Biology subjects

Feng, L.

Publications and source records attributed to Feng, L..

108 records · Page 6Linked to original sources

bioRxiv2020

Biochar effect - mediated ammonium transporter genes and GDH may be the core of improvement nitrogen assimilation in cotton seedling

Biochar enhancement of nitrogen efficiency in crops is highly essential not only to reduce costs of agricultural production but also to conserve resources, lower energy consumption for products of these fertilizers, strengthen soil health, and eventually helps in slowing climate change; however nitrogen efficiency physiology by biochar effects is not clear. Here, we reported on the morphological, nitrogen metabolism and cytokinin, at seedling stage, under different layers of biochar and limited urea conditions grown in soil culture. Expression profile of miRNAs and AOB was further studied in fine and medium roots. It showed active root absorption area, fresh weight, and nitrogen agronomic efficiency responded significantly under biochar and reduction by 20% urea condition in the surface soil layer. Also, NR and GPT activity in fine roots remarkably increased with cytokinin, but decreased significantly in medium roots, meanwhile both NR and GDH activity did so. GOGAT activity was to be dependent with biochar and urea locations. In addition, AMT1;1, gdh3 and gdh2 in fine roots showed their up-regulation with reduction 20% urea and biochar. It revealed that co-expression of gdh3 and gdh2 in fine roots significantly affected nitrogen assimilation under reduction 20% urea with biochar on surface soil at seedling stage. HighlightsThe co-expression of ammonium transporter gene and GDH induced by biochar effect improves nitrogen efficiency and seedling growth. These data emphasizes the importance of effects of cytokinin on nitrate reductase activity closely related to the position under biochar condition, which is a key element of enhancement nitrogen assimilation efficiency in cotton seedling. Biochar addition applied into 0 to 10cm soil had a more positive effect on seedling growth than that into 10 to 20cm soil layers.

plant biology↗

bioRxiv2020

Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1

The wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303 and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and showed here that these three resistance loci co-segregate in fine-mapping populations and share identical full-length genomic sequence of functional Wtk1. Independent EMS mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303 and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303- and YrH52-mediated resistances to yellow rust are encoded by a single locus Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks. HighlightWe demonstrate that Yr15, YrG303 and YrH52 resistances are encoded by the Wtk1 locus, but express variable resistance responses to yellow rust in a genetic background dependent manner.

genetics↗

bioRxiv2019

A comprehensive online database for exploring ~20,000 public Arabidopsis RNA-Seq libraries

Application of Next Generating Sequencing (NGS) technology in transcriptome profiling has greatly improved our understanding of transcriptional regulation at genome-wide scale in the last decade, and tens of thousands of RNA-sequencing (RNA-seq) libraries have been produced by the research community. However, accessing such huge amount of RNA-seq data poses a big challenge for groups that lack dedicated bioinformatic personnel or expensive computational resources. Here, we introduce the Arabidopsis RNA-seq database (ARS), a free, web-accessible, and user-friendly to quickly explore expression level of any gene in 20,000+ publicly available Arabidopsis RNA-seq libraries.

bioinformatics↗

bioRxiv2019

Natural naphthoquinones isolated from Lithospermum erythrorhizon suppress dextran sulfate sodium-induced murine experimental colitis

The purpose of this study was to explore the effects of natural shikonin and its derivatives on mice experimental colitis induced by dextran sulfate sodium, and to investigate the underlying mechanisms in vivo. Our results suggested that, intragastric administration of single compound like shikonin and its derivatives contributed to attenuating symptoms of malignant induced by DSS. Meanwhile, shikonin or its derivatives could also remarkably reduce the disease activity index and histopathological scores, suppress the levels of pro-inflammatory cytokines (including IL-6, IL-1{beta} and TNF-), while increase that of inflammatory cytokine IL-10 in serum. Additionally, both shikonin and alkanin were found to restrain the levels of COX-2, MPO and iNOS in serum and colonic tissues. Moreover, western blotting results demonstrated that shikonin and its derivatives could inhibit the activation of the NLRP3 inflammasome and the NF-{kappa}B signaling pathway, relieve the DSS-induced disruption of colonic epithelial tight junction (TJ) in colonic tissues. Further, docking simulation had been performed to prove that shikonin and its derivatives could bind to the active sites of NLRP3 inflammasome and the NF-{kappa}B to generate an effective inflammatory effect. Taken together, our experimental data can provide some evidence for the potential use of shikonin and its derivatives to treat the inflammatory bowel disease (IBD).

biochemistry↗

bioRxiv2019

sRNAanno --- a database repository of uniformly-annotated small RNAs in plants

Small RNAs (sRNAs) are essential regulatory molecules, including three mayor classes in plants, microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Except miRNAs, the other two classes are not well-annotated and collected in public databases for most sequenced plant genomes. We performed comprehensive sRNA annotation for 138 plant species, which have fully sequenced genomes and public next-generation-sequencing (NGS) sRNA data available. The results are available via an online repository called sRNAanno (www.plantsRNAs.org). Compared to plant miRNAs deposited in miRBase, we obtained much more miRNAs, which are more complete and reliable because of consistent and high-stringent criteria used in our miRNA annotation. sRNAanno also provides free access to genomic information for >16,000 PHAS loci and >21,000,000 hc-siRNA loci annotated from these 138 plants. On the basis of Integrative Genomics Viewer (IGV), we developed a visualization tool for browsing NGS sRNA data (IGV-sRNA), which have been integrated a series of new functions compatible to specific sRNA features. To make sRNA annotation an easy task, sRNAanno also provides free service of sRNA annotation to the community. In summary, sRNAanno and IGV-sRNA are great resources to facilitate the genomic and genetic research of plant small RNAs.

genomics↗

bioRxiv2019

The Study on Computer Vision-Assisted Cell Bank Construction and Screening & Classification

Computer vision technology plays an important role in screening and culturing cells. This paper proposes a method to construct a helper cell library based on cell image segmentation and screening. Firstly, cell culture and image acquisition were carried out. The main content is to use laboratory conditions to carry out different cell types. Through careful observation of the whole process of cell proliferation and passage, the representative pictures of different stages were taken. Analysis and summary of the relevant morphology, texture, color characteristics. Secondly, computer vision technology is used to segment cells and extract the main features such as cell perimeter and area. Explore the automatic information extraction method of cell bank, and complete the image segmentation of individual cell image from the whole picture. Finally, the cells were screened and identified. Investigate different pattern recognition methods and neural network structures, and prepare pictures of various cell pictures. The corresponding neural network and prediction program are constructed. This paper proposes an automatic image processing method for each image category in cell culture cycle, which improves the automation of production process. At the same time, compared with the design of a single algorithm for a certain type of cell, different algorithm design ideas are proposed for three types of pictures with different characteristics, which is closer to the dynamic change of cell morphology in the process of cell culture. This research has important application prospects in promoting cell factory research, cell bank construction and automatic screening.

bioinformatics↗

bioRxiv2019

In situ Fucosylation for Modulating Wnt Signaling in Live Cells

Wnt/{beta}-catenin signaling, also known as canonical Wnt signaling, regulates critical, context-dependent transcription in numerous (patho) physiological events. Amongst the well-documented mechanisms of canonical Wnt signaling, modification of N-glycans by L-fucose (Fuc) is the newest and the least understood. Using a combination of Chinese Hamster Ovary (CHO) cell mutants with different fucosylation levels and in situ cell-surface Fuc editing (ISF), we report that (1-3)-fucosylation of N-acetylglucosamine in the LacNAc (Gal{beta}(1-4)-GlcNAc) sequences of complex N-glycans modulates Wnt signaling by regulating the endocytosis of low density lipoprotein receptor-related protein 6 (LRP6). Pulse-chase experiments reveal that increasing N-glycan LacNAc fucosylation elevates endocytosis of lipid-raft-localized LRP6, leading to the suppression of Wnt-{beta}-catenin signaling. Inhibiting endocytosis by inhibiting dynamin 1, a GTPase responsible for endocytosis in eukaryotic cells, partially rescues Wnt signaling. Remarkably, inhibition of Wnt signaling by N-glycan LacNAc fucosylation is fully rescued by the addition of free Fuc to the medium, suggesting that endocytosis of N-glycan fucosylated LRP6 may be mediated by a receptor that recognizes the bound (1-3)-Fuc. This work provides the first evidence that in situ cell-surface fucosylation can be exploited to regulate a specific signaling pathway via endocytosis, revealing a novel regulatory mechanism linking glycosylation of a cell surface receptor with its intracellular signaling.

biochemistry↗

bioRxiv2019

TMEM16F phospholipid scramblase mediates trophoblast fusion and placental development

Cell-cell fusion or syncytialization is fundamental to the reproduction, development and homeostasis of multicellular organisms. In addition to various cell-type specific fusogenic proteins, cell surface externalization of phosphatidylserine (PS), a universal eat-me signal in apoptotic cells, has been observed in different cell-fusion events. Nevertheless, molecular underpinnings of PS externalization and cellular mechanisms of PS-facilitated cell-cell fusion are unclear. Here we report that TMEM16F, a Ca2+-activated phospholipid scramblase (CaPLSase), plays an indispensable role in placental trophoblast fusion by translocating PS to the cell surface independent of apoptosis. Consistent with its essential role in trophoblast fusion, the placentas from TMEM16F-deficient mice exhibit deficiency in syncytialization, placental developmental defects and perinatal lethality. Our findings thus identify a cell-cell fusion mechanism by which TMEM16F CaPLSase-dependent externalization of PS serves as a critical cell fusion signal to facilitate trophoblast syncytialization and placental development.

cell biology↗

bioRxiv2019

MicroRNA-378 suppressed osteogenesis of mesenchymal stem cells and impaired bone formation via inactivating Wnt/β-catenin signaling

MicroRNAs (miRNAs) have been reported to serve as silencers to repress gene expression at post-transcriptional level. Multiple miRNAs have been demonstrated to play important roles in osteogenesis. MiR-378, a conserved miRNA, was reported to mediate bone metabolism and influence bone development, but the detailed function and underlying mechanism remain obscure. In this study, the miR-378 transgenic (TG) mouse was developed to study the role of miR-378 in osteogenic differentiation as well as bone formation. The abnormal bone tissues and impaired bone quality were displayed in the miR-378 TG mice, and a delayed healing effect was observed during bone fracture of the miR-378 TG mice. The osteogenic differentiation of MSCs derived from this TG mouse was also inhibited. We also found that miR-378 mimics suppressed while anti-miR-378 promoted osteogenesis of human MSCs. Two Wnt family members Wnt6 and Wnt10a were identified as bona fide targets of miR-378, and their expression were decreased by this miRNA, which eventually induced the inactivation of Wnt/{beta}-catenin signaling. Finally, the sh-miR-378 modified MSCs were locally injected into the fracture sites in an established mouse fracture model. The results indicated that miR-378 inhibitor therapy could promote bone formation and stimulate healing process in vivo. In conclude, miR-378 suppressed osteogenesis and bone formation via inactivating Wnt/{beta}-catenin signaling, suggesting miR-378 may be a potential therapeutic target for bone diseases.

cell biology↗

bioRxiv2019

Correlation between Retinal Ganglion Cell Loss and Nerve Crush Force-Impulse Established with an Instrumented Tweezers in Mice

ObjectivesRodent models of optic nerve crush (ONC) have often been used to study degeneration and regeneration of retinal ganglion cells (RGCs) and their axons as well as the underlying molecular mechanisms. However, ONC results from different laboratories exhibit a range of RGC injury with varying degree of axonal damage. We developed an instrumented tweezers to measure optic nerve (ON) crush forces in real time and studied the correlation between RGC axon loss and force-impulse, the product of force and duration, applied through the instrumented tweezers in mice.\n\nMethodsA pair of standard self-closing #N7 tweezers were instrumented with miniature foil strain gauges at optimal locations on both tweezer arms. The instrumented tweezers were capable of recording the tip closure forces in the form of voltages, which were calibrated through load cells to corresponding tip closure forces over the operating range. Using the instrumented tweezers, the ONs of multiple mice were crushed with varied forces and durations and the axons in the immunostained sections of the crushed ONs were counted.\n\nResultsWe found that the surviving axon density correlated with crush force, with longer duration and stronger crush forces producing consistently more axon damage.\n\nDiscussionThe instrumented tweezers enable a simple technique for measurement of ONC forces in real-time for the first time. Using the instrumented tweezers, experimenters can quantify crush forces during ONC to produce consistent and predictable post-crush cell death. This should permit future studies a way to produce nerve damage more consistently than is available now.

neuroscience↗

bioRxiv2019

Analytical treatment interruption after short-term anti-retroviral therapy in a postnatally SHIV infected infant rhesus macaque model

To achieve long-term viral remission in HIV-infected children, novel strategies beyond early anti-retroviral therapy (ART) will be necessary. Identifying clinical predictors of time to viral rebound upon ART interruption will streamline the development of novel therapeutic strategies and accelerate their evaluation in clinical trials. However, identification of these biomarkers is logistically challenging in infants, due to sampling limitations and potential risks of treatment interruption. To facilitate identification of biomarkers predicting viral rebound, we have developed an infant rhesus macaque (RM) model of oral SHIV.CH505.375H.dCT challenge and analytical treatment interruption (ATI) after short-term ART. We used this model to characterize SHIV replication kinetics and virus-specific immune responses during short-term ART or post-ATI and demonstrated plasma viral rebound in 5 out of 6 (83%) infants. We observed a decline in humoral immune responses and partial dampening of systemic immune activation upon initiation of ART in these infants. Furthermore, we documented that infant and adult macaques have similar SHIV replication and rebound kinetics and equally potent virus-specific humoral immune responses. Finally, we validated our models by confirming a well-established correlate of time to viral rebound, namely pre-ART plasma viral load, as well as identified additional potential humoral immune correlates. Thus, this model of infant ART and viral rebound can be used and further optimized to define biomarkers of viral rebound following long-term ART as well as to pre-clinically assess novel therapies to achieve a pediatric HIV functional cure.\n\nIMPORTANCENovel interventions that do not rely on daily adherence to ART are needed to achieve sustained viral remission for perinatally infected children who currently rely on lifelong ART. Considering the risks and expense associated with ART-interruption trials, identification of biomarkers of viral rebound will prioritize promising therapeutic intervention strategies, including anti-HIV Env protein therapeutics. However, comprehensive studies to identify those biomarkers are logistically challenging in human infants, demanding the need for relevant non-human primate models of HIV rebound. In this study, we developed an infant RM model of oral Simian/Human Immunodeficiency virus infection expressing clade C HIV Env, and short-term ART followed by ATI, longitudinally characterizing immune responses to viral infection during ART and post-ATI. Additionally, we compared this infant RM model to an analogous adult RM rebound model and identified virologic and immunologic correlates of time to viral rebound post-ATI.

immunology↗

bioRxiv2019

The conserved metalloprotease invadolysin is present in invertebrate haemolymph and vertebrate blood

We identified invadolysin, a novel essential metalloprotease, for functions in chromosome structure, cell proliferation and migration. Invadolysin also plays an important metabolic role in insulin signaling and is the only protease known to localise to lipid droplets, the main lipid storage organelle in the cell. In silico examination of the protein sequence of invadolysin predicts not only protease and lipase catalytic motifs, but also post-translational modifications and the secretion of invadolysin. Here we show that the protease motif of invadolysin is important for its role in lipid accumulation, but not in glycogen accumulation. The lipase motif does not appear to be functionally important for accumulation of lipids or glycogen. Post-translational modifications likely contribute to modulating the level, localisation or activity of invadolysin. We identified a secreted form of invadolysin in the soluble fraction of invertebrate hemolymph (where we observe sexually dimorphic forms) and also vertebrate plasma, including in the extracellular vesicle fraction. Biochemical analysis for various post-translational modifications demonstrated that secreted invadolysin is both N-and O-glycosylated, but not apparently GPI-linked. The discovery of invadolysin in the extracellular milieu suggests a role for invadolysin in normal organismal physiology.\n\nSummary StatementIn this study, we show that the conserved metalloprotease invadolysin is present in invertebrate hemolymph and vertebrate blood, suggesting the protein may function in organismal physiology.

cell biology↗

bioRxiv2018

Genome sequencing analysis identifies high-risk Epstein-Barr virus subtypes for nasopharyngeal carcinoma

Epstein-Barr virus (EBV) infection is ubiquitous worldwide and associated with multiple cancers including nasopharyngeal carcinoma (NPC). The role of EBV viral genomic variation in NPC development and its striking endemicity in southern China has been poorly explored. Through large-scale genome sequencing and association study of EBV isolates from China, we identified two non-synonymous EBV variants within BALF2 strongly associated with NPC risk (conditional P value 1.75x10-6 for SNP162476_C and 3.23x10-13 for SNP163364_T), whose cumulative effects contributed to 83% of the overall risk in southern China. Phylogenetic analysis of the risk variants revealed a unique origin in southern China followed by clonal expansion. EBV BALF2 haplotype carrying the risk variants were shown to reduce viral lytic DNA replication, as a result potentially promoting viral latency. Our discovery has not only provided insight to the unique endemic pattern of NPC occurrence in southern China, but also paved the way for the identification of individuals at high risk of NPC and effective intervention program to reduce the disease burden in southern China.

genetics↗

bioRxiv2018

Neural correlates of auditory enhancement in humans

The perception of sensory events can be suppressed or enhanced by the surrounding spatial and temporal context in ways that help in detecting novel objects and establishing perceptual constancy. In the auditory system, the phenomenon known as auditory enhancement reflects a general principle of contrast enhancement, where a target sound embedded within a background sound becomes perceptually more salient if the background is presented first by itself. This effect is highly robust, producing an effective enhancement of the target of between 5 and 25 dB (more than two orders of magnitude in intensity), depending on the task. Despite their ubiquity in vision, neural correlates of auditory contrast enhancement have yet to be identified in humans. Here we used the auditory steady-state response to probe the neural response to a target sound under conditions of enhancement. The probe was simultaneously modulated in amplitude with two modulation frequencies, to distinguish cortical from subcortical contributions to this phenomenon. We found robust auditory cortical, but not subcortical, enhancement that correlates with behavior and is consistent with an early theoretical model that postulates neural adaptation of inhibition. Our findings provide empirical support for a previously unverified theory of auditory enhancement and point to new approaches for improving sensory prostheses for hearing loss, such as hearing aids and cochlear implants. Significance StatementA target sound embedded within a background sound becomes perceptually more salient if the background is presented first by itself. This phenomenon, where the target "pops out", is known as auditory enhancement. It reflects a general principle of contrast enhancement, and helps in the detection of new acoustic events in the environment and in establishing the perceptual constancy of speech and other biologically relevant sounds under varying acoustic conditions. We use EEG in humans to reveal a cortical correlate of this perceptual phenomenon that provides empirical support for a longstanding but previously unverified theoretical account.

neuroscience↗

bioRxiv2018

Protein Deacetylase CobB Interplays with c-di-GMP

As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis and DNA supercoiling in many bacteria. Using an E.coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Protein deacetylation assays showed that c-di-GMP inhibits CobB activity and thereby modulates the biogenesis of acetyl-CoA. Through mutagenesis studies, residues R8, R17 and E21 of CobB were shown to be required for c-di-GMP binding. Next, we found that CobB is an effective deacetylase of YdeH, a major diguanylate cyclase (DGC) of E.coli that is endogenously acetylated. Mass spectrometry analysis identified YdeH K4 as the major site of acetylation, and it could be deacetylated by CobB. Interestingly, deacetylation of YdeH enhances its stability and cyclase activity in c-di-GMP production. Thus, our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.

microbiology↗

bioRxiv2018

Conserved Roles of C. elegans and Human MANFs in Sulfatide Binding and Cytoprotection

Mesencephalic Astrocyte-Derived Neurotrophic Factor (MANF) is an endoplasmic reticulum (ER) protein that can be secreted and protect dopamine neurons and cardiomyocytes from ER stress and apoptosis. The mechanism of action of extracellular MANF has long been elusive. From a genetic screen for mutants with abnormal ER stress response, we identified the gene Y54G2A.23 as the evolutionarily conserved C. elegans MANF orthologue. We find that MANF binds to the lipid sulfatide, also known as 3-O-sulfogalactosylceramide present in serum and outer-cell membrane leaflets, directly in isolated forms and in reconstituted lipid micelles. Sulfatide binding promotes cellular MANF uptake and cytoprotection from hypoxia-induced cell death. Heightened ER stress responses of MANF-null C. elegans mutants and mammalian cells are alleviated by human MANF in a sulfatide-dependent manner. Our results demonstrate conserved roles of MANF in sulfatide binding and ER stress response, supporting sulfatide as a long-sought lipid mediator of MANFs cytoprotection.

cell biology↗

bioRxiv2017

Changing geographic patterns and risk factors for avian influenza A(H7N9) infection in China

The 5th epidemic wave in 2016-2017 of avian influenza A(H7N9) virus in China caused more human cases than any previous waves but the factors that may explain the recent range expansion and surge in incidence remain unknown. We investigated the effect of anthropogenic, poultry and wetland information and of market closures on all epidemic waves (1-5). Poultry predictor variables recently became much more important than before, supporting the assumption of much wider H7N9 transmission in the chicken reservoir, that could be linked to increases in pathogenicity. We show that the future range expansion of H7N9 to northern China may translate into a higher risk of coinciding peaks with those of seasonal influenza, leading to a higher risk of reassortments. Live-poultry market closures are showed to be effective in reducing the local incidence rates of H7N9 human cases, but should be paired with other prevention and control measures to prevent transmission.

epidemiology↗

bioRxiv2017

Allopatric divergence, local adaptation, and multiple Quaternary refugia in a long-lived tree (Quercus spinosa) from subtropical China

O_LIThe complex geography and climatic changes occurring in subtropical China during the Tertiary and Quaternary might have provided substantial opportunities for allopatric speciation. To gain further insight into these processes, we reconstruct the evolutionary history of Quercus spinosa, a common evergreen tree species mainly distributed in this area.\nC_LIO_LIForty-six populations were genotyped using four chloroplast DNA regions and 12 nuclear microsatellite loci to assess genetic structure and diversity, which was supplemented by divergence time and diversification rate analyses, environmental factor analysis, and ecological niche modeling of the species distributions in the past and at present.\nC_LIO_LIThe genetic data consistently identified two lineages: the western Eastern Himalaya-Hengduan Mountains lineage and the eastern Central-Eastern China lineage, mostly maintained by populations environmental adaptation. These lineages diverged through climate/orogeny-induced vicariance during the Neogene and remained separated thereafter. Genetic data strongly supported the multiple refugia (per se, interglacial refugia) or refugia within refugia hypotheses to explain Q. spinosa phylogeography in subtropical China.\nC_LIO_LIQ. spinosa population structure highlighted the importance of complex geography and climatic changes occurring in subtropical China during the Neogene in providing substantial opportunities for allopatric divergence.\nC_LI

evolutionary biology↗