Interactome between ASFV and host immune pathway proteins.

IMPORTANCE: African swine fever (ASF), caused by African swine fever virus (ASFV), has become a major crisis for the pork industry in recent years. The mechanism for ASFV pathology and the clinical symptoms difference of ASF between domestic pigs and reservoir hosts remain to be elucidated. We deciphered the comprehensive protein-protein interaction (PPI) network between ASFV and host immune pathways. The intensive PPI network contained both ASFV-host immune pathway PPI and ASFV-ASFV PPI information, providing a comprehensive ASFV-host interaction landscape. Furthermore, the ASFV-host PPI difference between domestic pigs and warthogs was explored, which will be instructive for exploring essential candidates involved in ASFV pathology. Moreover, we screened the inhibitory effect of ASFV proteins in the PPI with cGAS-STING pathway on IFN-I and NF-κB, further providing possible functions of ASFV-host PPI network in innate immune regulation.

Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils.

Both heavy metals and antibiotics exert selection pressure on bacterial resistance, and as they are commonly co-contaminated in the environment, they may play a larger role in bacterial resistance. This study examined how breeding cycles affect antibiotic resistance genes (ARGs) in chicken manure and the surrounding topsoils at 20, 50, 100, 200, and 300 m from twelve typical laying hen farms in the Ningxia Hui Autonomous Region of northwest China. Six antibiotics, seven heavy metals, ten mobile genetic elements (MGEs), and microbial community affected the ARGs profile in chicken dung and soil samples. Tetracycline antibiotic residues were prevalent in chicken manure, as were relatively high content of aureomycin during each culture period. Zinc (Zn) content was highest among the seven heavy metals in chicken feces. Chicken dung also enriched aminoglycosides, MLSB, and tetracycline ARGs, notably during brooding and high production. The farm had a minimal influence on antibiotics in the surrounding soil, but its effect on ARGs and MGEs closer to the farm (50 m) was stronger, and several ARGs and MGEs increased with distance. Manure microbial composition differed dramatically throughout breeding cycles and sampling distances. ARGs were more strongly related with antibiotics and heavy metals in manure than soil, whereas MGEs were the reverse. Antibiotics, heavy metals, MGEs, and bacteria in manure accounted 12.28%, 22.25%, 0.74%, and 0.19% of ARGs composition variance, respectively, according to RDA and VPA. Bacteria (2.89%) and MGEs (2.82%) only affected soil ARGs composition. These findings showed that heavy metals and antibiotics are the main factors affecting faecal ARGs and bacteria and MGEs soil ARGs. This paper includes antibiotic resistance data for large-scale laying hen husbandry in northwest China and a theoretical framework for decreasing antibiotic resistance.

Identification of Characteristic Peptides of Casein in Cow Milk Based on MALDI-TOF MS for Direct Adulteration Detection of Goat Milk.

It is widely acknowledged that casein is an important allergenic protein in milk which may cause danger to customers. The identification and confirmation of caseins through mass spectrometry requires the selection of suitable characteristic peptides. In this study, by means of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), the three most representative specific peptides of caseins in cow milk were screened out with mass-to-charge ratios (m/z) of 830, 1195, and 1759, respectively. By comparing 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA) MALDI matrices, it was found that DHB was more suitable for peptide detection with the limits of detection (LODs) of 0.1 mg/L for α, ß-casein. Furthermore, on the basis of verifying the characteristic peptides of casein from cow milk, this protocol was applied to goat milk authentication. Cow milk addition in goat milk was investigated by using the screened specific peptides. The results showed that the adulteration could be identified when the proportion of cow milk was 1% or more. When applied to inspect adulteration in five brands of commercial goat milk, specific peptides of bovine casein were detected in four of them. The method has the advantages of strong reliability, high throughput, simple preprocessing, and fast speed, which can provide powerful help for prewarning dairy allergen.

Highly efficient and robust π-FISH rainbow for multiplexed in situ detection of diverse biomolecules.

In the unprecedented single-cell sequencing and spatial multiomics era of biology, fluorescence in situ hybridization (FISH) technologies with higher sensitivity and robustness, especially for detecting short RNAs and other biomolecules, are greatly desired. Here, we develop the robust multiplex π-FISH rainbow method to detect diverse biomolecules (DNA, RNA, proteins, and neurotransmitters) individually or simultaneously with high efficiency. This versatile method is successfully applied to detect gene expression in different species, from microorganisms to plants and animals. Furthermore, we delineate the landscape of diverse neuron subclusters by decoding the spatial distribution of 21 marker genes via only two rounds of hybridization. Significantly, we combine π-FISH rainbow with hybridization chain reaction to develop π-FISH+ technology for short nucleic acid fragments, such as microRNA and prostate cancer anti-androgen therapy-resistant marker ARV7 splicing variant in circulating tumour cells from patients. Our study provides a robust biomolecule in situ detection technology for spatial multiomics investigation and clinical diagnosis.

Residue screening and analysis of enrofloxacin and its metabolites in real aquatic products based on ultrahigh-performance liquid chromatography coupled with high resolution mass spectrometry.

The abuse of enrofloxacin (ENR) in aquaculture and the lack of monitoring of other metabolites except ciprofloxacin (CIP) may lead to unknown harmful effects on human health. In this study, ENR metabolites were screened in real fish samples based on ultrahigh-performance liquid chromatography coupled with Q-Orbitrap mass spectrometry combined with Compound Discoverer software, and another metabolite deethylene-ENR besides CIP was detected and identified for the first time. Correspondingly, a method for the determination of ENR and CIP and the semi-quantitative analysis of deethylene-ENR in aquatic products was established. Method validation illustrated that excellent linearity and satisfactory recoveries of analytes were obtained. Limits of detection of ENR and CIP were both 0.1 µg kg-1, and their limits of quantification both 1 µg kg-1. CIP and deethylene-ENR were detected in 12 of 14 ENR-positive fish samples, so deethylene-ENR should be of concern as a possible risk candidate in aquatic products.

Determination of chlorpromazine and its metabolites in animal-derived foods using QuEChERS-based extraction, EMR-Lipid cleanup, and UHPLC-Q-Orbitrap MS analysis.

Chlorpromazine (CPZ) is abused in animal husbandry and can be extensively metabolized in humans and animals. However, the actual monitoring mainly focuses on the parent compound but lacks attention to its metabolites. A method was developed and validated firstly for identification and determination of CPZ and its four major metabolites in animal-derived foods using ultrahigh-performance liquid chromatography coupled with quadrupole-Orbitrap mass spectrometry in combination with QuEChERS preparation method. Satisfactory recoveries of analytes spiked in fish and pork samples ranged from 72 to 117 %, and limits of quantification were 2.0 and 1.0 µg kg-1 for fish and pork samples respectively. Moreover, through the hydrolysis experiments of CPZ, its hydrolysates, such as CPZ-sulfoxide, CPZ-N-oxide and CPZ-sulfoxide-N-oxide, were identified as potential risk compounds. The developed method has been successfully applied to the determination of CPZ and its metabolites in actual commercial samples, as well as to the screening of other CPZ-related risk compounds.

Construction of Attenuated Strains for Red-Spotted Grouper Nervous Necrosis Virus (RGNNV) via Reverse Genetic System.

The nervous necrosis virus (NNV) mainly attacks the central nervous system of fish to cause viral nervous necrosis, which is an acute and serious prevalent disease in fish. Among different genotypes of NNV, red-spotted grouper nervous necrosis virus (RGNNV) is the most widely reported, with the highest number of susceptible species. To better understand the pathogenicity of RGNNV, we first developed a reverse genetic system for recombinant RGNNV rescue using B7GG and striped snakehead (SSN-1) cells. Furthermore, we constructed attenuated RGNNV strains rRGNNV-B2-M1 and rRGNNV-B2-M2 with the loss of B2 protein expression, which grew slower and induced less Mx1 expression than that of wild-type RGNNV. Moreover, rRGNNV-B2-M1 and rRGNNV-B2-M2 were less virulent than the wild-type RGNNV. Our study provides a potential tool for further research on the viral protein function, virulence pathogenesis, and vaccine development of RGNNV, which is also a template for the rescue of other fish viruses.

[Distribution Characteristics of Antibiotics and Antibiotic Resistance Genes in Manure and Surrounding Soil of Poultry Farm in Ningxia].

Antibiotics and antibiotic resistance genes (ARGs) in livestock and poultry manure pose potential ecological risks. In order to understand the distribution characteristic of antibiotics and ARGs in manure and surrounding soils of poultry farms in Ningxia, the poultry manure and relative soil samples were collected from 12 layers of different poultry breeding farms. The compositions of antibiotics and ARGs in the samples were analyzed using UPLC-MS/MS and HT-qPCR. The results showed that:① tetracycline, aminoglycoside, and sulfonamide were the dominant antibiotics in poultry manure. The types and contents of antibiotics in poultry manure were different in different breeding periods. There were more types of antibiotics in the brooding period, the average content was high, and the initial stage showed the opposite trend. ② A small amount of antibiotics was detected in the surrounding soil only 20 m away from the poultry farm, and the poultry farm had little effect on the distribution of antibiotics in the surrounding soil. The content of quinolone in the soils with poultry manure application was significantly higher than that in the control and surrounding soil. ③ We detected 132-168 ARGs in poultry manure, and the number of aminoglycosides and tetracycline was higher. The relative abundance of ARGs in the rearing period was highest, and the initial stage showed the opposite trend. The total relative abundance of ARGs in the brooding period was highest, but the terminal period showed the opposite. There were 110 ARGs in poultry manure during all breeding periods. ④ There were 23-105 ARGs in the soils, and the number of aminoglycoside was highest, followed by multidrug ARGs. The poultry farm had a great effect on the number and relative abundance of ARGs in the surrounding soil. For example, the number and relative abundance of ARGs in the surrounding soil of poultry farms gradually decreased with the increase in the distance from the poultry farms. The number and relative abundance of ARGs in the soil with applied poultry manure were significantly increased; however, these values were lower than those in the soil 20 m away from the poultry farm. ⑤ ß-lactamases, aminoglycosides, and macrolide lincosamide-streptogramin B (MLSB) ARGs were all at risk of horizontal movement in manure, and chloramphenicol ARGs were at risk of horizontal movement in soil. Correlation analysis showed that the relative abundance of aminoglycoside, tetracycline, sulfonamide, ß-lactamase, and MLSB were not significantly correlated with their contents. ⑥ Different types of ARGs had related co-occurrence phenomena, such as the positive correlation between the relative abundance of ARGs in poultry manure, and aminoglycoside and ß-lactamases, MGEs, multidrugs and vancomycins. The relative abundances of ARGs in soil, aminoglycoside and tetracyclines, vancomycins, sulfonamides, and MLSBs; tetracyclines and MLSBs; etc., all showed a significant positive correlation. In short, the co-occurrence among the relative abundance of ARGs in soil was significantly stronger than that in poultry manure. These results could provide the theoretical basis for the site selection of poultry farms, the selection of antibiotic types and dosages for large-scale breeding of laying hens, and the application of poultry manure.

The Connectome and Chemo-Connectome Databases for Mice Brain Connection Analysis.

The various brain functions rely on the intricate connection networks and certain molecular characteristics of neurons in the brain. However, the databases for the mouse brain connectome and chemo-connectome are still inadequate, hindering the brain circuital and functional analysis. Here, we created mice brain connectome and chemo-connectome databases based on mouse brain projection data of 295 non-overlapping brain areas and in situ hybridization (ISH) data of 50 representative neurotransmission-related genes from the Allen Brain Institute. Based on this connectome and chemo-connectome databases, functional connection patterns and detailed chemo-connectome for monoaminergic nuclei were analyzed and visualized. These databases will aid in the comprehensive research of the mouse connectome and chemo-connectome in the whole brain and serve as a convenient resource for systematic analysis of the brain connection and function.

Neuron-derived neuropeptide Y fine-tunes the splenic immune responses.

The nervous and immune systems are closely entwined to maintain the immune balance in health and disease. Here, we showed that LPS can activate suprarenal and celiac ganglia (SrG-CG) neurons and upregulate NPY expression in rats. Single-cell sequencing analysis revealed that knockdown of the NPY gene in SrG-CG altered the proliferation and activation of splenic lymphocytes. In a neuron and splenocyte coculture system and in vivo experiments, neuronal NPY in SrG-CG attenuated the splenic immune response. Notably, we demonstrated that neuronal NPF in Drosophila exerted a conservative immunomodulatory effect. Moreover, numerous SNPs in NPY and its receptors were significantly associated with human autoimmune diseases, which was further supported by the autoimmune disease patients and mouse model experiments. Together, we demonstrated that NPY is an ancient language for nervous-immune system crosstalk and might be utilized to alleviate inflammatory storms during infection and to modulate immune balance in autoimmune diseases.

A spatial and cellular distribution of rabies virus infection in the mouse brain revealed by fMOST and single-cell RNA sequencing.

BACKGROUND: Neurotropic virus infection can cause serious damage to the central nervous system (CNS) in both humans and animals. The complexity of the CNS poses unique challenges to investigate the infection of these viruses in the brain using traditional techniques. METHODS: In this study, we explore the use of fluorescence micro-optical sectioning tomography (fMOST) and single-cell RNA sequencing (scRNA-seq) to map the spatial and cellular distribution of a representative neurotropic virus, rabies virus (RABV), in the whole brain. Mice were inoculated with a lethal dose of a recombinant RABV encoding enhanced green fluorescent protein (EGFP) under different infection routes, and a three-dimensional (3D) view of RABV distribution in the whole mouse brain was obtained using fMOST. Meanwhile, we pinpointed the cellular distribution of RABV by utilizing scRNA-seq. RESULTS: Our fMOST data provided the 3D view of a neurotropic virus in the whole mouse brain, which indicated that the spatial distribution of RABV in the brain was influenced by the infection route. Interestingly, we provided evidence that RABV could infect multiple nuclei related to fear independent of different infection routes. More surprisingly, our scRNA-seq data revealed that besides neurons RABV could infect macrophages and the infiltrating macrophages played at least three different antiviral roles during RABV infection. CONCLUSION: This study draws a comprehensively spatial and cellular map of typical neurotropic virus infection in the mouse brain, providing a novel and insightful strategy to investigate the pathogenesis of RABV and other neurotropic viruses.

Insights into stress degradation behavior of gibberellic acid by UHPLC Q-Exactive Orbitrap mass spectrometry.

Gibberellic acid (GA3) is widely applied in agriculture and food worldwide. Profiling the degradation products and their formation pattern under stress are helpful for deeply understanding GA3 regulating plant physiology and GA3 safety in agricultural crops. This study firstly investigated the degradation behavior of GA3. Different stress factors such as light, pH and temperatures were investigated through photolysis and hydrolysis experiments. Five degradation products were identified using ultra high-performance liquid chromatography Q-Exactive Orbitrap mass spectrometry (UHPLC Q-Exactive Orbitrap MS). Three degradation products were produced under ultraviolet photolysis conditions. Two isomers (iso-GA3 and gibberellenic acid) were formed under alkaline conditions. In order to characterize each degradation product, complete mass fragmentation pathways of all analytes were initially established. These results could provide a practical reference for the safety of agricultural products and the guidance for scientific application of GA3 and proposed storage conditions of GA3.

CoolBox: a flexible toolkit for visual analysis of genomics data.

BACKGROUND: Data visualization, especially the genome track plots, is crucial for genomics researchers to discover patterns in large-scale sequencing dataset. Although existing tools works well for producing a normal view of the input data, they are not convenient when users want to create customized data representations. Such gap between the visualization and data processing, prevents the users to uncover more hidden structure of the dataset. RESULTS: We developed CoolBox-an open-source toolkit for visual analysis of genomics data. This user-friendly toolkit is highly compatible with the Python ecosystem and customizable with a well-designed user interface. It can be used in various visualization situations like a Swiss army knife. For example, to produce high-quality genome track plots or fetch commonly used genomic data files with a Python script or command line, to explore genomic data interactively within Jupyter environment or web browser. Moreover, owing to the highly extensible Application Programming Interface design, users can customize their own tracks without difficulty, which greatly facilitate analytical, comparative genomic data visualization tasks. CONCLUSIONS: CoolBox allows users to produce high-quality visualization plots and explore their data in a flexible, programmable and user-friendly way.

RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription.

Like most DNA viruses, herpesviruses precisely deliver their genomes into the sophisticatedly organized nuclei of the infected host cells to initiate subsequent transcription and replication. However, it remains elusive how the viral genome specifically interacts with the host genome and hijacks host transcription machinery. Using pseudorabies virus (PRV) as model virus, we performed chromosome conformation capture assays to demonstrate a genome-wide specific trans-species chromatin interaction between the virus and host. Our data show that the PRV genome is delivered by the host DNA binding protein RUNX1 into the open chromatin and active transcription zone. This facilitates virus hijacking host RNAPII to efficiently transcribe viral genes, which is significantly inhibited by either a RUNX1 inhibitor or RNA interference. Together, these findings provide insights into the chromatin interaction between viral and host genomes and identify new areas of research to advance the understanding of herpesvirus genome transcription.

Delineating the organization of projection neuron subsets in primary visual cortex with multiple fluorescent rabies virus tracing.

The impressive functions of the brain rely on an extensive connectivity matrix between specific neurons, the architecture of which is frequently characterized by one brain nucleus/region connecting to multiple targets, either via collaterals of the same projection neuron or several, differentially specified neurons. Delineating the fine architecture of projection neuron subsets in a specific brain region could greatly facilitate its circuit, computational, and functional resolution. Here, we developed multiple fluorescent rabies viruses (RV) to delineate the fine organization of corticothalamic projection neuron subsets in the primary visual cortex (V1). By simultaneously retrograde labeling multiple distinct subsets of corticothalamic projection neurons in V1 from their target nuclei in thalamus (dLGN, LP, LD), we observed that V1-dLGN corticothalamic projection neurons were densely concentrated in layer VI, except for several sparsely scattered neurons in layer V, while V1-LP and V1-LD corticothalamic projection neurons were localized to both layers V and VI. Meanwhile, we observed a fraction of V1 corticothalamic projection neurons targeting two thalamic nuclei, which was further confirmed by fMOST whole-brain imaging. The multiple fluorescent RV tracing tools can be extensively applied to resolve the architecture of projection neuron subsets in certain brain regions, with a strong potential to delineate the computational and functional organization of these brain regions.

A new strategy to develop pseudorabies virus-based bivalent vaccine with high immunogenicity of porcine circovirus type 2.

Herpesvirus based multivalent vaccines have been extensively studied, whereas few of them have been successfully used in clinic and animal husbandry industry due to the low expression of foreign immunogens in herpesvirus. In this study, we developed a new strategy to construct herpesvirus based bivalent vaccine with high-level expression of foreign immunogen, by which the ORF2 gene encoding the major antigen protein Cap of porcine circovirus type 2 (PCV2), was highly expressed in pseudorabies virus (PRV). To obtain the high expression of PCV2 immunogen, tandem repeats of PCV2 ORF2 gene were firstly linked by protein quantitation ratioing (PQR) linker to reach equal expression of each ORF2 gene. Then, the multiple copies of ORF2 gene were respectively inserted into the gE and gG sites of PRV using CRISPR/Cas9 system, in which the expression of ORF2 gene was driven by endogenous strong promoters of PRV. Through this way, the highest yield of Cap protein was achieved in two copies of quadruple ORF2 gene insertion. Finally, in mice and pigs immunized with the bivalent vaccine candidate, we detected high titer of specific antibodies for PRV and neutralized antibodies for PCV2, and observed protective effect of the bivalent vaccine candidate against PRV challenge in immunized pigs, suggesting a potential clinical application of the bivalent vaccine candidate we constructed. Together, our strategy could be extensively applied to the generation of other multivalent vaccines, and will pave the way to construct herpesvirus based multivalent vaccines to effectively reduce the cost of vaccine.

Photolysis kinetics of cartap and nereistoxin in water and tea beverages under irradiation of simulated sunlight and ultraviolet under laboratory conditions.

Cartap applied widely in agricultural crops and tea plants is readily degraded into nereistoxin, resulting in a longer residual period and higher exposure risk to humans. The photolysis kinetics of cartap and nereistoxin in water and tea beverages was firstly investigated to explore the effect and mechanism of pesticide residue removal. Cartap and nereistoxin could be effectively photolyzed by ultraviolet and their photolysis rate increased with light intensity increasing. The photolysis percentage of cartap and nereistoxin in different solutions under ultraviolet irradiation of 200 W mercury lamp reached 81.8%-100.0% within 6 h. Relative to water solution, the water-soluble components in tea had an inhibition effect on the photodegradation of cartap and nereistoxin. This research provided a reference for the development of effective methods for the removal of cartap and its metabolite in water and tea beverages.

Single-cell atlas of domestic pig cerebral cortex and hypothalamus.

The brain of the domestic pig (Sus scrofa domesticus) has drawn considerable attention due to its high similarities to that of humans. However, the cellular compositions of the pig brain (PB) remain elusive. Here we investigated the single-nucleus transcriptomic profiles of five regions of the PB (frontal lobe, parietal lobe, temporal lobe, occipital lobe, and hypothalamus) and identified 21 cell subpopulations. The cross-species comparison of mouse and pig hypothalamus revealed the shared and specific gene expression patterns at the single-cell resolution. Furthermore, we identified cell types and molecular pathways closely associated with neurological disorders, bridging the gap between gene mutations and pathogenesis. We reported, to our knowledge, the first single-cell atlas of domestic pig cerebral cortex and hypothalamus combined with a comprehensive analysis across species, providing extensive resources for future research regarding neural science, evolutionary developmental biology, and regenerative medicine.

Residue pattern of chlorpyrifos and its metabolite in tea from cultivation to consumption.

BACKGROUND: Chlorpyrifos (CPF) is a broad-spectrum organophosphorus pesticide widely used to control tea geometrid (Ectropis oblique) and tea green leafhoppers (Empoasca pirisuga Matsumura) in tea trees. The major metabolite of CPF in water, plants, and animals is 3,5,6-trichloro-2-pyridinol, which is more toxic than CPF. However, the dissipation pattern of CPF in tea is unknown. RESULTS: An optimized QuEChERS sample preparation method combined with ultra-performance liquid chromatography-tandem mass spectrometry was applied to determine the residues of chlorpyrifos and its metabolite in tea during tea planting and green tea processing. During tea planting, the sum of chlorpyrifos and its metabolite dissipated rapidly with a half-life of 1.93 days for tea shoots. The residues of chlorpyrifos and its metabolite in made green tea were 96.89 and 35.88 µg kg-1 on the seventh day. The values for processing factors of chlorpyrifos and its metabolite were all less than 1, showing that each green tea manufacturing step was responsible for the reduction. The transfer rates of chlorpyrifos and its metabolite from made green tea to its infusion were 0.68-4.62% and 62.93-71.79%, respectively. CONCLUSION: The risk of chlorpyrifos was negligible to human health based on the hazard quotient, which was 7.4%. This study provides information relevant to the reasonable application of chlorpyrifos in tea planting and is potentially helpful for tea exporting and importing countries to establish harmonized maximum residue limits. © 2020 Society of Chemical Industry.