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.

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.

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.

Memantine can relieve the neuronal impairment caused by neurotropic virus infection.

Neurotropic viruses, such as the rabies virus (RABV) and Japanese encephalitis virus (JEV), induce neuronal dysfunction and complication, causing neuronal damage. Currently, there are still no effective clinical treatments for neuronal injury caused by neurotropic viruses. Memantine, a drug capable of passing through the blood-brain barrier, noncompetitively and reversibly binds to n-methyl- d-aspartic acid (NMDA) receptors. Memantine is used to treat Alzheimer's disease by blocking the activation of extra axonal ion channels, thus preventing neuronal degeneration by inhibiting the abnormal cytosolic Ca 2+ increase. To explore whether memantine can alleviate neurological disturbances caused by RABV and JEV, the following experiments were carried out: (1) for primary neurons cultured in vitro infected with RABV, the addition of memantine showed neuroprotection. (2) In the RABV challenge experiments, memantine had limited therapeutic effect, mildly extending the survival time of mice. In contrast, memantine significantly prolonged the survival time of mice infected with JEV, by reducing the intravascular cuff and inflammatory cell infiltration in mice. Furthermore, memantine decreases the amount of JEV virus in mice brain.

Advance in Stress for Depressive Disorder.

Stress is an adaptive response to environment aversive stimuli and a common life experience of one's daily life. Chronic or excessive stress especially that happened in early life is found to be deleterious to individual's physical and mental health, which is highly related to depressive disorders onset. Stressful life events are consistently considered to be the high-risk factors of environment for predisposing depressive disorders. In linking stressful life events with depressive disorder onset, dysregulated HPA axis activity is supposed to play an important role in mediating aversive impacts of life stress on brain structure and function. Increasing evidence have indicated the strong association of stress, especially the chronic stress and early life stress, with depressive disorders development, while the association of stress with depression is moderated by genetic risk factors, including polymorphism of SERT, BDNF, GR, FKBP5, MR, and CRHR1. Meanwhile, stressful life experience particularly early life stress will exert epigenetic modification in these risk genes via DNA methylation and miRNA regulation to generate long-lasting effects on these genes expression, which in turn cause brain structural and functional alteration, and finally increase the vulnerability to depressive disorders. Therefore, the interaction of environment with gene, in which stressful life exposure interplay with genetic risk factors and epigenetic modification, is essential in predicting depressive disorders development. As the mediator of environmental risk factors, stress will function together with genetic and epigenetic mechanism to influence brain structure and function, physiology and psychology, and finally the vulnerability to depressive disorders.

Adaptive gene profiling of Mycobacterium tuberculosis during sub-lethal kanamycin exposure.

Resistance to anti-tuberculosis drugs is a formidable obstacle to effective tuberculosis (TB) treatment and prevention globally. New forms of multidrug, extensive drug and total drug resistance Mycobacterium tuberculosis (Mtb) causing a serious threat to human as well as animal's population. Mtb shows diverse adaptability under stress conditions especially antibiotic treatment, however underlying physiological mechanism remained elusive. In present study, we investigated Mtb's response and adaptation with reference to gene expression during sub-lethal kanamycin exposure. Mtb were cultured under sub-lethal drug and control conditions, where half were sub-cultured every 3-days to observe serial adaptation under same conditions and the remaining were subjected to RNA-seq. We identified 98 up-regulated and 198 down-regulated responsive genes compared to control through differential analysis, of which Ra1750 and Ra3160 were the most responsive genes. In adaptive analysis, we found Ra1750, Ra3160, Ra3161, Ra3893 and Ra2492 up-regulation at early stage and gradually showed low expression levels at the later stages of drug exposure. The adaptive expression of Ra1750, Ra3160 and Ra3161 were further confirmed by real time qPCR. These results suggested that these genes contributed in Mtb's physiological adaptation during sub-lethal kanamycin exposure. Our findings may aid to edify these potential targets for drug development against drug resistance tuberculosis.

[Antimicrobial and anti-tumor activities of endophytes from Lycium barbarum of Ningxia].

The antimicrobial activity and cytotoxicity in vitro of the fermentation broth of 10 endophytic strains isolated from Lycium barbarum were determined to screen high activity endophytic strains. Sequences analysis of ITS and 16S rDNA was used for molecular identification of the strains. The results showed that 5 endophytic fungi had no inhibitory activity against the tested pathogens. Endophytic actinomycete strain AL6 had a certain inhibitory effect on 3 kinds of pathogenic fungi, and strain AL5 only had strong inhibitory activity against Staphylococcus aureus. However, the anti-tumor activity of endophytic fungi was significantly higher than that of actinomycetes. Four endophytic fungi strains exhibited the growth inhibition rate of above 50% against at least one of the tested tumor cells when the concentration of fermentation broth was 0.2 g•L⁻¹. Sequences analysis showed that 5 endophytic fungi strains belonged to genus Aspergillus, Penicillium and Emericella, and the 5 endophytic actinomycetes strains belonged to genus Aspergillus, Penicillium and Emericella. Aspergillus strain FL1 had stronger inhibitory activity against A549 and HeLa cells, and the IC50 values were 0.022，0.028 g•L⁻¹, respectively, which was worthy of further study.

Keeping CRISPR/Cas on-Target.

CRISPR/Cas, a microbial adaptive immune system, has recently been reshaped as a versatile genome editing approach, endowing genome engineering with high efficiency and robustness. The DNA endonuclease Cas, a component of CRISPR system, is directed to specific target within genomes by guide RNA (gRNA) and performs gene editing function. However, the system is still in its infancy and facing enormous challenges such as off-target mutation. Lots of attempts have been made to overcome such off-targeting and proven to be effective. In this review we focused on recent progress of increasing the CRISPR specificity realized by rational design of gRNA and modification of Cas9 endonuclease. Meanwhile the methods to screen off-target mutation and their effects are also discussed. Comprehensive consideration and rational design to reduce off-target mutation and selection of effective screening assay will greatly facilitate to achieve successful CRISPR/Cas system mediated gene editing.

[Screening and identification of antioxidant endophytes from Lycium barbarum of Ningxia].

In this paper, 29 endophytes were isolated from different organs and tissues of Lycium barbarum of Ningxia by tablet coating method, 18 of them was fungi, and 11 of them was actinomycetes. The endophytes quantity in the different tissues were leaves > flowers > roots >fruits; The hydroxyl radical scavenging activities of 11 endophytes were investigated by Fenton reaction, and total antioxidant capacities of them were examined by a. total antioxidant capacity test kit; culture features and strain-specific sequence analysis were employed to explore the diversity of the 11 endophytes. The result showed that 5 fungi and 6 actinomycetes that having antioxidant activity could be phylogenetically classified into 3 genera, 3 genera and 3 families, respectively. The total antioxidant capacity and hydroxyl radical scavenging activity of the 11 endophytes showed distinct difference. The antioxidant activity of Aspergillus were stronger, among which total antioxidant capacity of fL1 was (188.5 ± 0.549) U · mL⁻¹ and the IC50 was 0.3 mg · L⁻¹; the IC50 of strain fL1 was 0.42 mg · L⁻¹ and the total antioxidant capacity of fL9 was (113.63 ± 1.021) U · mL⁻¹, all of them were stronger than the positive control Vit C. The experimental results indicated that endophytic fungi of L. barbarum of Ningxia have a great developing and application prospect for the development of antioxidant agent.

A novel zwitterionic magnetic nanocomposite developed for non-invasive speciation analysis of inorganic chromium.

3-(2-Aminoethylamino)propyltriethoxysilane and carboxyethylsilanetriol sodium salt were grafted on silica-coated Fe3O4 nanoparticles via sol-gel process to prepare novel amine- and carboxyl-bifunctionalized magnetic nanocomposites (SMNPs-(NH2 + COOH)). After well characterized, this doubly functionalized material was used as magnetic solid-phase extraction (MSPE) adsorbent to separate and enrich inorganic chromium species followed by inductively coupled plasma-mass spectrometry detection. The optimization of MSPE operation parameters including pH was conducted. It is reasonably elucidated that the adsorption mechanisms of zwitterionic SMNPs-(NH2 + COOH) towards chromium species are electrostatic and/or coordination interactions. Cr(VI) and Cr(III) can be adsorbed around pH 3.0 and around 10.0 respectively with strong anti-interference ability not only from other co-existing ions but also from the two labile species each other, and eluted by dilute nitric acid solution. With a 15-fold enrichment factor, the limits of detection of Cr(VI) and Cr(III) were 0.008 and 0.009 µg L-1, respectively, profiting from the maximum adsorption capacities of 7.52 and 6.11 mg g-1. The just one magnetic extraction matrix based speciation scheme possesses excellent convenience and friendliness to Cr(VI) and Cr(III) without any oxidation or reduction prior to capture of these two species. This protocol has been successfully applied to the speciation analysis of inorganic chromium in real-world environmental water samples.

Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.

Technology for spatial multi-omics aids the discovery of new insights into cellular functions and disease mechanisms. Here we report the development and applicability of multi-omics in situ pairwise sequencing (MiP-seq), a method for the simultaneous detection of DNAs, RNAs, proteins and biomolecules at subcellular resolution. Compared with other in situ sequencing methods, MiP-seq enhances decoding capacity and reduces sequencing and imaging costs while maintaining the efficacy of detection of gene mutations, allele-specific expression and RNA modifications. MiP-seq can be integrated with in vivo calcium imaging and Raman imaging, which enabled us to generate a spatial multi-omics atlas of mouse brain tissues and to correlate gene expression with neuronal activity and cellular biochemical fingerprints. We also report a sequential dilution strategy for resolving optically crowded signals during in situ sequencing. High-throughput in situ pairwise sequencing may facilitate the multidimensional analysis of molecular and functional maps of tissues.

EphB regulates L1 phosphorylation during retinocollicular mapping.

Interaction of the cell adhesion molecule L1 with the cytoskeletal adaptor ankyrin is essential for topographic mapping of retinal ganglion cell (RGC) axons to synaptic targets in the superior colliculus (SC). Mice mutated in the L1 ankyrin-binding motif (FIGQY(1229)H) display abnormal mapping of RGC axons along the mediolateral axis of the SC, resembling mouse mutant phenotypes in EphB receptor tyrosine kinases. To investigate whether L1 functionally interacts with EphBs, we investigated the role of EphB kinases in phosphorylating L1 using a phospho-specific antibody to the tyrosine phosphorylated FIGQY(1229) motif. EphB2, but not an EphB2 kinase dead mutant, induced tyrosine phosphorylation of L1 at FIGQY(1229) and perturbed ankyrin recruitment to the membrane in L1-transfected HEK293 cells. Src family kinases mediated L1 phosphorylation at FIGQY(1229) by EphB2. Other EphB receptors that regulate medial-lateral retinocollicular mapping, EphB1 and EphB3, also mediated phosphorylation of L1 at FIGQY(1229). Tyrosine(1176) in the cytoplasmic domain of L1, which regulates AP2/clathrin-mediated endocytosis and axonal trafficking, was not phosphorylated by EphB2. Accordingly mutation of Tyr(1176) to Ala in L1-Y(1176)A knock-in mice resulted in normal retinocollicular mapping of ventral RGC axons. Immunostaining of the mouse SC during retinotopic mapping showed that L1 colocalized with phospho-FIGQY in RGC axons in retinorecipient layers. Immunoblotting of SC lysates confirmed that L1 was phosphorylated at FIGQY(1229) in wild type but not L1-FIGQY(1229)H (L1Y(1229)H) mutant SC, and that L1 phosphorylation was decreased in the EphB2/B3 mutant SC. Inhibition of ankyrin binding in L1Y(1229)H mutant RGCs resulted in increased neurite outgrowth compared to WT RGCs in retinal explant cultures, suggesting that L1-ankyrin binding serves to constrain RGC axon growth. These findings are consistent with a model in which EphB kinases phosphorylate L1 at FIGQY(1229) in retinal axons to modulate L1-ankyrin binding important for mediolateral retinocollicular topography.

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.

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.

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.

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.

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.

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.

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.