Biology subjects

Lu, W.

Publications and source records attributed to Lu, W..

At least 127 records · Page 7Linked to original sources

bioRxiv2022

Genetic and peripheral visual system changes underlie evolving butterfly mate preference

Many studies have linked genetic variation to behavior, but less is known about how that variation alters the neural circuits that drive behavior. We investigated the genetic and neurobiological basis of courtship preference variation in Heliconius butterflies, which use vision to identify appropriate mates based on wing color patterns. We found that Heliconius cydno preference variation was strongly associated with genetic variation and differential expression of senseless-2, a gene predominantly expressed in the eye. Further measurements of photoreceptor sensitivities revealed differences in inter-photoreceptor inhibition of ultraviolet-sensitive cells corresponding to courtship preference variation. Our results reveal a genetic basis for preference/cue co-evolution, suggest a link between sens-2 and visual system variation, and support the idea that changing peripheral neural computations can significantly alter essential behaviors. SummaryGenetic and expression variation of senseless-2 and inter-photoreceptor inhibition predict visual mate preference in a clade of diverse butterflies.

evolutionary biology↗

bioRxiv2022

Study on the interference of DicdsVg4 and DicdsVgR in egg formation in the ovary of Diaphorina citri (Kuwayama)

The ovary is the key organ in insect female oviposition. For the continuation of populations in nature, the whole life cycle of female adults is centred on reproduction. Vg and VgR genes are important in determining the synthesis and transport of vitellogenin. Therefore, Vg and VgR gene expression in insect females affects the formation of mature eggs in the ovary, which is very important. RNAi interference of Vg and VgR genes may become an important means to control D. citri populations. A study found that the expression of the DicVg4 and DicVgR genes was significantly affected by DicdsVg4 and DicdsVgR. DicVg4 and DicVgR gene expression interference could prevent the accumulation of vitellogenin in the ovaries of females, rendering ovaries unable to form mature eggs normally and leading to the production of abnormal eggs and nymphs. After knockdown of DicVg4 and DicVgR gene expression, the proportion of ovarian mature eggs was only 8.33 {+/-} 1.67% and 7.75 {+/-} 0.5% in the 10-d developmental stage, the proportion of negative control group ovarian mature eggs was 13.19 {+/-} 0.14% in the 10-d developmental stage, and the proportion of ovarian mature eggs in the interference group was 0.00 {+/-} 0.00% in the 5, 15, 20, 25, and 30-d developmental stages. These results provide a theoretical basis for the use of mixed polygene interference technology to control damage from D. citri populations.

biochemistry↗

bioRxiv2022

Piezo mechanosensory channels regulate centrosome integrity

Piezo1 and 2 are evolutionarily conserved mechanosensory cation channels known to function on the cell surface by responding to external pressure and transducing a mechanically activated Ca2+ current. Here we show that both Piezo1 and 2 also exhibit concentrated intracellular localization at centrosomes. Both Piezo1 and 2 loss-of-function and Piezo1 activation by the small molecule Yoda1 produced supernumerary centrosomes due to inappropriate centriole disengagement. Using a centrosome-localized GCaMP Ca2+-sensitive reporter, we show that perturbations in Piezo modulate Ca2+ local concentration at centrosomes. We designed a photoactivable Yoda1 analog (caged-Yoda1) and revealed that its photoactivation specifically at centrosomes leads to rapid premature centriole disengagement within minutes. We identified the sorting nexin Snx5, which is involved in endocytic uptake and trafficking, as a protein-interactor with the conserved Piezo C-terminal domain, and Snx5 also co-localizes with Piezo1 and 2 at centrosomes. Moreover, inhibition of Polo-like-kinase 1 (PLK1) abolishes Yoda1-induced centriole disengagement. Collectively, these data suggest that Piezo1 and 2 in pericentrosomal endosomes control centrosome integrity, likely by maintaining local Ca2+ within a defined range through mechanotransduction of cell intrinsic forces from microtubules.

cell biology↗

bioRxiv2022

Shisa7-dependent regulation of GABAA receptor single-channel gating kinetics

GABAA receptors (GABAARs) mediate the majority of fast inhibitory transmission throughout the brain. Although it is widely known that pore-forming subunits critically determine receptor function, it is unclear whether their single-channel properties are modulated by GABAAR-associated transmembrane proteins. We previously identified Shisa7 as a GABAAR auxiliary subunit that modulates the trafficking, pharmacology, and kinetic properties of these receptors. In particular, Shisa7 accelerates receptor deactivation; however, the underlying mechanisms by which Shisa7 controls GABAAR kinetics have yet to be determined. Here we have performed single-channel recordings and find that while Shisa7 does not change channel slope conductance, it reduces the frequency of openings. Importantly, Shisa7 modulates GABAAR gating by decreasing the duration and open probability (Po) within bursts. Kinetic analysis of dwell times, activation modeling, and macroscopic simulations indicate that Shisa7 accelerates GABAAR deactivation by governing the time spent between close and open states during gating. Together, our data provide a mechanistic basis for how Shisa7 controls GABAAR gating kinetics and reveal for the first time that GABAAR single-channel properties can be modulated by an auxiliary subunit. These findings shed light on processes that shape the temporal dynamics of GABAergic transmission.

neuroscience↗

bioRxiv2022

An intergeneric recombinant geminivirus causes soybean stay-green disease

Soybean is one of the most valuable legume crops in the world with high nutritional value. Recently, the outbreak of soybean stay-green syndrome has swept the soybean production in the Huang-Huai-Hai region of China, resulting in huge yield losses, which has become an epidemic and prominent problem in soybean production. However, the cause of the stay-green syndrome remains obscure. Here, we report a novel intergeneric recombinant geminivirus which causes soybean stay-green symptoms. Viral small RNA-based screening identified a new recombinant geminvirus from field soybean stay-green samples. The complete genome sequence of the virus contains 2762 nucleotide (nt) and appears to be an intergeneric recombinant virus in which protein coding for coat protein (V1) is similar to member of genus Mastrevirus, whereas proteins coding for V2, C2, C3 are most similar to those of viruses in the Maldovirus genus, and C1 and C4 are most similar to virus in genus Begomovirus. Inoculation of the infectious clone of the recombinant geminivirus through Agrobacterium rhizogenes causes typical soybean stay-green syndrome which resembles field symptoms including delayed leaf senescence, flat pods and abnormal seeds. The recombinant geminivirus can be detected in seed coat but not in cotyledon and embryo, thus failing to be transmitted by seeds. Moreover, the genome variation and epidemiological dynamic analysis were also carried out to help the continuous epidemiological surveillance of this emerging geminivirus. Collectively, this new geminivirus is tentatively named soybean stay-green associated virus (SoSGV). Our determination of the causal agent of soybean stay-green disease will bolster efforts to develop effective management strategies to control this prevalent disease in the field.

microbiology↗

bioRxiv2022

Harringtonine has the effects of double blocking SARS-CoV-2 membrane fusion

Fusion with host cell membrane is the main mechanism of infection of SARS-CoV-2. Here, we propose a new strategy to double block SARS-CoV-2 membrane fusion by using Harringtonine (HT), a small-molecule antagonist. By using cell membrane chromatography (CMC), we found that HT specifically targeted the SARS-CoV-2 S protein and host cell TMPRSS2, and then confirmed that HT can inhibit pseudotyped virus membrane fusion. Furthermore, HT successfully blocked SARS-CoV-2 infection, especially in the delta and Omicron mutant. Since HT is a small-molecule antagonist, it is minimally affected by the continuous variation of SARS-CoV-2. Our findings show that HT is a potential small-molecule antagonist with a new mechanism of action against SARS-CoV-2 infection, and thus HT mainly targets the S protein, and thus, greatly reduces the damage of the S proteins autotoxicity to the organ system, has promising advantages in the clinical treatment of COVID-19.

pharmacology and toxicology↗

bioRxiv2022

An atlas of plant full-length RNA reveals tissue-specific and evolutionarily-conserved regulation of poly(A) tail length

Introductory paragraphPoly(A) tail is a hallmark of eukaryotic mRNA and its length plays an essential role in regulating mRNA metabolism1-3. However, a comprehensive resource for plant poly(A) tail length has yet to be established. Here, we applied a poly(A)-enrichment-free, Nanopore-based method4,5 to profile full-length RNA with poly(A) tail information in plants. Our atlas contains over 120 million polyadenylated mRNA molecules from seven different tissues of Arabidopsis, as well as the shoot tissue of maize, soybean and rice. In most tissues, the size of plant poly(A) tails shows peaks at approximately 20 and 45 nt, presumably the sizes protected by one and two poly(A) binding proteins (PABP), respectively2,6, while the poly(A) tails in pollen exhibit a distinct pattern with strong peaks centered at 55 and 80 nt. Moreover, poly(A) tail length is regulated in a gene-specific manner -- mRNAs with short half-lives in general have long poly(A) tails, while mRNAs with long half-lives are featured with relatively short poly(A) tails that peak at ~45 nt, suggesting that protection of poly(A) tail in this size by PABP is essential for mRNA stability. Across species, poly(A) tails in the nucleus are almost twice as long as in the cytoplasm, implying a conserved rapid shortening process of poly(A) tail occurs before the mRNA is stabilized in cytoplasm. Our comprehensive dataset lays the groundwork for future functional and evolutionary studies on poly(A) tail length regulation in plants.

molecular biology↗

bioRxiv2022

HIF-1α Contributes to the Progression of Chronic Obstructive Pulmonary Disease

BackgroundHypoxia-inducible factor-1 (HIF-1) plays an important regulatory role in inflammatory and hypoxic diseases. Higher HIF-1 level was found in lungs of chronic obstructive pulmonary disease (COPD) patients, however, its role in cigarette smoke (CS)-induced COPD has not been fully studied. Digoxin has been showed to inhibit HIF-1 translation and block HIF-1 activity and thus is often used as the HIF-1 inhibitor. Therefore, in the present study, we chose digoxin as the inhibitor to investigate whether HIF-1 contributes to the progression of COPD and possible mechanism. MethodsCS-exposed mice were intragastrically treated with different doses of digoxin, and COPD-associated phenotypes such as pathological changes in lungs, inflammation, lung function and mucus secretion in airways were evaluated. Meanwhile, CSE-treated A549 cells were administrated with digoxin or S7959. Moreover, EMT-associated markers together with HIF-1\TGF-{beta}1\Smad3 signaling pathway were detected both in vivo and in vitro. ResultsThe level of HIF-1 was significantly increased in lungs of COPD mice and CSE-exposed A549 cells, which was markedly suppressed by digoxin. Moreover, digoxin inhibited CS-induced inflammatory responses, lung function decline, and mucus hyper-secretion in COPD mouse model. In in vitro studies, digoxin decreased CSE-induced pro-inflammatory cytokine release. Importantly, CS-induced or CSE-induced EMT and up-regulation of HIF-1/TGF-{beta}1/Smad pathway was inhibited by digoxin. Additionally, S7959 mitigated CSE-induced EMT in A549 cells. ConclusionsDigoxin can protect CS-induced COPD and prevent CS-induced EMT possibly through HIF-1/TGF-{beta}1/Smad3 signaling pathway. This study suggests HIF1- could be a potential intervention target for COPD prevention and treatment, especially for EMT in CS-induced COPD.

molecular biology↗

bioRxiv2021

TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics

Computational Pathology (CPath) has seen rapid growth in recent years, driven by advanced deep learning (DL) algorithms. These algorithms typically share the same sequence of steps. However, due to the sheer size and complexity of handling large multi-gigapixel whole-slide images, there is no open-source software library that provides a generic end-to-end API for pathology image analysis using best practices for CPath. Most researchers have designed custom pipelines from the bottom-up, restricting the development of advanced CPath algorithms to specialist users. To help overcome this bottleneck, we present TIAToolbox, a Python toolbox designed to make CPath more accessible to new and advanced CPath scientists and pathologists alike. We provide a usable and adaptable library with efficient, cutting-edge and unit-tested tools for data loading, pre-processing, model inference, post-processing and visualization. This enables all kinds of users to easily build upon recent DL developments in the CPath literature. TIAToolbox provides a user-friendly modular API to enable seamless integration of advanced DL algorithms. We show with the help of examples how state-of-the-art DL algorithms can be streamlined using TIAToolbox.

bioengineering↗

bioRxiv2021

Potential inhibitors for blocking the interaction of the coronavirus SARS-CoV-2 spike protein and its host cell receptor ACE2

The outbreak of SARS-CoV-2 continues to pose a serious threat to human health and social and economic stability. In this study, we established an anti-coronavirus drug screening platform based on the Homogeneous Time Resolved Fluorescence (HTRF) technology and the interaction between the coronavirus S protein and its host receptor ACE2. This platform is a rapid, sensitive, specific, and high throughput system. With this platform, we screened two compound libraries of 2,864 molecules and identified three potential anti-coronavirus compounds: tannic acid (TA), TS-1276 (anthraquinone), and TS-984 (9-Methoxycanthin-6-one). Our in vitro validation experiments indicated that TS-984 strongly inhibits the interaction of the coronavirus S-protein and the human cell ACE2 receptor. This data suggests that TS-984 is a potent blocker of the interaction between the S-protein and ACE2, which might have the potential to be developed into an effective anti-coronavirus drug. SIGNIFICANCEThe ongoing pandemic of COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made a serious threat to public health worldwide. Given the urgency of the situation, researchers are attempting to repurpose existing drugs for treating COVID-19. In this present study, we screened two compound libraries of 2,864 molecules and identified a potent inhibitor (TS-984) for blocking the coronavirus S-protein and the human cell ACE2 receptor. TS-984 might have the potential to be developed into an effective anti-coronavirus drug for treating COVID-19.

pharmacology and toxicology↗

bioRxiv2021

Multiscale mechanical models of DNA nanotubes: A theoretical basis for the design and tuning of DNA nanocarriers

DNA nanostructures are one of potential candidates for drug carriers due to their good biocompatibility and non-specificity in vivo. A reliable prediction about mechanical properties of artificial DNA structures is desirable to improve the efficiency of DNA drug carriers, however there is only a handful of information on mechanical functionalities of DNA nanotubes (DNTs). This paper focuses on quantifying the multiscale correlations among DNT deformation, packaging conditions and surrounding factors to tune mechanical properties of DNTs. By combining WLC statistical mechanics model, Parsegians mesoscopic liquid crystal model and Eulers continuum beam theory, we developed a multiscale DNA-frame model; then theoretically characterize the initial packed states of DNTs for the first time, and reveal the diversity mechanism in mechanical properties of DNTs induced by interchain interactions and initial packed states. Moreover, the study of parameters, such as packaging conditions and environmental factors, provides a potential control strategy for tuning mechanical properties of DNTs. These conclusions provide a theoretical basis for accurately controlling the property and deformation of DNT in various DNT dynamic devices, such as DNA nanocarriers.

biophysics↗

bioRxiv2021

Intestinal SEC16B modulates obesity by controlling dietary lipid absorption

Genome-wide association studies (GWAS) have identified genetic variants in SEC16 homolog B (SEC16B) locus to be associated with obesity and body mass index (BMI) in various populations. SEC16B encodes a scaffold protein located at endoplasmic reticulum (ER) exit sites that is implicated to participate in the trafficking of COPII vesicles in mammalian cells. However, the function of SEC16B in vivo, especially in lipid metabolism, has not been investigated. Here we demonstrated that intestinal SEC16B is required for dietary lipid absorption in mice. We showed that Sec16b intestinal knockout (IKO) mice, especially female mice, were protected from HFD-induced obesity. Loss of SEC16B in intestine dramatically reduced postprandial serum triglyceride output upon intragastric lipid load or during overnight fasting and high-fat diet (HFD) refeeding. Further studies showed that intestinal SEC16B deficiency impaired apoB lipidation and chylomicron secretion. These results revealed that SEC16B plays important roles in dietary lipid absorption, which may shed light on the association between variants in SEC16B and obesity in human.

physiology↗

bioRxiv2021

A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines

A prion-like RNA-binding protein, CPEB3, can regulate local translation in dendritic spines. CPEB3 monomers repress translation, whereas CPEB3 aggregates activate translation of its target mRNAs. However, the CPEB3 aggregates, as long-lasting prions, may raise the problem of unregulated translational activation. Here, we propose a computational model of the complex structure between CPEB3 RNA-binding domain (CPEB3-RBD) and small ubiquitin-like modifier protein 2 (SUMO2). Free energy calculations suggest that the allosteric effect of CPEB3-RBD/SUMO2 interaction can amplify the RNA-binding affinity of CPEB3. Combining with previous experimental observations on the SUMOylation mode of CPEB3, this model suggests an equilibrium shift of mRNA from binding to deSUMOylated CPEB3 aggregates to binding to SUMOylated CPEB3 monomers in basal synapses. This work shows how a burst of local translation in synapses can be silenced following a stimulation pulse, and explores the CPEB3/SUMO2 interplay underlying the structural change of synapses and the formation of long-term memories.

molecular biology↗

bioRxiv2021

NAD precursors cycle between host tissues and the gut microbiome

Nicotinamide adenine dinucleotide (NAD) is an essential redox cofactor in both mammals and microbes. Here we use isotope tracing to investigate the precursors supporting NAD synthesis in the gut microbiome. We find that preferred dietary NAD precursors are absorbed in the proximal part of the gastrointestinal tract and not available to microbes in the distal gut. Instead, circulating host nicotinamide enters the gut lumen and supports gut microbiome NAD synthesis. In addition, the microbiome converts nicotinamide, originating from the host circulation, into nicotinic acid. Host tissues uptake and utilize this microbiome-derived nicotinic acid for NAD synthesis, maintaining circulating nicotinic acid levels even in the absence of dietary consumption. Moreover, the main route from oral nicotinamide riboside, a widely used nutraceutical, to host NAD is via conversion into nicotinic acid by the gut microbiome. Thus, NAD precursors cycle between the host and gut microbiome to maintain NAD homeostasis.

physiology↗

bioRxiv2021

A novel mechanism of bulk cytoplasmic transport by cortical dynein in Drosophila ovary

Cytoplasmic dynein, a major minus-end directed microtubule motor, plays essential roles in eukaryotic cells. Drosophila oocyte growth is mainly dependent on the contribution of cytoplasmic contents from the interconnected sister cells, nurse cells. We have previously shown that cytoplasmic dynein is required for Drosophila oocyte growth, and assumed that it transports cargoes along microtubule tracks from nurse cells to the oocyte. Here we report that instead transporting cargoes along microtubules into the oocyte, cortical dynein actively moves microtubules in nurse cells and from nurse cells to the oocyte via the cytoplasmic bridges, the ring canals. We demonstrate this microtubule movement is sufficient to drag even inert cytoplasmic particles through the ring canals to the oocyte. Furthermore, replacing dynein with a minus-end directed plant kinesin linked to the actin cortex is sufficient for transporting organelles and cytoplasm to the oocyte and driving its growth. These experiments show that cortical dynein can perform bulk cytoplasmic transport by gliding microtubules along the cell cortex and through the ring canals to the oocyte. We propose that the dynein-driven microtubule flow could serve as a novel mode of cargo transport for fast cytoplasmic transfer to support rapid oocyte growth.

cell biology↗

bioRxiv2021

Paradoxical excitation of lateral habenula neurons by propofol involves enhanced presynaptic release of glutamate

Sleep is a fundamental physiological process conserved across most species. As such, deficits in sleep can result in a myriad of psychological and physical health issues. However, the mechanisms underlying the induction of sleep are relatively unknown. Interestingly, general anesthetics cause unconsciousness by positively modulating GABA-A receptors (GABAARs). Based on this observation, it is hypothesized that GABAARs play a critical role in modulating circuits involved in sleep to promote unconsciousness. Recently, the lateral habenula (LHb) has been demonstrated to play a role in sleep physiology and sedation. Specifically, propofol has been shown to excite LHb neurons to promote sedation. However, the mechanism by which this occurs is unknown. Here, we utilize whole-cell voltage and current clamp recordings from LHb neurons obtained from 8-10 week old male mice to determine the physiological mechanisms for this phenomenon. We show that bath application of 1.5M propofol is sufficient to increase LHb neuronal excitability involving synaptic transmission, but not through modulation of intrinsic properties. Additionally, although there is increased LHb neuronal excitability, GABAARs localized postsynaptically on LHb neurons are still responsive to propofol, as indicated by an increase in the decay time. Lastly, we find that propofol increases the synaptic drive onto LHb neurons involving enhanced presynaptic release of both glutamate and GABA. However, the greatest contributor to the potentiated synaptic drive is the increased release of glutamate which shifts the balance of synaptic transmission towards greater excitation. Taken together, this study is the first to identify the physiological basis for why LHb neurons are excited by propofol, rather than inhibited, and as a result promote sedation.

neuroscience↗

bioRxiv2021

Nicotinic modulation insecticides act on diverse receptor subtypes with distinct subunit compositions

Insect nicotinic acetylcholine receptors (nAChRs) are ligand gated ion channels mainly expressed in the central nervous system of insects. They are the directed targets of nicotinic modulation insecticides including neonicotinoids, the most widely used insecticides in the world. However, the resistance development from pests and the negative impacts on the pollinators affect their applications and create demand for the alternatives. Thus, it is very important to understand the mode of action of these insecticides at the molecular level, which is actually unclear for more than 30 years. In this study, we systematically examined the susceptibility of ten Drosophila melanogaster nAChR subunits mutants against eleven nicotinic modulation insecticides. Our results showed that there are several subtypes of nAChRs with distinct subunits compositions that are responsible for the toxicity of different insecticides, respectively. At least three of them are the major molecular targets of seven structurally similar neonicotinoids in vivo. On the other hand, the spinosyns may exclusively act on the 6 homomeric nAChR but not any other heteromeric pentamers. Behavioral assays using thermogenetic tools further confirmed the bioassay results and support the idea that receptor activation rather than inhibition leads to the insecticidal effects of neonicotinoids. The present findings reveal native nAChR subunit interactions with various insecticides and have important implications for resistance management and the development of novel insecticides targeting this important ion channels. Author SummaryThe neonicotinoids and spinosyns make up about 27% of the insecticides by world market value. Novel insecticides like sulfoxaflor, flupyradifurone and triflumezopyrim are developed as alternatives due to the negative effects of neonicotinoids on pollinators. Although all act via insect nicotinic acetylcholine receptors, the mode of action is unclear. Our work shows that these insecticides act on diverse receptor subtypes with distinct subunit compositions. This finding could lead to the development of more selective insecticides to control pests with minimal effects on beneficial insects.

genetics↗

bioRxiv2021

Slow TCA flux implies low ATP production in tumors

The tricarboxylic acid (TCA) cycle oxidizes carbon substrates to carbon dioxide, with the resulting high energy electrons fed into the electron transport chain to produce ATP by oxidative phosphorylation. Healthy tissues derive most of their ATP from oxidative metabolism, and the remainder from glycolysis. The corresponding balance in tumors remains unclear. Tumors upregulate aerobic glycolysis (the Warburg effect), yet they also typically require an intact TCA cycle and electron transport chain1-6. Recent studies have measured which nutrients contribute carbon to the tumor TCA metabolites7,8, but not tumor TCA flux: how fast the cycle turns. Here, we develop and validate an in vivo dynamic isotope tracing-mass spectrometry strategy for TCA flux quantitation, which we apply to all major mouse organs and to five tumor models. We show that, compared to the tissue of origin, tumor TCA flux is markedly suppressed. Complementary glycolytic flux measurements confirm tumor glycolysis acceleration, but the majority of tumor ATP is nevertheless made aerobically, and total tumor ATP production is suppressed compared to healthy tissues. In murine pancreatic cancer, this is accommodated by downregulation of the major energy-using pathway in the healthy exocrine pancreas, protein synthesis. Thus, instead of being hypermetabolic as commonly assumed, tumors apparently make ATP at a lower than normal rate. We propose that, as cells de-differentiate into cancer, they eschew ATP-intensive processes characteristic of the host tissue, and that the resulting suppressed ATP demand contributes to the Warburg effect and facilitates cancer growth in the nutrient-poor tumor microenvironment.

cancer biology↗