revealed heterogeneity between tumor samples as well as mesothelioma primary cultures. ADAR2 expression levels are higher in BRCA1-associated protein 1 wild-type tumors, with corresponding changes in RNA editing in transcripts and 3UTR. ADAR2 knockdown and rescue models indicated a role in cell proliferation, altered cell cycle, increased sensitivity to antifolate treatment and type-1 interferon signaling upregulation, leading to changes in the microenvironment in vivo. Our data indicate that RNA editing contributes to mesothelioma heterogeneity and highlights an important role of ADAR2 not only in growth regulation in mesothelioma but also chemotherapy response, in addition to regulating inflammatory response downstream of sensing nucleic acid structures.

cancer biology↗

bioRxiv2022

Nutrient and moisture limitation reveal keystone metabolites that link switchgrass rhizosphere metabolome and microbiome dynamics

Plants exude large quantities of rhizosphere metabolites that can modulate composition and activity of microbial communities in response to environmental stress. While rhizodeposition dynamics have been associated with rhizosphere microbiome succession, and may be particularly impactful in stressful conditions, specific evidence of these connections has rarely been documented. Here, we grew the bioenergy crop switchgrass (Panicum virgatum) in a marginal soil, under nutrient limited, moisture limited, +nitrogen (N), and +phosphorus (P) conditions, to identify links between rhizosphere chemistry, microbiome dynamics, and abiotic stressors. To characterize links between rhizosphere microbial communities and metabolites, we used 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics. We measured significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of diverse bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions enhanced the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin, ectoine, and acetylcholine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were found in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions. SignificancePlants and microorganisms release metabolites that mediate rhizosphere host-microbe interactions and modulate plant adaptation to environmental stresses. However, the molecular mechanisms that underpin rhizosphere metabolite-microbiome dynamics, their functional relationships, and the biological role of plant- or microbial-produced soil metabolites remain largely unknown. Here, we found the abundances of specific classes of rhizosphere soil metabolites were responsive to abiotic stressors, and also connected to specific shifts in the rhizosphere microbial community and plant phenotypes. We propose a suite of understudied rhizosphere compounds as keystone metabolites that may structure the rhizosphere microbiome and influence plant metabolism in response to nutrient availability. These links between rhizosphere metabolites and microbial communities point to research avenues where we might leverage plant-microbe interactions to engineer enhanced rhizosphere microbiome function, plant and ecosystem health.

microbiology↗

bioRxiv2022

NISNet3D: Three-Dimensional Nuclear Synthesis and Instance Segmentation for Fluorescence Microscopy Images

The primary step in tissue cytometry is the automated distinction of individual cells (segmentation). Since cell borders are seldom labeled, researchers generally segment cells by their nuclei. While effective tools have been developed for segmenting nuclei in two dimensions, segmentation of nuclei in three-dimensional volumes remains a challenging task for which few tools have been developed. The lack of effective methods for three-dimensional segmentation represents a bottleneck in the realization of the potential of tissue cytometry, particularly as methods of tissue clearing present researchers with the opportunity to characterize entire organs. Methods based upon deep-learning have shown enormous promise, but their implementation is hampered by the need for large amounts of manually annotated training data. In this paper we describe 3D Nuclei Instance Segmentation Network (NISNet3D), a deep learning-based approach in which training is accomplished using synthetic data, profoundly reducing the effort required for network training. We compare results obtained from NISNet3D with results obtained from eight existing techniques.

cell biology↗

bioRxiv2022

Regulation of pDC Fate Determination by Histone Deacetylase 3

Dendritic cells (DCs), the key antigen-presenting cells, are primary regulators of immune responses. Transcriptional regulation of DC development had been one of the major research interests in DC biology, however, the epigenetic regulatory mechanisms during DC development remains unclear. Here, we report that Histone deacetylase 3 (Hdac3), an important epigenetic regulator, is highly expressed in pDCs, and its deficiency profoundly impaired the development of pDCs. Significant disturbance of homeostasis of hematopoietic progenitors was also observed in HDAC3-deficient mice, manifested by altered cell numbers of these progenitors and defective differentiation potentials for pDCs. Using the in vitro Flt3L supplemented DC culture system, we further demonstrated that HDAC3 was required for the differentiation of pDCs from progenitors at all developmental stages. Mechanistically, HDAC3 deficiency resulted in enhanced expression of cDC1-associated genes, owing to markedly elevated H3K27 acetylation (H3K27ac) at these gene sites in BM pDCs. In contrast, the expression of pDC-associated genes was significantly downregulated, leading to defective pDC differentiation. SummaryThis work reveals for the first time that HDAC3 is required for the development of pDCs and maintenance of homeostasis of hematopoietic progenitors with DC differentiation potential. Mechanistically, HDAC3 promotes pDC development by repressing the expression of cDC1 associated genes in a deacetylase dependent manner.

immunology↗

bioRxiv2022

FBXO11 deficiency in mice impairs lung development and aggravates cigarette smoke-induced airway fibrosis

Small airway fibrosis is a common pathology of chronic obstructive pulmonary disease (COPD) and contributes to airflow obstruction. However, the underlying fibrogenic mechanism is poorly understood. Epithelial-mesenchymal transition (EMT) has been proposed as a driver of fibrosis. EMT occurs in the airways of COPD patients and smokers, but it remains elusive whether EMT may contribute to airway fibrosis. We previously reported that FBXO11 is a critical suppressor of EMT and Fbxo11 deficiency in mice causes neonatal lethality and EMT in epidermis. Here, we found that Fbxo11-deficient mouse embryonic lungs showed impaired epithelial differentiation, excess fibroblast cells surrounding the airways, and thickened interstitial mesenchyme. We further generated conditional mutant mice to ablate Fbxo11 selectively in the club airway epithelial cells in adult mice, which induced partial EMT in the airways. To determine the effect of EMT on airway fibrosis, Fbxo11 conditional mutant mice were exposed to cigarette smoke. Airway-specific loss of Fbxo11 markedly enhanced smoking-induced airway fibrotic remodeling and collagen deposition. Taken together, our study suggests that EMT in the airway epithelium exacerbates cigarette smoke-induced airway fibrosis.

cell biology↗

bioRxiv2022

CAR-T Engager Proteins Optimize Anti-CD19 CAR-T Cell Therapies for Lymphoma

B cell lymphoma therapy has been transformed by CD19-targeting cellular therapeutics that induce high clinical response rates and impressive remissions in relapsed and refractory patients. However, approximately half of all patients who respond to CD19-directed cell therapy relapse, the majority within six months. One characteristic of relapse is loss or reduction of CD19 expression on malignant B cells. We designed a unique therapeutic to prevent and reverse relapses due to lost or reduced CD19 expression. This novel biologic, a CAR T Engager, binds CD20 and displays the CD19 extracellular domain. This approach increases the apparent CD19 antigen density on CD19-positive/CD20-positive lymphoma cells, and prevents CD19 antigen-oss induced relapse, as CD19 bound to CD20 remains present on the cell surface. We demonstrate that this novel therapeutic prevents and reverses lymphoma relapse in vitro and prevents CD19-negative lymphoma growth and relapse in vivo.

cancer biology↗

bioRxiv2022

Ecological Dynamics Imposes Fundamental Challenges in Microbial Source Tracking

Quantifying the contributions of possible environmental sources ("sources") to a specific microbial community ("sink") is a classical problem in microbiology known as microbial source tracking (MST). Solving the MST problem will not only help us understand how microbial communities were formed, but also have far-reaching applications in pollution control, public health, and forensics. Numerous computational methods, referred to as MST solvers hereafter, have been developed in the past and applied to various real datasets to demonstrate their utility across different contexts. Yet, those MST solvers do not consider microbial interactions and priority effects in microbial communities. Here, we revisit the performance of several representative MST solvers. We show compelling evidence that solving the MST problem using existing MST solvers is impractical when ecological dynamics plays a role in community assembly. In particular, we clearly demonstrate that the presence of either microbial interactions or priority effects will render the MST problem mathematically unsolvable for any MST solver. We further analyze data from fecal microbiota transplantation studies, finding that the state-of-the-art MST solvers fail to identify donors for most of the recipients. Finally, we perform community coalescence experiments to demonstrate that the state-of-the-art MST solvers fail to identify the sources for most of the sinks. Our findings suggest that ecological dynamics imposes fundamental challenges in solving the MST problem using computational approaches.

microbiology↗

bioRxiv2022

DINAVID: A Distributed and Networked Image Analysis System for Volumetric Image Data

BackgroundThe advancement of high content optical microscopy has enabled the acquisition of very large 3D image datasets. Image analysis tools and three dimensional visualization are critical for analyzing and interpreting 3D image volumes. The analysis of these volumes require more computational resources than a biologist may have access to in typical desktop or laptop computers. This is especially true if machine learning tools are being used for image analysis. With the increased amount of data analysis and computational complexity, there is a need for a more accessible, easy-to-use, and efficient network-based/cloud-based 3D image processing system. ResultsThe Distributed and Networked Analysis of Volumetric Image Data (DINAVID) system was developed to enable remote analysis of 3D microscopy images for biologists. DINAVID is a server/cloud-based system with a simple web interface that allows biologists to upload 3D volumes for analysis and visualization. DINAVID is designed using open source tools and has two main sub-systems, a computational system for 3D microscopy image processing and analysis as well as a 3D visualization system. ConclusionsIn this paper, we will present an overview of the DINAVID system and compare it to other tools currently available for microscopy image analysis.

cell biology↗

bioRxiv2022

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson's disease data

BackgroundOpen science and collaboration are necessary to facilitate the advancement of Parkinsons disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities. ObjectiveTo coordinate a virtual hackathon to develop novel PD research tools. Methods49 early career scientists from 12 countries collaborated in a virtual 3-day hackathon event in May 2021, during which they built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. ResultsEach team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. ConclusionHackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early career researchers. The resources generated can be used to accelerate research on the genetics of PD.

genetics↗

bioRxiv2022

An Ensemble Learning and Slice Fusion Strategy for Three-Dimensional Nuclei Instance Segmentation

Automated microscopy image analysis is a fundamental step for digital pathology and computer aided diagnosis. Most existing deep learning methods typically require post-processing to achieve instance segmentation and are computationally expensive when directly used with 3D microscopy volumes. Supervised learning methods generally need large amounts of ground truth annotations for training whereas manually annotating ground truth masks is laborious especially for a 3D volume. To address these issues, we propose an ensemble learning and slice fusion strategy for 3D nuclei instance segmentation that we call Ensemble Mask R-CNN (EMR-CNN) which uses different object detectors to generate nuclei segmentation masks for each 2D slice of a volume and propose a 2D ensemble fusion and a 2D to 3D slice fusion to merge these 2D segmentation masks into a 3D segmentation mask. Our method does not need any ground truth annotations for training and can inference on any large size volumes. Our proposed method was tested on a variety of microscopy volumes collected from multiple regions of organ tissues. The execution time and robustness analyses show that our method is practical and effective.

cell biology↗

bioRxiv2022

Resilience to anxiety and anhedonia after predator scent stress is accompanied by increased nucleus accumbens mGlu5 in female rats

Despite the higher prevalence of post-traumatic stress disorder (PTSD) in women, the majority of preclinical neuroscience research has been conducted utilizing male subjects. We have found that male rats exposed to the predator scent 2,4,5-trimethyl-3-thiazoline (TMT) show heterogenous development of long-term anxiety-like behavior and conditioned fear to the TMT environment. Stress-Resilient males exhibit increased mGlu5 mRNA expression in the basolateral amygdala (BLA) and prefrontal cortex. Here we sought to determine whether the same behavioral and genetic responses would be observed in female rats exposed to TMT. Sprague-Dawley rats were exposed to TMT for ten minutes, while Controls were exposed to an unscented environment. Anxiety and anhedonia were assessed 7-14 days later with elevated plus maze (EPM), acoustic startle response (ASR), light/dark box, and sucrose preference test. TMT-exposed females spent less time in the EPM open arms and exhibited greater startle amplitude, and reduced sucrose intake compared to Controls. Median split analyses conducted on EPM and sucrose intake yielded phenotypes that displayed behavior in the light/dark box consistent with EPM and sucrose testing. Unlike male Susceptible rats, female Susceptible rats showed no freezing when re-exposed to the TMT context, nor did Resilient female rats present elevated BLA mGlu5 mRNA levels. Instead, Susceptible females had greater BLA mGlu5 than Resilient or Control rats. This work indicates that, as in humans, rats exhibit sex-dependent responses to stress. This translational animal model may provide insight into how females are uniquely affected by PTSD.

neuroscience↗

bioRxiv2022

Self-avoidance alone does not explain the function of Dscam1 in mushroom body axonal wiring

Alternative splicing of Drosophila Dscam1 into 38,016 isoforms provides neurons with a unique molecular code for self-recognition and self-avoidance. A canonical model suggests that homophilic binding of identical Dscam1 isoforms on sister branches of mushroom body (MB) axons supports segregation with high fidelity, even when only a single isoform is expressed. Here we generated a series of mutant flies with a single exon 4, 6, or 9 variant, encoding 1,584, 396, or 576 potential isoforms, respectively. Surprisingly, most of the mutants in the latter two groups exhibited obvious defects in the growth, branching, and segregation of MB axonal sister branches. This demonstrates that repertoires of 396 and 576 Dscam1 isoforms were not sufficient for normal patterning of axonal branches. Moreover, reducing Dscam1 levels largely reversed the defects caused by reduced isoform diversity, suggesting a functional link between Dscam1 expression levels and isoform diversity. Taken together, these results indicate that canonical self-avoidance alone does not explain the function of Dscam1 in MB axonal wiring.

neuroscience↗