Integrative proteomics and metabolomics study reveal enhanced immune responses by COVID-19 vaccine booster shot against Omicron SARS-CoV-2 infection.

Since its outbreak in late 2021, the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely reported to be able to evade neutralizing antibodies, becoming more transmissible while causing milder symptoms than previous SARS-CoV-2 strains. Understanding the underlying molecular changes of Omicron SARS-CoV-2 infection and corresponding host responses are important to the control of Omicron COVID-19 pandemic. In this study, we report an integrative proteomics and metabolomics investigation of serum samples from 80 COVID-19 patients infected with Omicron SARS-CoV-2, as well as 160 control serum samples from 80 healthy individuals and 80 patients who had flu-like symptoms but were negative for SARS-CoV-2 infection. The multiomics results indicated that Omicron SARS-CoV-2 infection caused significant changes to host serum proteome and metabolome comparing to the healthy controls and patients who had flu-like symptoms without COVID-19. Protein and metabolite changes also pointed to liver dysfunctions and potential damage to other host organs by Omicron SARS-CoV-2 infection. The Omicron COVID-19 patients could be roughly divided into two subgroups based on their proteome differences. Interestingly, the subgroup who mostly had received full vaccination with booster shot had fewer coughing symptom, changed sphingomyelin lipid metabolism, and stronger immune responses including higher numbers of lymphocytes, monocytes, neutrophils, and upregulated proteins related to CD4+ T cells, CD8+ effector memory T cells (Tem), and conventional dendritic cells, revealing beneficial effects of full COVID-19 vaccination against Omicron SARS-CoV-2 infection through molecular changes.

Chemistry-specific responses due to rice-microbe interactions in the rhizosphere to counteract mefenacet stress.

The widespread use of herbicides has raised considerable concern with regard to their harmful consequences on plant growth, crop yield and the soil ecological environment. It has been well documented that colonization of rhizobacteria in the plant root system has a positive effect on activation of plant defenses to protect the plant from damage. Using the platform of high-throughput analysis with tandem mass spectrometry and Illumina sequencing, we identified the specific activated rhizobacteria, the key growth stimulating substances and the metabolic pathways involved in seedling stage tolerance to mefenacet stress in rice. The relative abundance of beneficial rhizospheremicrobes such as Acidobacteria and Firmicutes increased with mefenacet treatment, indicating that the rhizosphere recruited some beneficial microbes to resist mefenacet stress. Mefenacet treatment induced alterations in several interlinked metabolic pathways, many of which were related to activation of defense response signaling, especially the indole-3-pyruvate pathway. Indole-3-acetaldehyde and indole-3-ethanol from this pathway may act as flexible storage pools for indole-3-acetic acid (IAA). Our findings also suggest that a significant increase of IAA produced by the enrichment of beneficial rhizospheremicrobes, for example genus Bacillus, alleviated the dwarfing phenomenon observed in hydroponic medium following mefenacet exposure, which may be a key signaling molecule primarily for phytostimulation and phytotolerance in microbe-plant interactions.

RNA-Seq analysis in giant pandas reveals the differential expression of multiple genes involved in cataract formation.

BACKGROUND: The giant panda (Ailuropoda melanoleuca) is an endangered mammalian species native to China. Fewer than 2500 giant pandas are known to exist, many of which are bred in captivity as a means to preserve and repopulate the species. Like other captive mammals, giant pandas acquire age-related cataracts, reducing their quality of life. Recent comparative genome-wide methylation analysis revealed 110 differentially methylated genes associated with cataract formation including six also associated with the formation of age-related cataracts in humans. RESULTS: To investigate the pathological pathway in greater detail, here we used RNA-Seq analysis to investigate the differential expression profiles of genes in three giant pandas with cataracts and three healthy controls. We identified more than 700 differentially expressed genes, 29 of which were selected for further analysis based on their low q-value. We found that many of the genes encoded regulatory and signaling proteins associated with the control of cell growth, migration, differentiation and apoptosis, supporting previous research indicating a key role for apoptosis in cataract formation. CONCLUSION: The identification of genes involved in the formation of age-related cataracts could facilitate the development of predictive markers, preventative measures and even new therapies to improve the life of captive animals.

Laterality in Responses to Acoustic Stimuli in Giant Pandas.

Cerebral lateralization is a common feature present in many vertebrates and is often observed in response to various sensory stimuli. Numerous studies have proposed that some vertebrate species have a right hemisphere or left hemisphere dominance in response to specific types of acoustic stimuli. We investigated lateralization of eight giant pandas (Ailuropoda melanoleuca) by using a head turning paradigm and twenty-eight acoustic stimuli with different emotional valences which included twenty-four conspecific and four non-conspecific acoustic stimuli (white noise, thunder, and vocalization of a predator). There was no significant difference in auditory laterality in responses to conspecific or non-conspecific sounds. However, the left cerebral hemisphere processed the positive stimuli, whereas neither of the two hemispheres exhibited a preference for processing the negative stimuli. Furthermore, the right hemisphere was faster than the left hemisphere in processing emotional stimuli and conspecific stimuli. These findings demonstrate that giant pandas exhibit lateralization in response to different acoustic stimuli, which provides evidence of hemispheric asymmetry in this species.

Modulation of steroid metabolism and xenobiotic biotransformation responses in zebrafish (Danio rerio) exposed to triadimefon.

The widely used fungicide triadimefon (TDF) has been detected in aquatic environments, and appears to disrupt steroid homeostasis; however, the toxic effects on fish reproduction triggered by TDF via the key receptor signaling pathways remain largely unknown. The present study showed that TDF (0.069, 0.138, 0.690 mg/L) exposure not only caused disordered germ cell maturation, but also decreased spawned egg production. In order to better understand this reproductive inhibition, we investigated the effects of TDF based on quantitative PCR, Western blot and mass spectrometry methodology in zebrafish. Due to the preferential accumulation of TDF in the liver, a general pattern of up-regulation of genes involved in biotransformation pathway was observed. A significant increase in abcb4 expression appeared to be responsible for TDF excretion. TDF-induced receptors (AhR2 and PXR) changed many genes involved in steroid metabolism, and subsequent disruptions in steroid homeostasis, which might be the key biological pathway in TDF reproductive toxicity. However, due to the different metabolic demands, the transcript profiles involved in steroid metabolism in zebrafish exhibited a sex-specific expression pattern. For example, the increase in gene expression of ahr2 was accompanied by a reduction in the rate of E2 biosynthesis resulting from the diminished cyp19a1a expression, and in turn led to down-regulation of esr1 and vtg1 in the liver, supporting the anti-estrogenic effect of TDF in male fish. In contrast, the increase in E2 production was accompanied by an increase in Esr1 protein expression caused by TDF and paralleled the increase in ahrr1 expression, suggesting that TDF may induce estrogenic activity through AhR-ER interactions in females. In addition, over-induction of cyp3a65 activity mediated through pxr, which helped to accelerate the transformation from TDF to triadimenol in the liver, appeared to elevate T metabolite rate in females. The down-regulation of fshß transcript in males further suggested that TDF might adversely affect normal gametogenesis and induce reproductive toxicity.

[Simultaneous determination of six novel acetolactate synthase inhibitor herbicide residues in oil crops based on ultrasound assisted extraction liquid chromatography-tandem mass spectrometry].

Ultrasound-assisted extraction coupled with liquid chromatography-tandem mass spectrometry (UAE-LC-MS/MS) was used to develop a trace multi-residue detection method for six novel acetolactate synthase (ALS) inhibitor herbicide residues (mesosulfuron-methyl, halosulfuron-methyl, bispyribac-sodium, pyriminobac-methyl, orthosulfamuron, and ethoxysulfuron) in oil crops. In this study, the recoveries of the six herbicides based on ultrasound-assisted and QuEChERS extraction methods were compared, and five adsorbent materials (C18, PSA, GCB, Florisil, and EMR) were optimized based on their purification and adsorption capacities. The results showed that the ultrasound-assisted extractions gave recoveries greater than 90% for the six compounds. Furthermore, EMR showed little adsorption for the six compounds and a reduced matrix effect by effective removal of the oil lipids. The six herbicide residues had good linearities in the concentrations ranging from 0.05 to 500.0 µg/L, and the correlation coefficients were greater than 0.9984. The limits of detection and limits of quantification for this method were 0.08-0.8 µg/kg and 0.25-2.5 µg/kg, respectively. The recoveries of the six pesticides at three spiked levels in four matrices (rapeseed, soybean, peanut, and sunflower seed) ranged from 70.7% to 103.8%, with relative standard deviations of 0.8%-9.2%. This method was successfully applied to the simultaneous determination of six ALS inhibitor herbicide residues in oil crops.

Analysis of four sulfonylurea herbicides in cereals using modified Quick, Easy, Cheap, Effective, Rugged, and Safe sample preparation method coupled with liquid chromatography-tandem mass spectrometry.

A modified Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) sample preparation method, coupled with liquid chromatography-electrospray ionization tandem mass spectrometry, has been developed for the simultaneous analysis of four commonly used sulfonylurea herbicides, ethoxysulfuron, halosulfuron-methyl, mesosulfuron-methyl and orthosulfamuron, in rice, maize, wheat and soybean. Adsorption of the analytes onto the primary-secondary amine used in the clean-up step was avoided by using 1% formic acid in acetonitrile as the extraction solvent to maintain the acidic herbicides in a non-ionized state. Trueness studies were carried out at three levels (2.5, 25 and 250 µg/kg for ethoxysulfuron and 5, 50 and 500 µg/kg for the other three analytes). Promising trueness (70.2%-119.8%) was achieved for all herbicides in all matrices after clean-up, with relative standard deviations (RSDr) < 18.6%. Satisfactory matrix effects (-19.7% to 14.8%) were also obtained. Good linearity of the calibration curves was achieved, with determination coefficients (r) ≥ 0.9956, when the concentration of ethoxysulfuron was in the range 0.5-50 µg/L and that of the other three analytes was in the range 1.0-500 µg/L. The RSDwR for within-laboratory reproducibility was 5.7%. The validated method was successfully used to analyze real samples.