Biology subjects

Huang, P.

Publications and source records attributed to Huang, P..

At least 163 records · Page 9Linked to original sources

bioRxiv2019

DCT4 - a new member of the dicarboxylate transporter family in C4 grasses.

Malate transport shuttles atmospheric carbon into the Calvin-Benson cycle during NADP-ME C4 photosynthesis. Previous characterizations of several plant dicarboxylate transporters (DCT) showed that they efficiently exchange malate across membranes. Here we identify and characterize a previously unknown member of the DCT family, DCT4, in Sorghum bicolor. We show that SbDCT4 exchanges malate across membranes and its expression pattern is consistent with a role in malate transport during C4 photosynthesis. SbDCT4 is not syntenic to the characterized photosynthetic gene ZmDCT2, and an ortholog is not detectable in the maize reference genome. We found that the expression patterns of DCT family genes in the leaves of Z. mays, and S. bicolor varied by cell type. Our results suggest that sub-functionalization of members of the DCT family for the transport of malate into the bundle sheath (BS) plastids occurred during the process of independent recurrent evolution of C4 photosynthesis in grasses of the PACMAD clade. This study confirms the value of using both syntenic information and gene expression profiles to assign orthology in evolutionarily related genomes.

plant biology↗

bioRxiv2019

Dynamic changes in rhythmic and arrhythmic neural signatures in the subthalamic nucleus induced by anaesthesia and intubation

BackgroundSubcortical structures including the basal ganglia have been proposed to be crucial for arousal, consciousness, and behavioural responsiveness. However, how basal ganglia contributes to the loss and recovery of consciousness during anaesthesia has not been well characterized.\n\nMethodsIn this study, using local field potentials (LFPs) from subthalamic nucleus (STN) and scalp electroencephalogram in 12 Parkinsons disease patients, we investigate STN neural signatures during propofol general anaesthesia and during intubation as an arousal intervention in anaesthesia.\n\nResultsPropofol-induced anaesthesia resulted in changes in multiple frequency bands in STN LFPs, including increased low-frequency activities (slow-wave oscillation, delta, theta, and alpha bands) and decreased higher-frequency activities. This was also accompanied by increased STN-frontal cortical coherence in alpha frequency band. Beta and high-gamma activities in the STN temporally increased during intubation compared to the status of loss of consciousness. We also show that the dynamic changes in the high frequency activities (80-180 Hz) in STN LFPs induced by propofol and intubation correlated with power-law exponent in the power spectra between 2 and 80 Hz.\n\nConclusionsOur findings suggest that anaesthesia and intubation induced changes in the STN LFPs in multiple frequency bands. They are also consistent with the hypothesis that the power-law exponent in the power spectra between 2 and 80 Hz reflect the excitation/inhibition balance in the STN, which is modulated by anaesthesia and intubation, and further modulate the high frequency activity.

neuroscience↗

bioRxiv2019

Large-scale Genetic Analysis Identifies 66 Novel Loci for Asthma

We carried out a genome-wide association study (GWAS) for asthma in UK Biobank, followed by a meta-analysis with results from the Trans-National Asthma Genetic Consortium (TAGC). 66 novel genomic regions were identified, bringing the number of known asthma susceptibility loci to 211. Significant gene-sex interactions were also observed where susceptibility alleles, either individually or as a function of polygenic risk scores, increased asthma risk to a greater extent in men than women. Bioinformatics analyses demonstrated that asthma-associated variants were enriched for colocalizing to regions of open chromatic in immune cells and identified candidate causal genes at 52 of the novel loci, including CD52. An anti-CD52 (-CD52) antibody mimicked the immune cell-depleting effects of an FDA-approved human -CD52 antibody and reduced allergen-induced airway hyperreactivity in mice. These results further elucidate the genetic architecture of asthma, provide evidence that the immune system plays a prominent role in its pathogenesis, and suggest that CD52 represents a potentially novel therapeutic target for treating asthma.

genetics↗

bioRxiv2019

Improved motion correction of submillimetre 7T fMRI time series with boundary-based registration (BBR)

Ultra-high field functional magnetic resonance imaging (fMRI) has allowed us to acquire images with submillimetre voxels. However, in order to interpret the data clearly, we need to accurately correct head motion and the resultant distortions. Here, we present a novel application of Boundary Based Registration (BBR) to realign functional Magnetic Resonance Imaging (fMRI) data and evaluate its effectiveness on a set of 7T submillimetre data, as well as millimetre 3T data for comparison. BBR utilizes the boundary information from high contrast present in structural data to drive registration of functional data to the structural data. In our application, we realign each functional volume individually to the structural data, effectively realigning them to each other. In addition, this realignment method removes the need for a secondary aligning of functional data to structural data for purposes such as laminar segmentation or registration to data from other scanners. We demonstrate that BBR realignment outperforms standard realignment methods across a variety of data analysis methods. Further analysis shows that this benefit is an inherent property of the BBR cost function and not due to the difference in target volume. Our results show that BBR realignment is able to accurately correct head motion in 7T data and can be utilized in preprocessing pipelines to improve the quality of 7T data.

neuroscience↗

bioRxiv2019

The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene

Diverse wild and weedy crop relatives hold genetic variants underlying key evolutionary innovations of crops under domestication. Here, we provide genome resources and probe the genetic basis of domestication traits in green millet (Setaria viridis), a close wild relative of foxtail millet (S. italica). Specifically, we develop and exploit a platinum-quality genome assembly and de novo assemblies for 598 wild accessions to identify loci underlying a) response to climate, b) a key loss of shattering trait that permits mechanical harvest, and c) leaf angle, a major predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLES1) as a novel gene for seed shattering, which is rendered non-functional via a retrotransposon insertion in SiLes1, the domesticated loss-of-shattering allele of S. italica. Together these results and resources project S. viridis as a key model species for complex trait dissection and biotechnological improvement of panicoid crops.

genomics↗

bioRxiv2019

Metronomic capecitabine as an immune modulator in glioblastoma patients reduces myeloid-derived suppressor cells

BackgroundMyeloid-derived suppressor cells (MDSCs) are elevated in glioblastoma (GBM) patient circulation, present in tumor tissue, and associated with poor prognosis. While low-dose chemotherapy reduces MDSCs in preclinical models, the use of this strategy to reduce MDSCs in GBM patients has yet to be evaluated. MethodsA phase 0/1 dose-escalation clinical trial was conducted in recurrent glioblastoma patients treated 5-7 days prior to surgery with low-dose chemotherapy via capecitabine followed by concomitant low-dose capecitabine and bevacizumab. Clinical outcomes, including progression-free and overall survival, were measured, along with safety and toxicity profiles. Over the treatment time course, circulating MDSC levels were measured by multi-parameter flow cytometry, and tumor tissue immune profiles were assessed via mass cytometry time-of-flight. ResultsA total of 11 patients were enrolled across escalating dose cohorts of 150, 300, and 450 mg bid, with a progression-free survival of 5.8 months (range of 1.8-27.8 months) and an overall survival of 11.5 months (range of 3->28.0 months) from trial enrollment. No serious adverse events related to the drug combination were observed. Compared to pre-treatment baseline, circulating MDSCs were found to be higher after surgery in the 150 mg treatment arm and lower in the 300 mg and 450 mg treatment arms. Increased cytotoxic immune infiltration was observed after low-dose capecitabine compared to untreated GBM patients in the 300 mg and 450 mg treatment arms. ConclusionsLow-dose, metronomic capecitabine in combination with bevacizumab is well tolerated in GBM patients and was associated with a reduction in circulating MDSC levels and an increase in cytotoxic immune infiltration into the tumor microenvironment. Trial registrationNCT02669173 FundingThis research was funded by the Cleveland Clinic, Case Comprehensive Cancer Center, Musella Foundation, and B*CURED. Capecitabine was provided in kind by Mylan Pharmaceuticals.

clinical trials↗

bioRxiv2019

The preparation of cyclopentadecanone and cyclopentadecanolide from Malania oleifera Chum oil

The macrocyclic musks are of central importance in the fragrance industry. The preparation of cyclopentadecanone and cyclopentadecanolide from Malania oleifera Chum oil were investigated. Preparation method of cyclopentadecanone is three steps process: first fatty acid double bonds of Malania oleifera Chum oil are cut off by ozonolysis; second ozonides are converted into methyl esters by esterification; afterwards cyclopentadecanone was achieved from through acyloin condensation, reduction and separation with 38.5 % overall yield. The preparation coyfclopentadecanolide is two step process: first by ozonolysis triglycerides of {omega}-hydroxycarboxylic acids synthesized from malania oleifera chum oil by ozonolysis; and it were catalytically transformed to macrocyctic lactones, and a 63% yield of cyclopentadecanolide was obtained. The effect of different ester groups on cyclization of ,{omega}-difatty acid alkyl ester, and effect of catalysts on cyclization of {omega}-hydroxycarboxylic acid triglyceride were investigated.

scientific communication and education↗

bioRxiv2019

A Cys2/His2 zinc finger protein acts as a repressor of gibberellins biosynthesis by regulating SD1/OsGA20ox2 in rice (Oryza sativa L.)

Gibberellins (GAs) play important roles in the regulation of plant growth and development. The green evolution gene SD1 encoding gibberellin 20-oxidase 2 (GA20ox2) has been widely used in modern rice breeding. However, the molecular mechanism of how SD1/OsGA20ox2 expression is regulated remains unclear. Here we report a Cys2/His2 zinc finger protein ZFP207 acting as a transcriptional repressor of OsGA20ox2. ZFP207 was mainly accumulated in young tissues and more specifically in culm nodes. ZFP207-overexpression (ZFP207OE) plants displayed semi-dwarfism phenotype and small grains by modulating cell length. RNA interference of ZFP207 caused higher plant and longer grains. The endogenous bioactive GA levels were significantly reduced in ZFP207OE plants and application of exogenous GA3 rescued the semi-dwarf phenotype. The in vivo and in vitro studies showed that ZFP207 repressed the expression of OsGA20ox2 via binding to its promoter region. Together, ZFP207 acts as a transcriptional repressor of gibberellins biosynthesis and it may play a critical role in plant growth and development through fine-tuning GA biosynthesis in rice.

molecular biology↗

bioRxiv2019

Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition

Higher-order chromatin organization such as A/B compartments, TADs and chromatin loops are temporarily disrupted during mitosis. These structures are thought to organize aspects of gene regulation, and thus it is important to understand how they are re-established after mitosis. We examined the dynamics of chromosome reorganization by Hi-C at defined time points following exit from mitosis in highly purified, synchronous cell populations. We observed that A/B compartments are rapidly established and progressively gain in strength following mitotic exit. Contact domain formation occurs from the \"bottom-up\" with smaller sub-TADs forming initially, followed by convergence into multi-domain TAD structures. CTCF is strongly retained at a significant fraction of sites on mitotic chromosomes and immediately resumes full binding at ana/telophase, the earliest tested time point. In contrast, cohesin is completely evicted from mitotic chromosomes and resumes focal binding with delayed kinetics. The formation of CTCF/cohesin co-anchored structural loops follows the kinetics of cohesin positioning. Stripe-shaped contacts anchored by CTCF grow in length, consistent with a loop extrusion process after mitosis. Interactions between cis-regulatory elements can form rapidly, preceding CTCF/cohesin anchored structural loops. Strikingly, we identified a group of rapidly emerging transient contacts between cis-regulatory elements in ana/telophase, that are dissolved upon G1 entry, co-incident with the establishment of inner boundaries or nearby interfering loops. Our findings indicate that distinct but mutually influential forces drive post-mitotic chromatin re-configuration to shape compartments, contact domains, cis-element contacts, and CTCF/cohesin dependent loops.

genomics↗

bioRxiv2019

iRhom2 serves as a facilitator in obesity by enhancing adipose inflammation and insulin resistance

Chronic inflammation of adipose tissues contributes to obesity-triggered insulin resistance. Unfortunately, the potential molecular mechanisms regarding obesity associated systemic inflammation and metabolic disorder remain complicated. Here we display that inactive rhomboid-like protein 2 (iRhom2) is increased in mice fat with adipose inflammation. After 16 weeks on a high fat diet (HFD), obesity, chronic inflammation in adipose tissues and insulin resistance are markedly mitigated in iRhom2-knockout (iRhom2 KO) mice, but exaggerated in iRhom2-overactivated mice. The adverse impressions of iRhom2 on adipose inflammation and associated pathologies are determined in db/db mice. Also, we further exhibit that in response to HFD, iRhom2 KO mice and mice with deletion only in myeloid cells showed less severe adipose inflammation and insulin resistance than the control groups. Conversely, transplantation of bone marrow cells from normal mice to iRhom2 KO mice unleashed the severity of systemic inflammation and metabolic dysfunction after HFD ingestion. In conclusion, we identify iRhom2 as a key regulator that promotes obesity-associated metabolic disorder. Loss of iRhom2 from macrophages in adipose tissues inhibited the inflammation and insulin resistance. iRhom2 might be a therapeutic target for obesity-induced metabolic dysfunction.\n\nSignificanceIncreased inactive rhomboid-like protein 2 signaling has recently been shown to trigger inflammation-associated activation of innate immune responses. Herein we investigate that this signal also plays a crucial role in obesity-triggered adipose tissue inflammation infiltration and metabolic disorder, beyond the well-known assignment in innate immune supervision. Also, we have reported the iRhom2 as a key promoter in regulating metabolic function, which enhances obesity-stimulated inflammation and systemic insulin resistance by up regulation of macrophages pro-inflammatory activation. Our current study indicates that targeting the iRhom2 signaling in adipose tissues could possibly be an efficient strategy to mitigating obesity-associated systemic inflammation and metabolic dysfunction.

pathology↗

bioRxiv2019

Conduit integrity is compromised during acute lymph node expansion

Lymph nodes (LNs) work as filtering organs, constantly sampling peripheral cues. This is facilitated by the conduit network, a parenchymal tubular-like structure formed of bundles of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo 5-fold expansion with every adaptive immune response and yet these ECM-rich structures are not permanently damaged. Whether conduit integrity and filtering functions are affected during cycles of LN expansion and resolution is not known. Here we show that the conduit structure is disrupted during acute LN expansion but FRC-FRC contacts remain intact. In homeostasis, polarised FRCs adhere to the underlying substrate to deposit ECM ba-solaterally. ECM production by FRCs is regulated by the C-type lectin CLEC-2, expressed by dendritic cells (DCs), at transcriptional and secretory levels. Inflamed LNs maintain conduit size-exclusion, but flow becomes leaky, which allows soluble antigens to reach more antigen-presenting cells. We show how dynamic communication between peripheral tissues and LNs changes during immune responses, and describe a mechanism that enables LNs to prevent inflammation-induced fibrosis. HighlightsO_LIFRCs use polarized microtubule networks to guide matrix deposition C_LIO_LICLEC-2/PDPN controls matrix production at transcriptional and post-transcriptional levels C_LIO_LIFRCs halt matrix production and decouple from conduits during acute LN expansion C_LIO_LIConduits leak soluble antigen during acute LN expansion C_LI

immunology↗

bioRxiv2018

FT/FD-GRF5 repression loop directs growth to increase soybean yield

Major advances in crop yield are eternally needed to cope with population growth. To balance vegetative and reproductive growth plays an important role in agricultural yield. To extend vegetative phase can increase crop yield, however, this strategy risks loss of yield in the field as crops may not mature in time before winter come. Here, we identified a repression feedback loop between GmFTL/GmFDL and GmGRF5-1 (Glycine-max-Flowering-Locus-T/Glycine-max-FDL and Glycine-max-GROWTH-REGULATING-FACTOR5-1), which functions as a pivotal regulator in balancing vegetative and reproductive phases in soybean. GmFTL/GmFDL and GmGRF5-1 directly repress gene expression each other. Additionally, GmGRF5-1 enhances vegetative growth by directly enhancing expression of photosynthesis- and auxin synthesis-related genes. To modulate the loop, such as fine-tuning GmFTL expression to trade-off vegetative and reproductive growth, increases substantially soybean yield in the field. Our findings not only uncover the mechanism balancing vegetative and reproductive growth, but open a new window to improve crop yield.

plant biology↗

bioRxiv2018

Notch signalling maintains Hedgehog responsiveness via a Gli-dependent mechanism during spinal cord patterning in zebrafish

Spinal cord patterning is orchestrated by multiple cell signalling pathways. Neural progenitors are maintained by Notch signalling, whereas ventral neural fates are specified by Hedgehog (Hh) signalling. However, how dynamic interactions between Notch and Hh signalling drive the precise pattern formation is still unknown. We applied the PHRESH (PHotoconvertible REporter of Signalling History) technique to analyse cell signalling dynamics in vivo during zebrafish spinal cord development. This approach reveals that Notch and Hh signalling display similar spatiotemporal kinetics throughout spinal cord patterning. Notch signalling functions upstream to control Hh response of neural progenitor cells. Using gain- and loss-of-function tools, we demonstrate that this regulation occurs not at the level of upstream regulators or primary cilia, but rather at the level of Gli transcription factors. Our results indicate that Notch signalling maintains Hh responsiveness of neural progenitors via a Gli-dependent mechanism in the spinal cord.

developmental biology↗

bioRxiv2018

Heterogeneity of Sonic Hedgehog Response Dynamics and Fate Specification in Single Neural Progenitors

During neural tube patterning, a gradient of Sonic hedgehog (Shh) signaling specifies ventral progenitor fates. The cellular response to Shh is processed through a genetic regulatory network (GRN) to specify distinct fate decisions. This process integrates Shh response level, duration and other inputs and is affected by noise in signaling and cell position. How reliably Shh response profile predicts the fate choice of a single cell is unclear. Here we use live imaging to track neural progenitors in developing zebrafish and quantify both Shh and fate reporters in single cells over time. We found that there is significant heterogeneity between Shh response and fate choice in single cells. We quantitatively modeled reporter intensities to obtain single cell response levels over time and systematically evaluated their correlation with cell fate specification. Motor neuron progenitors (pMN) exhibit a high degree of variability in their Shh responses, which is particularly prominent in the posterior neural tube where the Shh response dynamics are similar to those of the more ventrally fated lateral floor plate cells (LFPs). Our results highlight the precision limit of morphogen-interpretation GRNs in small and dynamic target cell fields.

developmental biology↗

bioRxiv2018

Single cell dynamics of embryonic muscle progenitor cells in zebrafish

Muscle stem cells hold a great therapeutic potential in regenerating damaged muscles. However, the in vivo behavior of muscle stem cells during muscle growth and regeneration is still poorly understood. Using zebrafish as a model, we describe the in vivo dynamics and function of dermomyotome cells, a population of embryonic muscle progenitor cells. Dermomyotome cells are located in a superficial layer external to muscle fibers and express many extracellular matrix (ECM) genes including col1a2. Utilizing a new col1a2 transgenic line, we show that dermomyotome cells display a ramified morphology with dynamic cellular processes. Cell lineage tracing demonstrates that col1a2+ dermomyotome cells contribute to normal muscle growth as well as muscle injury repair. Combination of live imaging and single cell clonal analysis reveals a highly-choreographed process of muscle regeneration. Activated dermomyotome cells change from the quiescent ramified morphology to a polarized and elongated morphology and generate daughter cells that fuse with existing muscle fibers. Ablation of the dermomyotome severely compromises muscle injury repair. Our work provides a dynamic view of embryonic muscle progenitor cells during zebrafish muscle regeneration.\n\nSummary statementLive imaging and single cell clonal analysis reveal dynamic behaviors of zebrafish embryonic muscle progenitor cells in quiescence and activation.

developmental biology↗

bioRxiv2018

Global immune fingerprinting in glioblastoma reveals immune-suppression signatures associated with prognosis

Abstract/SummaryGlioblastoma (GBM) remains uniformly lethal, and, despite a large accumulation of immune cells in the microenvironment, there is limited anti-tumor immune response, even with newly developed immune checkpoint therapies. To overcome these challenges and enhance the efficacy of immunotherapies, a comprehensive understanding of the immune system in GBM and changes during disease progression is required. Here, we integrated multi-parameter flow cytometry and mass cytometry time of flight (CyTOF) analysis of patient blood to determine changes in the immune system among tumor types and over disease progression. Utilizing multi-parameter flow cytometry analysis in a cohort of over 250 patients with brain tumors ranging from benign to malignant primary and metastatic, we found that GBM patients had a significant elevation in myeloid-derived suppressor cells (MDSCs) in blood, but not immunosuppressive T regulatory cells. We validated these findings in GBM patient tissue and found that increased numbers of MDSCs in recurrent GBM portended poor prognosis. CyTOF analysis of peripheral blood from a cohort of newly diagnosed GBM patients revealed that reduction in MDSC frequency over time is accompanied by a concomitant increase in dendritic cells and natural killer cells. This reduced MDSC profile was present in GBM patients with extended survival and was similar to that of low-grade glioma (LGG) patients. Our findings provide a rationale for developing strategies to target MDSCs, which are elevated in GBM patients and predict poor prognosis, either by directly targeting or by shifting the immune profile to induce differentiation toward the immune profile of LGGs.

cancer biology↗

bioRxiv2018

Prospective Motion correction improves the sensitivity of fMRI pattern decoding

We evaluated the effectiveness of prospective motion correction (PMC) on a simple visual task when no deliberate subject motion was present. The PMC system utilizes an in-bore optical camera to track an external marker attached to the participant via a custom-moulded mouthpiece. The study was conducted at two resolutions (1.5mm vs 3mm) and under three conditions (PMC On and Mouthpiece On vs PMC Off and Mouthpiece On vs PMC Off and Mouthpiece Off). Multiple data analysis methods were conducted, including univariate and multivariate approaches, and we demonstrated that the benefit of PMC is most apparent for multi-voxel pattern decoding at higher resolutions. Additional testing on two participants showed that our inexpensive, commercially available mouthpiece solution produced comparable results to a dentist-moulded mouthpiece. Our results showed that PMC is increasingly important at higher resolutions for analyses that require accurate voxel registration across time.

neuroscience↗

bioRxiv2018

Functional repair after ischemic injury through high efficiency in situ astrocyte-to-neuron conversion

Mammalian brains have largely lost internal neural regeneration capability except for a few discrete neurogenic niches. After brain injury, the cerebral cortex is especially difficult to repair due to its extremely low rate of adult neurogenesis. Previous studies have converted glial cells into neurons, but the total number of neurons generated is rather limited, casting doubt about its therapeutic potential. Here, we demonstrate that high-efficiency neuroregeneration can be achieved in adult mammalian brains by making use of an engineered AAV Cre-FLEX system to convert a large number of reactive astrocytes into functional neurons. Specifically, using a combination of GFAP::Cre and FLEX-NeuroD1 AAV system, we were able to regenerate enough new neurons from astrocytes to cover about 40% of the neurons lost from an ischemic injury (400 NeuN+ new neurons/mm2), compared to previously reported an average of <1% of cortical neurons (2-8 NeuN+ neurons/mm2) in an ischemic-injured adult mammalian cortex. Importantly, this in situ astrocyte-to-neuron conversion process also improved survival of injured pre-existing neurons, (additional 400 neurons/mm2), leading to a repaired motor cortex with layered cortical structures. Moreover, NeuroD1-converted neurons not only form functional neural circuits but also rescue motor and memory deficits after ischemic injury. Our results establish the proof-of-principle that a highly efficient in situ astrocyte-to-neuron conversion approach provides a novel treatment for neurological disorders that are in need of new neurons.

neuroscience↗