Biology subjects

Li, B.

Publications and source records attributed to Li, B..

At least 469 records · Page 26Linked to original sources

bioRxiv2021

Bacterial Rdl2 dsRNA increased the insecticidal activity of GABAR blockers and allosteric modulators against Plutella xylostella

The utilization of RNA interference (RNAi) for pest management has garnered global interest. The bioassay results suggested the knockout of PxRdl2 significantly increased the insecticidal activities of the{gamma} -aminobutyric acid receptor (GABAR) targeting compounds (Fipronil, two pyrazoloquinazolines and two isoxazolines), thereby presenting a viable target gene for RNAi-mediated pest control. Consequently, we suggest enhancing the insecticidal activities of GABAR-targeting compounds by knockdown the transcript level of PxRdl2. Furthermore, PxRdl2 dsRNA was expressed in HT115 Escherichia coli to reduce costs and protect dsRNA against degradation. In comparison to in vitro synthesized dsRNA, the recombinant bacteria (ds-B) exhibited superior interference efficiencies and greater stability when exposed to UV irradiation. Collectively, our results provide a new strategy of insecticide spray which combined synergistically with insecticidal activities by suppressing PxRdl2 using ds-B, and may be beneficial for reducing the usage of insecticide and slowing pest resistance.

pharmacology and toxicology↗

bioRxiv2021

Mechano-transduction via the pectin-FERONIA complex regulates ROP6 GTPase signaling in Arabidopsis

During growth and morphogenesis, plant cells respond to mechanical stresses resulting from spatiotemporal changes in the cell wall that bear high internal turgor pressure. Microtubule (MT) arrays are re-organized to align in the direction of maximal tensile stress to guide the synthesis of cellulose, reinforcing the local cell wall. However, how mechanical forces regulate MT re-organization remains largely unknown. Here, we demonstrate that mechanical signaling that is based on the CrRLK1L subfamily receptor kinase FERONIA (FER) regulates the reorganization of cortical MT in cotyledon epidermal pavement cells (PC) in Arabidopsis. Recessive mutations in FER compromised MT response to mechanical perturbations such as single cell ablation, compression and Isoxaben treatment in these pavement cells. These perturbations promoted the activation of ROP6 GTPase that acts directly downstream of FER. Furthermore, defects in the ROP6 signaling pathway negated the reorganization of cortical MTs induced by these stresses. Finally, reduction in highly demethylesterified pectin, which binds the extracellular malectin domain of FER and is required for FER-mediated ROP6 activation, also impacted mechanical induction of cortical MT reorganization. Taken together our results suggest that the FER-pectin complex senses and/or transduce mechanical forces to regulate MT organization through activating the ROP6 signaling pathway in Arabidopsis.

cell biology↗

bioRxiv2021

N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner

BackgroundEpigenetic marks, such as DNA methylation, play pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6A methylation, the epitranscriptome, is functionally conserved for ripening control. ResultsHere we show that m6A methylation, which has been revealed to regulate ripening of tomato, a typical climacteric fruit, displays a dramatic change at ripening onset of strawberry, a classical non-climacteric fruit. The m6A modification in the coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m6A around the stop codons and within the 3 untranslated regions is generally negatively correlated with the abundance of the mRNAs. We identified thousands of transcripts with m6A hypermethylation in the CDS regions, including those of NCED5, ABAR, and AREB1 in the abscisic acid (ABA) biosynthesis and signaling pathway. We demonstrated that the methyltransferases MTA and MTB are indispensable for normal ripening of strawberry fruit, and MTA-mediated m6A modification promotes mRNA stability of NCED5 and AREB1, while facilitates translation of ABAR. ConclusionOur findings uncover that m6A methylation regulates ripening of non-climacteric strawberry fruit by targeting ABA pathway, which is distinct from that in climacteric tomato fruit.

developmental biology↗

bioRxiv2021

Recovery of high-qualitied Genomes from a deep-inland Salt Lake Using BASALT

Metagenomic binning enables the in-depth characterization of microorganisms. To improve the resolution and efficiency of metagenomic binning, BASALT (Binning Across a Series of AssembLies Toolkit), a novel binning toolkit was present in this study, which recovers, compares and optimizes metagenomic assembled genomes (MAGs) across a series of assemblies from short-read, long-read or hybrid strategies. BASALT incorporates self-designed algorithms which automates the separation of redundant bins, elongate and refine best bins and improve contiguity. Evaluation using mock communities revealed that BASALT auto-binning obtained up to 51% more number of MAGs with up to 10 times better MAG quality from microbial community at low (132 genomes) and medium (596 genomes) complexity, compared to other binners such as DASTool, VAMB and metaWRAP. Using BASALT, a case-study analysis of a Salt Lake sediment microbial community from northwest arid region of China was performed, resulting in 426 non-redundant MAGs, including 352 and 69 bacterial and archaeal MAGs which could not be assigned to any known species from GTDB (ANI < 95%), respectively. In addition, two Lokiarchaeotal MAGs that belong to superphylum Asgardarchaeota were observed from Salt Lake sediment samples. This is the first time that candidate species from phylum Lokiarchaeota was found in the arid and deep-inland environment, filling the current knowledge gap of earth microbiome. Overall, BASALT is proven to be a robust toolkit for metagenomic binning, and more importantly, expand the Tree of Life.

bioinformatics↗

bioRxiv2021

Cinnamoyl-CoA Reductase 1 (CCR1) and CCR2 Function Divergently in Tissue Lignification, Flux Control and Cross-talk with Glucosinolate Pathway in Brassica napus

Cinnamoyl-CoA reductase (CCR) is the entry point of lignin pathway and a crucial locus in dissection and manipulation of associated traits, but its functional dissection in Brassicaceae plants is largely lagged behind though Arabidopsis thaliana CCR1 has been characterized to certain extent. Here, 16 CCR genes are identified from Brassica napus and its parental species B. rapa and B. oleracea. Brassicaceae CCR genes are divided into CCR1 subfamily and CCR2 subfamily with divergent organ-specificity, yellow-seed trait participation and stresses responsiveness. CCR1 is preferential in G- and H-lignins biosynthesis and vascular development, while CCR2 has a deviation to S-lignin biosynthesis and interfascicular fiber development. CCR1 has stronger effects on lignification-related development, lodging resistance, phenylpropanoid flux control and seed coat pigmentation, whereas CCR2 controls sinapates levels. CCR1 upregulation could delay bolting and flowering time, while CCR2 upregulation weakens vascular system in leaf due to suppressed G lignin accumulation. Besides, CCR1 and CCR2 are deeply but almost oppositely linked with glucosinolates metabolism through inter-pathway crosstalk. Strangely, upregulation of both CCR1 and CCR2 could not enhance resistance to UV-B and S. sclerotiorum though CCR2 is sharply induced by them. These results provide systemic dissection on Brassica CCRs and CCR1-CCR2 divergence in Brassicaceae. HighlightBrassicaceae contains two types of Cinnamoyl-CoA reductase. As revealed in Brassica napus, they are divergently involved in lignin monomer biosynthesis, tissue lignification, phenylpropanoid flux control, and inter-pathway crosstalk with glucosinolates.

plant biology↗

bioRxiv2021

An ultrasensitive GRAB sensor for detecting extracellular ATP in vitro and in vivo

The purinergic transmitter ATP (adenosine 5-triphosphate) plays an essential role in both the central and peripheral nervous systems, and the ability to directly measure extracellular ATP in real time will increase our understanding of its physiological functions. We developed an ultrasensitive GPCR Activation-Based ATP sensor called GRABATP1.0, with a robust fluorescence response to extracellular ATP when expressed in several cell types. This sensor has sub-second kinetics, ATP affinity in the range of tens of nanomolar, and can be used to localize ATP release with subcellular resolution. Using this sensor, we monitored ATP release under a variety of in vitro and in vivo conditions, including primary hippocampal neurons, a zebrafish model of injury-induced ATP release, and LPS-induced ATP-release events in individual astrocytes in the mouse cortex measured using in vivo two-photon imaging. Thus, the GRABATP1.0 sensor is a sensitive, versatile tool for monitoring ATP release and dynamics under both physiological and pathophysiological conditions.

neuroscience↗

bioRxiv2021

Young and Undamaged rMSA Improves the Longevity of Mice

Improvement of longevity is an eternal dream of human beings. Here we report that a single protein recombinant mouse serum albumin (rMSA) improved the lifespan and healthspan of C57BL/6N mice. The median lifespan extensions were 17.6% for female and 20.3% for male, respectively. The grip strength of rMSA-treated female and male mice increased by 29.6% and 17.4%, respectively. Meanwhile, the percentage of successful escape increased 23.0% in rMSA-treated male mice using the Barnes Maze test. The rMSA used in this study is young and almost undamaged. We define the concept "young and undamaged" to any protein without any unnecessary modifications by four parameters: intact free thiol (if any), no advanced glycation end-product, no carbonylation, and no homocysteinylation. Here "young and undamaged" rMSA is much younger and less damaged than the endogenous serum albumin from young mice at 1.5 months of age. We predict that young and undamaged proteins altogether can further improve the longevity.

biochemistry↗

bioRxiv2021

Parallel Characterization of cis-Regulatory Elements for Multiple Genes UsingCRISPRpath

Current pooled CRISPR screens for cis-regulatory elements (CREs) can only accommodate one gene based on its expression level. Here, we describe CRISPRpath, a scalable screening strategy for parallelly characterizing CREs of genes linked to the same biological pathway and converging phenotypes. We demonstrate the ability of CRISPRpath for simultaneously identifying functional enhancers of six genes in the 6-thioguanine-induced DNA mismatch repair pathway using both CRISPR interference (CRISPRi) and CRISPR nuclease (CRISPRn) approaches. 60% of the identified enhancers are known promoters with distinct epigenomic features compared to other active promoters, including increased chromatin accessibility and interactivity. Furthermore, by imposing different levels of selection pressure, CRISPRpath can distinguish enhancers exerting strong impact on gene expression from those exerting weak impact. Our results offer a nuanced view of cis-regulation and demonstrate that CRISPRpath can be leveraged for understanding the complex gene regulatory program beyond transcriptional output at scale.

genomics↗

bioRxiv2021

Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer Cells

Precision medicine depends critically on developing treatment strategies that can selectively target cancer cells with minimal adverse effects. Identifying unique transcriptional regulators of oncogenic signaling, and targeting cancer-cell-specific enhancers that may be active only in specific tumor cell lineages, could provide the necessary high specificity, but a scarcity of functionally validated enhancers in cancer cells presents a significant hurdle to this strategy. We address this limitation by carrying out large-scale functional screens for pro-growth enhancers using highly multiplexed CRISPR-based perturbation and sequencing in multiple cancer cell lines. We used this strategy to identify 488 pro-growth enhancers in a colorectal cancer cell line and 22 functional enhancers for the MYC and MYB key oncogenes in an additional nine cancer cell lines. The majority of pro-growth enhancers are accessible and presumably active only in cancer cells but not in normal tissues, and are enriched for elements associated with poor prognosis in colorectal cancer. We further identify master transcriptional regulators and demonstrate that the cancer pro-growth enhancers are modulated by lineage-specific transcription factors acting downstream of growth signaling pathways. Our results uncover context-specific, potentially actionable pro-growth enhancers from cancer cells, yielding insight into altered oncogenic transcription and revealing potential therapeutic targets for cancer treatment.

cancer biology↗

bioRxiv2021

Outer membrane vesicles derived from Salmonella Typhimurium can deliver Shigella flexneri 2a O-polysaccharide antigen to prevent lethal pulmonary infection in mice

The threat to health from shigellosis has become quite serious in many developing countries, causing severe diarrhea. Shigella flexneri 2a (S. flexneri 2a) is the principal species responsible for this endemic disease. Although there have been multiple attempts to design a vaccine against Shigellosis, one that is effective has not yet been developed. Lipopolysaccharide (LPS) is both an essential virulence factor and a protective antigen against Shigella, due to its outer domain, termed O-polysaccharide antigen. In the present study, S. flexneri 2a O-polysaccharide antigen was innovatively bio-synthesized in Salmonella and attached to core-lipid A by the ligase WaaL, and thus purified outer membrane vesicles (OMVs) were used as a vaccine for subsequent research. Here, we identified the expression of the heterologous polysaccharide antigen and described the isolation, characterization, and immune protection efficiency of the OMV vaccine. The expression of S. flexneri 2a did not affect the formation of Salmonella OMVs or their cytotoxicity. Furthermore, the results of the animal experiments indicated that immunization of the mice both intranasally and intraperitoneally with the OMV vaccine induced significant specific anti-Shigella LPS antibodies in both vaginal secretions and fluid from bronchopulmonary lavage, in addition to within sera. The OMV vaccine immunized by both routes of administration provided significant protection against virulent S. flexneri 2a infection, as judged by a serum bactericidal assay (SBA), opsonization assay, challenge experiment, and pathological analysis. The present study firstly indicates that the proposed vaccination strategy represents a novel and improved approach to control Shigellosis by the combination of bioconjugation of Salmonella glycosyl carrier lipid and OMV. In addition, the strategy of genetic manipulation described here is ideally suited for designs based on other Shigella serotypes, allowing the development of a Shigella vaccine with broad-protection.

microbiology↗

bioRxiv2020

Development of next-generation sequencing-based sterility test

The sterility testing methods described in pharmacopoeias require an incubation period of 14 days to obtain analysis results. An alternative method that can significantly shorten the detection time and improve the accuracy is in urgent need to meet the sterility testing requirements of regenerative medicine products with a short shelf life. In this study, we developed the next-generation sequencing-based sterility test (NGSST) based on sequencing and multiple displacement amplification. The NGSST can be finished within 48 hours with five steps including whole genome amplification, sequencing, alignment, sterility testing report, and microorganism identification. We use RPKM ratio to minorize the influence of environmental bacteria and determine its cutoff based AUC curve. The NGSST showed high sensitivity in reporting contaminates at 0.1 CFU in supernatant of biological product or 1 CFU in cell suspension. Furthermore, we identified microorganisms in 5 primary umbilical cord mesenchymal stem cell samples that were tested positive by BacT/ALERTR 3D. Overall, the NGSST can serve as a promising alternative for sterility testing of biological products.

microbiology↗

bioRxiv2020

Super-robust data storage in DNA by de Bruijn graph-based decoding

DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. The major technical challenges include various errors, such as the strand breaks, rearrangements, and indels that frequently arise during DNA synthesis, amplification, sequencing, and preservation. Through a de novo assembly strategy, we developed an algorithm based on the de Bruijn graph and greedy path search (DBGPS) to address these issues. DBGPS shows distinct advantages in handling DNA breaks, rearrangements, and indels. The robustness of DBGPS is demonstrated by accelerated aging, multiple independent data retrievals, deep error-prone PCR, and large data scale simulations. Remarkably, 6.8 MB of data can be retrieved accurately from a seriously corrupted sample that has been treated at 70 {degrees}C for 70 days. With DBGPS, we were able to achieve a logical density of 1.30 bits/cycle and a physical density of 295 PB/g. One-Sentence SummaryA de Bruijn graph-based de novo assembly algorithm for DNA data storage enables fast and robust data readouts even with DNA samples that have been severely corrupted.

bioinformatics↗

bioRxiv2020

Linkage disequilibrium under polysomic inheritance

The influence of genetic drift on linkage disequilibrium in finite populations has been extensively studied in diploids. However, to date the effects of ploidy on LD has not been extensively studied. We here extend the linkage disequilibrium measure D and Burrows {Delta} statistic to include polysomic inheritance, as well as their corresponding squared correlation coefficients r2 and [Formula], where the former is for phased genotypes and the latter for unphased genotypes. Weir & Hills double non-identity framework is also extended to include polysomic inheritance, and the expressions of double non-identity coefficients are derived under five mating systems. On this basis, the approximated expectations of estimated r2 and [Formula] at equilibrium state, d2 and{delta} 2, are derived under five mating systems. We assess the behaviors of the estimated r2 and [Formula] and the influence of the recombination rate on d2 or{delta} 2, simulate the application of estimating effective population size, and evaluate the statistical performance of the method of estimating.

genetics↗

bioRxiv2020

Construction of a liquid-liquid phase separation system from the gel-sol transition of elongated protein microgels in a crowding agent

Liquid proteinaceous materials have been frequently found in cells or tissues and are crucial for various biological processes. Unlike their solid-state counterparts, liquid-state protein compartments are challenging to engineer and control at the microscale. Conventionally, gelation (sol-gel transition) of biological molecules has been thought to be the intermediate step between liquid-liquid phase separation (LLPS) states and insoluble aggregates that are related to protein functions, malfunctions and even diseases. However, the opposite process, i.e., the gel-sol transition of materials, has not been broadly explored. Here we describe a thermoresponsive gel-sol transition of a protein in a crowded environment that results in a demixed LLPS state, contradicting the common consequence of a one-phase protein solution by the end of such transition at elevated temperature without crowding agents. We also demonstrate a simple method to monitor the gel-sol transition by showing that elongated gelatin microgels can evolve towards a spherical morphology in the crowding agents because of interfacial tension. The LLPS system was explored for the diffusion of small particles for drug-release application scenarios. Our results demonstrate a route for the rapid construction of LLPS models, where the gel-sol transition of the protein-rich phase is monitorable. The models are featured with tunable size and dimensional monodispersity of dispersed condensates. The present study can be employed in biophysics and bioengineering with practices such as 3D printing and temperature sensing.

biophysics↗

bioRxiv2020

A comprehensive catalogue of regulatory variants in the cattle transcriptome

Characterization of genetic regulatory variants acting on the transcriptome of livestock is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here, we build a cattle Genotype-Tissue Expression atlas (cattle GTEx, http://cgtex.roslin.ed.ac.uk/) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 11,642 RNA-Seq datasets. We describe the landscape of the transcriptome across over 100 tissues and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 24 major tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association study (TWAS) and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.

genomics↗

bioRxiv2020

The role of macrophage scavenger receptor 1 (Msr1) in prion pathogenesis

The progression of prion diseases is accompanied by the accumulation of prions in the brain. Ablation of microglia enhances prion accumulation and accelerates disease progression, suggesting that microglia play a neuroprotective role by clearing prions. However, the mechanisms underlying the phagocytosis and clearance of prion are largely unknown. The macrophage scavenger receptor 1 (Msr1) is an important phagocytic receptor expressed by microglia in the brain, and is involved in the uptake and clearance of soluble amyloid-{beta}. We therefore asked whether Msr1 might play a role in prion clearance, and assessed the scavenger function of Msr1 in prion pathogenesis. We found that Msr1 expression was upregulated in prion-infected mouse brains. However, Msr1 deficiency did not change prion disease progression or lesion patterns. Prion deposition in Msr1 deficient mice was similar to their wild type littermates. In addition, prion-induced neuroinflammation was not affected by Msr1 ablation. We conclude that Msr1 does not play a major role in prion pathogenesis.

neuroscience↗

bioRxiv2020

Sex-specific stress-related behavioral phenotypes and central amygdala dysfunction in a mouse model of 16p11.2 microdeletion

Substantial evidence indicates that a microdeletion on human chromosome 16p11.2 is linked to neurodevelopmental disorders including autism spectrum disorders (ASD). Carriers of this deletion show divergent symptoms besides the core features of ASD, such as anxiety and emotional symptoms. The neural mechanisms underlying these symptoms are poorly understood. Here we report mice heterozygous for a deletion allele of the genomic region corresponding to the human 16p11.2 microdeletion locus (i.e., the 16p11.2 del/+ mice) have sex-specific anxiety-related behavioral and neural circuit changes. We found that female, but not male 16p11.2 del/+ mice showed enhanced fear generalization - a hallmark of anxiety disorders - after auditory fear conditioning, and displayed increased anxiety-like behaviors after physical restraint stress. Notably, such sex-specific behavioral changes were paralleled by an increase in activity in central amygdala neurons projecting to the globus pallidus in female, but not male 16p11.2 del/+ mice. Together, these results reveal female-specific anxiety phenotypes related to 16p11.2 microdeletion syndrome and a potential underlying neural circuit mechanism. Our study therefore identifies previously underappreciated sex-specific behavioral and neural changes in a genetic model of 16p11.2 microdeletion syndrome, and highlights the importance of investigating female-specific aspects of this syndrome for targeted treatment strategies.

neuroscience↗

bioRxiv2020

A Mycobacterium tuberculosis effector protein attacks host innate immunity by acting as an unusual ubiquitinating enzyme

Protein kinase G (PknG), a eukaryotic type serine-threonine protein kinase (STPK) in Mycobacterium tuberculosis (Mtb), is secreted into the cytosol of infected macrophages to promote intracellular survival of mycobacteria and has been considered as a promising therapeutic target for tuberculosis (TB) treatment. However, the molecular details of Mtb PknG-host intracellular interactions remain obscure. Here, we demonstrate that PknG serves as both the ubiquitin-activating enzyme (E1) and the ubiquitin ligase (E3) to promote ubiquitination and degradation of tumor necrosis factor receptor-associated factor 2 (TRAF2) and TGF-{beta}-activated kinase 1 (TAK1), and thus inhibits the NF-{kappa}B-mediated host innate immune responses. Surprisingly, PknG promotes the attachment of ubiquitin (Ub) to ubiquitin-conjugating enzyme (E2) UbcH7 via an isopeptide bond (UbcH7 K82-Ub), instead of a usual C86-Ub thiol-ester bond, and then promotes the discharge of Ub from UbcH7 by acting as an isopeptidase before attaching Ub to its substrates TRAF2 and TAK1. These results demonstrate that Mtb PknG promotes ubiquitination of the key components of the host innate immunity by acting as an unusual ubiquitinating enzyme to suppress innate immunity. Our findings provide a potential TB treatment via targeting unconventional ubiquitinating activities of PknG. SignificanceMycobacterium tuberculosis (Mtb) protein kinase G (PknG), which is critical for Mtb intracellular survival, is a promising target for tuberculosis (TB) treatment. However, the molecular mechanisms underlying PknG-host interactions remain largely unclear. Here we demonstrate that PknG serves as both the ubiquitin-activating enzyme and the ubiquitin ligase to promote the ubiquitination and degradation of tumor necrosis factor receptor-associated factor 2 (TRAF2) and TGF-{beta}-activated kinase 1 (TAK1), thus inhibiting NF-{kappa}B signaling activation. PknG promotes the attachment of ubiquitin to ubiquitin-conjugating enzyme UbcH7 via an isopeptide bond, instead of a usual thiol-ester bond, and releases the ubiquitin from UbcH7 by acting as an isopeptidase. These findings provide important information for rational development of TB treatment via targeting unconventional ubiquitinating activity of PknG.

microbiology↗