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Zhu, F.

Publications and source records attributed to Zhu, F..

At least 73 records · Page 4Linked to original sources

An anti-steatosis response regulated by oleic acid through lipid droplet-mediated ERAD enhancement

Although excessive lipid accumulation is a hallmark of obesity-related pathologies, some lipids are beneficial. Oleic acid (OA), the most abundant monounsaturated fatty acid (FA), promotes health and longevity. Here we show that OA benefits C. elegans by activating the endoplasmic reticulum (ER)-resident transcription factor SKN-1A (Nrf1/NFE2L1) in a lipid homeostasis response. SKN-1A/Nrf1 is cleared from the ER by the ER-associated degradation (ERAD) machinery and stabilized when proteasome activity is low, and canonically maintains proteasome homeostasis. Unexpectedly, OA increases nuclear SKN-1A levels independently of proteasome activity, through lipid droplet (LD)-mediated enhancement of ERAD. In turn, SKN-1A reduces steatosis by reshaping the lipid metabolism transcriptome, and mediates longevity from OA provided through endogenous accumulation, reduced H3K4 trimethylation, or dietary supplementation. Our findings reveal a surprising mechanism of FA signal transduction, and a lipid homeostasis pathway that provides strategies for opposing steatosis and aging, and may mediate benefits of the OA-rich Mediterranean diet.

cell biology↗

Systemic pesticides in a solitary bee pollen food store affect larval development and increase pupal mortality

Solitary bees are often exposed to various pesticides applied for pest control on farmland while providing pollination services to food crops1. Increasing evidence suggests that sublethal toxicity of agricultural pesticides affects solitary bees differently than the social bees used to determine regulatory thresholds like honey bees and bumblebees2-4. Studies on solitary bees are challenging because of the difficulties in obtaining large numbers of eggs or young larvae for bioassays. Here we show the toxic and sublethal developmental effects of four widely used plant systemic pesticides on the Japanese orchard bee (Osmia cornifrons). Pollen food stores of this solitary bee were treated with different concentrations of three insecticides (acetamiprid, flonicamid, and sulfoxaflor) and a fungicide (dodine). Eggs were transplanted to the treated pollen and larvae were allowed to feed on the pollen stores after egg hatch. The effects of chronic ingestion of contaminated pollen were measured until adult eclosion. This year-long study revealed that chronic exposure to all tested pesticides delayed larval development and lowered larval and adult body weights. Additionally, exposure to the systemic fungicide resulted in abnormal larval defecation and increased mortality at the pupal stage, indicating potential risk to bees from fungicide exposure. These findings demonstrate potential threats to solitary bees from systemic insecticides and fungicides and will help making policy decisions for mitigating these effects.

ecology↗

A parallel channel of state-dependent sensory signaling from the cholinergic basal forebrain to the auditory cortex

Cholinergic basal forebrain (CBF) signaling exhibits multiple timescales of activity with classic, slow signals related to brain and behavioral states and faster, phasic signals reflecting behavioral events, including movement and reinforcement. Recent evidence suggests that the CBF may also exhibit fast, sensory-evoked responses. It remains unknown, however, whether such sensory signals target the sensory cortex and how they relate to local functional topography. Moreover, the extent to which fast and slow CBF activity interact has been largely unexplored. Here, we used simultaneous two-channel, two-photon imaging of CBF axons and auditory cortical (AC) neurons to reveal that CBF axons project a robust, non-habituating, and stimulus-specific sensory signal to the AC. Individual axon segments exhibited heterogeneous but stable tuning to auditory stimuli allowing stimulus identity to be decoded from the population. However, CBF axons displayed no tonotopy and their frequency tuning was uncoupled from that of nearby cortical neurons. Chemogenetic suppression revealed the auditory thalamus as a principal source of auditory information to the CBF. Finally, slow fluctuations in cholinergic activity modulated the fast, sensory-evoked signals in the same axons, suggesting that a multiplexed combination of fast and slow signals is projected from the CBF to the AC. Taken together, our work demonstrates a novel, non-canonical function of the CBF as a parallel channel of state-dependent sensory signaling to the sensory cortex that provides repeated representations of a broad range of sound stimuli at all points on the tonotopic map.

neuroscience↗

SARS-COV-2 Omicron variant predicted to exhibit higher affinity to ACE-2 receptor and lower affinity to a larger range of neutralizing antibodies, using a rapid assessment platform

Rapid assessment of whether a pandemic pathogen may have increased transmissibility or be capable of evading existing vaccines and therapeutics is critical to mounting an effective public health response. Over the period of seven days, we utilized rapid computational prediction methods to evaluate potential public health implications of the emerging SARS-CoV-2 Omicron variant. Specifically, we modeled the structure of the Omicron variant, examined its interface with human angiotensin converting enzyme 2 (ACE-2) and evaluated the change in binding affinity between Omicron, ACE-2 and publicly known neutralizing antibodies. We also compared the Omicron variant to known Variants of Concern (VoC). Seven of the 15 Omicron mutations occurring in the spike protein receptor binding domain (RBD) occur at the ACE-2 cell receptor interface, and therefore may play a critical role in enhancing binding to ACE-2. Our estimates of Omicron RBD-ACE-2 binding affinities indicate that at least two of RBD mutations, Q493R and N501Y, contribute to enhanced ACE-2 binding, nearly doubling delta-delta-G (ddG) free energies calculated for other VoCs. Binding affinity estimates also were calculated for 55 known neutralizing SARS-CoV-2 antibodies. Analysis of the results showed that Omicron substantially degrades binding for more than half of these neutralizing SARS-CoV-2 antibodies, and for roughly 10 times as many of the antibodies than the currently dominant Delta variant. This early study lends support to use of rapid computational risk assessments to inform public health decision-making while awaiting detailed experimental characterization and confirmation.

bioinformatics↗

A deep learning framework for inference of single-trial neural population activity from calcium imaging with sub-frame temporal resolution

In many brain areas, neural populations act as a coordinated network whose state is tied to behavior on a moment-by-moment basis and millisecond timescale. Two-photon (2p) calcium imaging is a powerful tool to probe network-scale computation, as it can measure the activity of many individual neurons, monitor multiple cortical layers simultaneously, and sample from identified cell types. However, estimating network state and dynamics from 2p measurements has proven challenging because of noise, inherent nonlinearities, and limitations on temporal resolution. Here we describe RADICaL, a deep learning method to overcome these limitations at the population level. RADICaL extends methods that exploit dynamics in spiking activity for application to deconvolved calcium signals, whose statistics and temporal dynamics are quite distinct from electrophysiologically-recorded spikes. It incorporates a novel network training strategy that capitalizes on the timing of 2p sampling to recover network dynamics with high temporal precision. In synthetic tests, RADICaL infers network state more accurately than previous methods, particularly for high-frequency components. In real 2p recordings from sensorimotor areas in mice performing a "water grab" task, RADICaL infers network state with close correspondence to single-trial variations in behavior, and maintains high-quality inference even when neuronal populations are substantially reduced.

neuroscience↗

Selective Vulnerability of Tripartite Synapses in Amyotrophic Lateral Sclerosis.

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder. Separate lines of evidence suggest that synapses and astrocytes play a role in the pathological mechanisms underlying ALS. Given that astrocytes make specialised contacts with some synapses, called tripartite synapses, we hypothesise that tripartite synapses could act as the fulcrum of disease in ALS. To test this hypothesis, we have performed an extensive microscopy-based investigation of synapses and tripartite synapses in the spinal cord of ALS model mice and post-mortem human tissue from ALS cases. We reveal widescale synaptic changes at the early symptomatic stages of the SOD1G93a mouse model. Super-resolution microscopy reveals that large complex postsynaptic structures are lost in ALS mice. Most surprisingly, tripartite synapses are selectively lost while non-tripartite synapses remain in equal number to healthy controls. Finally, we also observe a similar selective loss of tripartite synapses in human post-mortem ALS spinal cords. From these data we conclude that tripartite synaptopathy is a key hallmark of ALS.

neuroscience↗

Calcium-independent but voltage-dependent secretion (CiVDS) mediates synaptic transmission in a mammalian central synapse

A central principle of synaptic transmission is that action potential-induced presynaptic neurotransmitter release occurs exclusively via Ca2+-dependent secretion (CDS). The discovery and mechanistic investigations of Ca2+-independent but voltage-dependent secretion (CiVDS) have demonstrated that the action potential per se is sufficient to trigger neurotransmission in the somata of primary sensory and sympathetic neurons in mammals. One key question remains, however, whether CiVDS contributes to central synaptic transmission. Here we report, in the central transmission from presynaptic (dorsal root ganglion) to postsynaptic (spinal dorsal horn) neurons, (1) excitatory postsynaptic currents (EPSCs) are mediated by glutamate transmission through both CiVDS (up to 87%) and CDS; (2) CiVDS-EPSCs are independent of extracellular and intracellular Ca2+; (3) CiVDS is >100 times faster than CDS in vesicle recycling with much less short-term depression; (4) the fusion machinery of CiVDS includes Cav2.2 (voltage sensor) and SNARE (fusion pore). Together, an essential component of activity-induced EPSCs is mediated by CiVDS in a central synapse.

neuroscience↗

Structure and function of one unclassified-class glutathione S-transferase in Leptinotarsa decemlineata

Arthropod Glutathione S-transferases (GSTs) constitute a large family of multifunctional enzymes that are mainly associated with xenobiotic or stress adaptation. GST-mediated xenobiotic adaptation is through direct metabolism or sequestration of xenobiotics, and/or indirectly by providing protection against oxidative stress induced by xenobiotic exposure. To date, the roles of GSTs in xenobiotic adaptation in the Colorado potato beetle (CPB), a notorious agriculture pest of plants within Solanaceae have not been well studied. Here, we functionally expressed and characterized an unclassified-class GST, LdGSTu1. The three-dimensional structure of the LdGSTu1 was solved with a resolution up to 1.8 [A] by x-ray crystallography. Recombinant LdGSTu1 was used to determine enzyme activity and kinetic parameters using 1-chloro-2,4-dinitrobenzene (CDNB), GSH, p-nitrophenyl acetate (PNA) as substrates. The enzyme kinetic parameters and enzyme-substrate interaction studies demonstrated that LdGSTu1 could catalyze the conjugation of GSH to both CDNB and PNA, with a higher turnover number for CDNB than PNA. The LdGSTu1 enzyme inhibition assays demonstrated that the enzymatic conjugation of GSH to CDNB could be inhibited by multiple pesticides, suggesting a potential function of LdGSTu1 in xenobiotic adaptation.

biophysics↗

Sequence determinants of human gene regulatory elements

DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. To obtain a global and unbiased view of the relative importance of different sequence determinants in gene expression, we measured transcriptional activity of DNA sequences that are in aggregate [~]100 times longer than the human genome in three different cell types. We show that enhancers can be classified to three main types: classical enhancers1, closed chromatin enhancers and chromatin-dependent enhancers, which act via different mechanisms and differ in motif content. Transcription factors (TFs) act generally in an additive manner with weak grammar, with classical enhancers increasing expression from promoters by a mechanism that does not involve specific TF-TF interactions. Few TFs are strongly active in a cell, with most activities similar between cell types. Chromatin-dependent enhancers are enriched in forkhead motifs, whereas classical enhancers contain motifs for TFs with strong transactivator domains such as ETS and bZIP; these motifs are also found at transcription start site (TSS)-proximal positions. However, some TFs, such as NRF1 only activate transcription when placed close to the TSS, and others such as YY1 display positional preference with respect to the TSS. TFs can thus be classified into four non-exclusive subtypes based on their transcriptional activity: chromatin opening, enhancing, promoting and TSS determining factors - consistent with the view that the binding motif is the only atomic unit of gene expression.

genomics↗

The molecular infrastructure of glutamatergic synapses in the mammalian forebrain

Glutamatergic synapses form the vast majority of connections within neuronal circuits, but how these subcellular structures are molecularly organized within the mammalian brain is poorly understood. Conventional electron microscopy using chemically fixed, metal- stained tissue has identified a proteinaceous, membrane-associated thickening called the postsynaptic density (PSD). Here, we combined mouse genetics and cryo-electron tomography to determine the 3D molecular architecture of fresh isolated and anatomically intact synapses in the adult forebrain. The native glutamatergic synapse did not consistently show a higher density of proteins at the postsynaptic membrane thought to be characteristic of the PSD. Instead, a synaptoplasm consisting of cytoskeletal elements, macromolecular complexes and membrane-bound organelles extended throughout the pre- and post- synaptic compartments. Snapshots of active processes gave insights into membrane remodeling processes. Clusters of up to 60 ionotropic glutamate receptors were positioned inside and outside the synaptic cleft. Together, these information-rich tomographic maps present a detailed molecular framework for the coordinated activity of synapses in the adult mammalian brain.

neuroscience↗

NOMA: a high-throughput microchip for robust sequential measurements of secretions from the same single-cells

Despite recent advances in single-cell analysis technologies, lacking simple methods to keep the live single-cells traceable for longitudinal detection reliably poses a significant obstacle in single-cell secretion analysis. Here we reported the high-density NOMA (narrow-opening microwell array) microchip that realized the retention of[≥] 97% of trapped single cells in dedicated spatial locations during repetitive detection procedures, verified with both adherent and suspension cells by two researchers independently. We applied it in monitoring single-cell protein secretions sequentially from the same single cells, and we found the digital protein secretion patterns dominate the protein secretion. We also demonstrated the microchip for longitudinally tracking IL-8 and the CD81+EV secretions from the same single-cells over days, which revealed the presence of "super secretors" within the cell population be more persistent to secrete protein or extracellular vesicle for an extended period. The NOMA platform reported here is simple, robust, and easy to operate for tracking sequential measurements from the same single cells, representing a novel and informative tool to inspire new observations in biomedical research. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/427049v4_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@aa69c7org.highwire.dtl.DTLVardef@6bc79org.highwire.dtl.DTLVardef@3fcbbforg.highwire.dtl.DTLVardef@597f4b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

ATGs ubiquitination is required for circumsporozoite protein to subvert host innate immunity against malaria liver stage

Although exoerythrocytic forms (EEFs) of liver stage malaria parasite in parasitophorous vacuole (PV) encountered with robust host innate immunity, EEFs can still survive and successfully complete infection of hepatocytes, and the underlying mechanism is largely unknown. Here, we showed that sporozoite circumsporozoite protein (CSP) translocated from the parasitophorous vacuole into the hepatocyte cytoplasm significantly inhibited the killing of exo-erythrocytic forms (EEFs) by interferon-gamma (IFN-{gamma}). Attenuation of IFN-{gamma}-mediated killing of EEFs by CSP was dependent on its ability to reduce the levels of autophagy-related genes (ATGs) in hepatocytes. The ATGs downregulation occurred through its enhanced ubiquitination mediated by E3 ligase NEDD4, an enzyme that was upregulated by CSP when it translocated from the cytoplasm into the nucleus of hepatocytes via its nuclear localization signal (NLS) domain. Thus, we have revealed an unrecognized role of CSP in subverting host innate immunity and shed new light for a prophylaxis strategy against liver-stage infection.

microbiology↗

Unveiling unexpected complexity and multipotentiality of early heart fields

Complex organs are composed of a multitude of specialized cell types which assemble to form functional biological structures. How these cell types are created and organized remains to be elucidated for many organs including the heart, the first organ to form during embryogenesis. Here, we show the ontogeny of mammalian mesoderm at high-resolution single cell and genetic lineage/clonal analyses, which revealed an unexpected complexity of the contribution and multi-potentiality of mesodermal progenitors to cardiac lineages creating distinct cell types forming specific regions of the heart. Single-cell transcriptomics of Mesp1 lineage-traced cells during embryogenesis and corresponding trajectory analyses uncovered unanticipated developmental relationships between these progenitors and lineages including two mesodermal progenitor sources contributing to the first heart field (FHF), an intraembryonic and a previously uncharacterized extraembryonic-related source, that produce distinct cardiac lineages creating the left ventricle. Lineage-tracing studies revealed that these extraembryonic-related FHF progenitors reside at the extraembryonic-intraembryonic interface in gastrulating embryos and generate cardiac cell types that form the epicardium and the dorsolateral regions of the left ventricle and atrioventricular canal myocardium. Clonal analyses further showed that these progenitors are multi-potent, creating not only cardiomyocytes and epicardial cell types but also extraembryonic mesoderm. Overall, these results reveal unsuspected multiregional origins of the heart fields, and provide new insights into the relationship between intraembryonic cardiac lineages and extraembryonic tissues and the associations between congenital heart disease and placental insufficiency anomalies.

developmental biology↗

ERK signaling licenses SKN-1A/NRF1 for proteasome production and proteasomal stress resistance

The ubiquitin-proteasome system is vital for cell growth and homeostasis, but for most cancers proteasomal inhibition has not been effective as a therapy. Normal and cancer cells adapt to proteasomal stress through an evolutionarily conserved recovery response, in which the transcription factor NRF1 upregulates proteasome subunit genes. Starting with a C. elegans screen to identify regulators of the recovery response, here we show that this response depends upon phosphorylation of NRF1 on a single residue by the growth factor-activated kinase ERK1/2. Inhibition of this phosphorylation impairs NRF1 nuclear localization and proteasome gene activation, sensitizes C. elegans and cancer cells to proteasomal stress, and synergizes with proteasome inhibition to retard human melanoma growth in vivo in a mouse model. The evolutionarily conserved ERK1/2-NRF1 axis couples proteasome production to growth signaling, and represents a promising new strategy for expanding the range and efficacy of proteasomal inhibition therapy in cancer.

cell biology↗

Silencing NADPH-Cytochrome P450 reductase affects imidacloprid susceptibility, fecundity, and embryonic development in Leptinotarsa decemlineata

The Colorado potato beetle (CPB) is a prominent insect pest of potatoes, tomatoes and eggplants all over the world, however, the management of CPB remains a challenging task for more than one hundred years. We have successfully developed bacteria-expressed dsRNA-mediated feeding RNA interference (RNAi) approach in our previous study. A critical step towards field management of CPB via feeding RNAi is to identify effective and environmentally safe target genes. NADPH-Cytochrome P450 reductase (CPR) plays a central role in cytochrome P450 action. The full length Leptinotarsa decemlineata CPR (LdCPR) cDNA was isolated from an imidacloprid resistant population. The LdCPR gene was ubiquitously expressed in all stages tested but showed an increase in expression during the early stage of embryonic development. The bacteria-expressed dsRNA-mediated feeding RNAi of LdCPR in adults caused systemic knock down expression of the gene coding for LdCPR in both adults and their eggs. Suppression of LdCPR expression increased susceptibility of imidacloprid in resistant beetles, as well as a significant decrease of fecundity in female beetles (29% less eggs/day) and the hatching rate (47%) of their eggs. These data suggest that LdCPR plays important roles in insecticide detoxification and biosynthetic pathways of endogenous compounds and may serve as an essential target to control CPB. HIGHLIGHTSO_LIHigh expression of LdCPR was observed in the egg stage. C_LIO_LISilencing of LdCPR reduced the CPR enzymatic activities. C_LIO_LILdCPR knockdown increased imidacloprid susceptibility. C_LIO_LILdCPR knockdown decreased the fecundity and enhanced embryonic lethality. C_LI

pharmacology and toxicology↗

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

BackgroundCis-regulatory elements such as enhancers and promoters are crucial for directing gene expression in the human heart. Dysregulation of these elements can result in many cardiovascular diseases that are major leading causes of morbidity and mortality worldwide. In addition, genetic variants associated with cardiovascular disease risk are enriched within cis-regulatory elements. However, the location and activity of these cis-regulatory elements in individual cardiac cell types remains to be fully defined. MethodsWe performed single nucleus ATAC-seq and single nucleus RNA-seq to define a comprehensive catalogue of candidate cis-regulatory elements (cCREs) and gene expression patterns for the distinct cell types comprising each chamber of four non-failing human hearts. We used this catalogue to computationally deconvolute dynamic enhancers in failing hearts and to assign cardiovascular disease risk variants to cCREs in individual cardiac cell types. Finally, we applied reporter assays, genome editing and electrophysiogical measurements in in vitro differentiated human cardiomyocytes to validate the molecular mechanisms of cardiovascular disease risk variants. ResultsWe defined >287,000 candidate cis-regulatory elements (cCREs) in human hearts at single-cell resolution, which notably revealed gene regulatory programs controlling specific cell types in a cardiac region/structure-dependent manner and during heart failure. We further report enrichment of cardiovascular disease risk variants in cCREs of distinct cardiac cell types, including a strong enrichment of atrial fibrillation variants in cardiomyocyte cCREs, and reveal 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Two such risk variants residing within a cardiomyocyte-specific cCRE at the KCNH2/HERG locus resulted in reduced enhancer activity compared to the non-risk allele. Finally, we found that deletion of the cCRE containing these variants decreased KCNH2 expression and prolonged action potential repolarization in an enhancer dosage-dependent manner. ConclusionsThis comprehensive atlas of human cardiac cCREs provides the foundation for not only illuminating cell type-specific gene regulatory programs controlling human hearts during health and disease, but also interpreting genetic risk loci for a wide spectrum of cardiovascular diseases.

genomics↗

PhenoImage: an open-source GUI for plant image analysis

High-throughput genotyping coupled with molecular breeding approaches has dramatically accelerated crop improvement programs. More recently, improved plant phenotyping methods have led to a shift from manual measurements to automated platforms with increased scalability and resolution. Considerable effort has also gone into the development of large-scale downstream processing of the imaging datasets derived from high-throughput phenotyping (HTP) platforms. However, most available tools require some programing skills. We developed PhenoImage - an open-source GUI based cross-platform solution for HTP image processing with the aim to make image analysis accessible to users with either little or no programming skills. The open-source nature provides the possibility to extend its usability to meet user-specific requirements. The availability of multiple functions and filtering parameters provides flexibility to analyze images from a wide variety of plant species and platforms. PhenoImage can be run on a personal computer as well as on high-performance computing clusters. To test the efficacy of the application, we analyzed the LemnaTec Imaging system derived RGB and fluorescence shoot images from two plant species: sorghum and wheat differing in their physical attributes. In the study, we discuss the development, implementation, and working of the PhenoImage. HighlightPhenoImage is an open-source application designed for analyzing images derived from high-throughput phenotyping.

plant biology↗

Loss-of-function of Fbxo10, encoding a post-translational regulator of BCL2 in lymphomas, has no discernible effect on BCL2 or B lymphocyte accumulation in mice

Regulation of the anti-apoptotic BCL2 protein determines cell survival and is frequently abnormal in B cell lymphomas. An evolutionarily conserved post-translational mechanism for over-expression of BCL2 in human B cell lymphomas and the BCL2 paralogue CED-9 in Caenorhabditis elegans results from loss-of-function mutations in human FBXO10 and its C.elegans paralogue DRE-1, a BCL2/CED-9-binding subunit of the SKP-CULLIN-FBOX (SCF) ubiquitin ligase. Here, we tested the role of FBXO10 in BCL2 regulation by producing mice with two different CRISPR/Cas9-engineered Fbxo10 mutations: an Asp54Lys (E54K) missense mutation in the FBOX domain and a Cys55SerfsTer55 frameshift (fs) truncating mutation. Mice homozygous for either mutant allele were born at the expected Mendelian frequency and appeared normal in body weight and appearance as adults. Spleen B cells from homozygous mutant mice did not have increased BCL2 protein, nor were the numbers of mature B cells or germinal centre B cells increased as would be expected if BCL2 was increased. Other lymphocyte subsets that are also regulated by BCL2 levels also displayed no difference in frequency in homozygous Fbxo10 mutant mice. These results support one of two conclusions: either FBXO10 does not regulate BCL2 in mice, or it does so redundantly with other ubiquitin ligase complexes. Possible candidates for the latter include FBXO11 or ARTS-XIAP. The difference between the role of FBXO10 in regulating BCL2 protein levels in C. elegans and in human DLBCL, relative to single-gene deficient mouse leukocytes, should be further investigated.

immunology↗