Comparative Extracellular Proteomics of Aeromonas hydrophila Reveals Iron-Regulated Secreted Proteins as Potential Vaccine Candidates

In our previous study, several iron-related outer membrane proteins in Aeromonas hydrophila, a serious pathogen of farmed fish, conferred high immunoprotectivity to fish, and were proposed as potential vaccine candidates. However, the protective efficacy of these extracellular proteins against A. hydrophila remains largely unknown. Here, we identified secreted proteins that were differentially expressed in A. hydrophila LP-2 in response to iron starvation using an iTRAQ-based quantitative proteomics method. We identified 341 proteins, of which 9 were upregulated in response to iron starvation and 24 were downregulated. Many of the differently expressed proteins were associated with protease activity. We confirmed our proteomics results with Western blotting and qPCR. We constructed three mutants by knocking out three genes encoding differentially expressed proteins (Δorf01830, Δorf01609, and Δorf03641). The physiological characteristics of these mutants were investigated. In all these mutant strains, protease activity decreased, and Δorf01609, and Δorf01830 were less virulent in zebrafish. This indicated that the proteins encoded by these genes may play important roles in bacterial infection. We next evaluated the immune response provoked by the six iron-related recombinant proteins (ORF01609, ORF01830, ORF01839, ORF02943, ORF03355, and ORF03641) in zebrafish as well as the immunization efficacy of these proteins. Immunization with these proteins significantly increased the zebrafish immune response. In addition, the relative percent survival (RPS) of the immunized zebrafish was 50–80% when challenged with three virulent A. hydrophila strains, respectively. Thus, these extracellular secreted proteins might be effective vaccine candidates against A. hydrophila infection in fish

Quantitative Proteomics Reveals Antibiotics Resistance Function of Outer Membrane Proteins in Aeromonas hydrophila

Outer membrane proteins (OMPs) play essential roles in antibiotic resistance, particularly in Gram-negative bacteria; however, they still have many unidentified functions regarding their behavior in response to antibiotic stress. In the current work, quantitative tandem mass tag labeling-based mass spectrometry was used to compare the outer membrane related proteins between an oxytetracycline-resistant (OXY-R) and its original control stain (OXY-O) in Aeromonas hydrophila. Consequently, a total of 261 commonly altered proteins in two biological repeats were identified including 29 proteins that increased and 28 that decreased. Gene ontology analysis showed that the expression of transport proteins was significantly reduced, and translation-related proteins were downregulated in the OXY-R strain. After using western blotting to validate selected altered proteins, eight OMP-related genes were knocked out and their roles in antibiotic resistance were further evaluated. The survival assays showed that some mutants such as ΔAHA_4281, ΔAHA_2766, ΔAHA_2282, ΔAHA_1181, and ΔAHA_1280 affected the susceptibility of A. hydrophila to antimicrobials. Moreover, the minimum inhibitory concentration assay showed that these candidate mutants also respond differently to other types of antibiotics. Our results reveal several novel outer membrane related proteins of A. hydrophila that play important roles in antibiotic resistance, and as such, may be helpful for screening studies to identify novel drug targets

The quality difference in five oolong tea accessions under different planting management patterns in south Fujian of China

IntroductionOolong tea, celebrated for its significance in Chinese tea culture, was the subject of investigation in this study.MethodsFive varieties of Minnan oolong tea were sampled, each cultivated under two distinct management approaches: conventional management and natural growth methods. The study aimed to discern variations in sensory attributes, encompassing appearance and liquor color, alongside the analysis of chemical composition.Results and discussionThe results indicated that oolong tea cultivated through conventional manual management generally exhibited qualities in terms of shape and foliage appearance, in contrast to those grown naturally. However, naturally grown oolong tea tended to exhibit more favorable aroma and taste profiles compared to conventionally managed counterparts. Furthermore, the content of water extract, amino acids, polyphenols, caffeine, and other pivotal chemical constituents were typically higher in naturally grown tea varieties compared to conventionally managed ones. Conversely, catechin content was found to be more abundant in traditionally managed bushes than in those grown naturally. These findings emphasize the significance of implementing appropriate natural growth management practices to enhance the quality of Minnan oolong tea and maintain ecological sustainability

Extended Wiener-Khinchin theorem for quantum spectral analysis

The classical Wiener-Khinchin theorem (WKT), which can extract spectral information by classical interferometers through Fourier transform, is a fundamental theorem used in many disciplines. However, there is still need for a quantum version of WKT, which could connect correlated biphoton spectral information by quantum interferometers. Here, we extend the classical WKT to its quantum counterpart, i.e., extended WKT (e-WKT), which is based on two-photon quantum interferometry. According to the e-WKT, the difference-frequency distribution of the biphoton wavefunctions can be extracted by applying a Fourier transform on the time-domain Hong-Ou-Mandel interference (HOMI) patterns, while the sum-frequency distribution can be extracted by applying a Fourier transform on the time-domain NOON state interference (NOONI) patterns. We also experimentally verified the WKT and e-WKT in a Mach-Zehnder interference (MZI), a HOMI and a NOONI. This theorem can be directly applied to quantum spectroscopy, where the spectral correlation information of biphotons can be obtained from time-domain quantum interferences by Fourier transform. This may open a new pathway for the study of light-matter interaction at the single photon level.Comment: 13 pages, 5 figure

Metagenomics-based exploration of key soil microorganisms contributing to continuously planted Casuarina equisetifolia growth inhibition and their interactions with soil nutrient transformation

Casuarina equisetifolia (C. equisetifolia) is an economically important forest tree species, often cultivated in continuous monoculture as a coastal protection forest. Continuous planting has gradually affected growth and severely restricted the sustainable development of the C. equisetifolia industry. In this study, we analyzed the effects of continuous planting on C. equisetifolia growth and explored the rhizosphere soil microecological mechanism from a metagenomic perspective. The results showed that continuous planting resulted in dwarfing, shorter root length, and reduced C. equisetifolia seedling root system. Metagenomics analysis showed that 10 key characteristic microorganisms, mainly Actinoallomurus, Actinomadura, and Mycobacterium, were responsible for continuously planted C. equisetifolia trees. Quantitative analysis showed that the number of microorganisms in these three genera decreased significantly with the increase of continuous planting. Gene function analysis showed that continuous planting led to the weakening of the environmental information processing-signal transduction ability of soil characteristic microorganisms, and the decrease of C. equisetifolia trees against stress. Reduced capacity for metabolism, genetic information processing-replication and repair resulted in reduced microbial propagation and reduced microbial quantity in the rhizosphere soil of C. equisetifolia trees. Secondly, amino acid metabolism, carbohydrate metabolism, glycan biosynthesis and metabolism, lipid metabolism, metabolism of cofactors and vitamins were all significantly reduced, resulting in a decrease in the ability of the soil to synthesize and metabolize carbon and nitrogen. These reduced capacities further led to reduced soil microbial quantity, microbial carbon and nitrogen, microbial respiration intensity, reduced soil enzyme nutrient cycling and resistance-related enzyme activities, a significant reduction in available nutrient content of rhizosphere soils, a reduction in the ion exchange capacity, and an impediment to C. equisetifolia growth. This study provides an important basis for the management of continuously planted C. equisetifolia plantations

Minute-Cadence Observations of the LAMOST Fields with the TMTS V. Machine Learning Classification of TMTS Catalogues of Periodic Variable Stars

Periodic variables are always of great scientific interest in astrophysics. Thanks to the rapid advancement of modern large-scale time-domain surveys, the number of reported variable stars has experienced substantial growth for several decades, which significantly deepened our comprehension of stellar structure and binary evolution. The Tsinghua University-Ma Huateng Telescopes for Survey (TMTS) has started to monitor the LAMOST sky areas since 2020, with a cadence of 1 minute. During the period from 2020 to 2022, this survey has resulted in densely sampled light curves for ~ 30,000 variables of the maximum powers in the Lomb-Scargle periodogram above the 5sigma threshold. In this paper, we classified 11,638 variable stars into 6 main types using XGBoost and Random Forest classifiers with accuracies of 98.83% and 98.73%, respectively. Among them, 5301 (45.55%) variables are newly discovered, primarily consisting of Delta Scuti stars, demonstrating the capability of TMTS in searching for short-period variables. We cross-matched the catalogue with Gaia's second Data Release (DR2) and LAMOST's seventh Data Release (DR7) to obtain important physical parameters of the variables. We identified 5504 Delta Scuti stars (including 4876 typical Delta Scuti stars and 628 high-amplitude Delta Scuti stars), 5899 eclipsing binaries (including EA-, EB- and EW-type) and 226 candidates of RS Canum Venaticorum. Leveraging the metal abundance data provided by LAMOST and the Galactic latitude, we discovered 8 candidates of SX Phe stars within the class of "Delta Scuti stars". Moreover, with the help of Gaia color-magnitude diagram, we identified 9 ZZ ceti stars.Comment: 20 pages, 14 figures, accepted to MNRA

Sustained organic amendments utilization enhances ratoon crop growth and soil quality by enriching beneficial metabolites and suppressing pathogenic bacteria

IntroductionOrganic soil amendments such as filter mud (FM) and biochar (BC) can potentially influence the abundance and composition of metabolites. However, our current understanding of the stimulatory effects of FM and BC’s long-term impact on stress-regulating metabolites, such as abscisic acid (ABA), jasmonic acid (JA), melatonin, and phenyllactic acid (PLA), and these substrates regulatory effects on disease-causing bacteria in sugarcane ratooning field, which is susceptible to nutrients depletion, diseases, etc., remain poorly understood. Additionally, little is known about how the long-term interaction of these substrates and compounds influences sugarcane ratooning soil enzyme activities, nutrient cycling, and crop growth performance.MethodsTo answer these questions, we adopted metabolomics tools combined with high-throughput sequencing to explore the stimulatory effects of the long-term addition of FM and BC on metabolites (e.g., PLA and abscisic aldehyde) and quantify these substrates’ regulatory effects on disease-causing bacteria, soil enzyme activities, nutrient cycling, and crop growth performance.ResultsThe result revealed that ratoon crop weight, stem diameter, sugar content, as well as soil physico-chemical properties, including soil nitrate (NH3+-N), organic matter (OM), total nitrogen (TN), total carbon (TC), and β-glucosidase, marked a significant increase under the BC and FM-amended soils. Whereas soil available potassium (AK), NO3–N, cellulase activity, and phosphatase peaked under the BC-amended soil, primarily due to the enduring effects of these substrates and metabolites. Furthermore, BC and FM-amended soils enriched specific stress-regulating metabolites, including JA, melatonin, abscisic aldehyde, etc. The sustained effects of both BC and FM-amended soils suppressed disease-causing bacteria, eventually promoting ratooning soil growth conditions. A number of key bioactive compounds had distinct associations with several beneficial bacteria and soil physico-chemical properties.DiscussionThis study proves that long-term BC and FM application is one of the eco-friendly strategies to promote ratoon crop growth and soil quality through the enrichment of stress-regulating metabolites and the suppression of disease-causing bacteria

Minute-cadence Observations of the LAMOST Fields with the TMTS: III. Statistic Study of the Flare Stars from the First Two Years

Tsinghua University-Ma Huateng Telescopes for Survey (TMTS) aims to detect fast-evolving transients in the Universe, which has led to the discovery of thousands of short-period variables and eclipsing binaries since 2020. In this paper, we present the observed properties of 125 flare stars identified by the TMTS within the first two years, with an attempt to constrain their eruption physics. As expected, most of these flares were recorded in late-type red stars with $G_{\rm BP}-G_{\rm RP}$ > 2.0 mag, however, the flares associated with bluer stars tend to be on average more energetic and have broader profiles. The peak flux (F_peak) of the flare is found to depend strongly on the equivalent duration (ED) of the energy release, i.e., $F_{{\rm peak}} \propto {\rm ED}^{0.72\pm0.04}$, which is consistent with results derived from the Kepler and Evryscope samples. This relation is likely related to the magnetic loop emission, while -- for the more popular non-thermal electron heating model -- a specific time evolution may be required to generate this relation. We notice that flares produced by hotter stars have a flatter $F_{{\rm peak}} \propto {\rm ED}$ relation compared to that from cooler stars. This is related to the statistical discrepancy in light-curve shape of flare events with different colors. In spectra from LAMOST, we find that flare stars have apparently stronger H alpha emission than inactive stars, especially at the low temperature end, suggesting that chromospheric activity plays an important role in producing flares. On the other hand, the subclass having frequent flares are found to show H alpha emission of similar strength in their spectra to that recorded with only a single flare but similar effective temperature, implying that the chromospheric activity may not be the only trigger for eruptions.Comment: 17 pages, 15 figures, 2 tables, refereed version. For associated data files, see https://cdsarc.cds.unistra.fr/viz-bin/cat/J/MNRAS/523/219

Effect of reduced nitrogen fertilizer application combined with biochar on nitrogen utilization of flue-cured tobacco and its association with functional gene expressions of the nitrogen cycle in rhizosphere soil

Studies have shed light on the impact of the co-application of inorganic fertilizer and biochar on soil fertility, health, and crop growth performance and yield. However, insufficient literature exists regarding the appropriate nitrogen reduction ratio for enhancing soil quality and maximizing crop nitrogen utilization following the application of biochar in a continuous tobacco-rice rotation field. Here, we explored nitrogen absorption and utilization patterns of tobacco crops, as well as the response characteristics of functional genes related to soil nitrogen cycling subjected to the interaction of reduced nitrogen utilization ratios following biochar application in a long-term tobacco-rice rotation field. The results showed that the treatments with 10% (T2) and 20% (T3) nitrogen reduction combined with biochar (30 t∙ha−1) promoted nitrogen utilization efficiency and nitrogen harvest index of tobacco plants. In the second year of the experiment, T2 and T3 significantly increased the nitrogen harvest index by 3.85% and 5.78% compared with the conventional nitrogen application treatment (T1), respectively. We believe that the increase in abundance of nitrification, nitrogen fixation, and ammonification genes, including nxrA, nifH, and UreC in the rhizosphere soil, precipitate the high nitrogen absorption and utilization efficiency in the biochar combined with nitrogen reduction treatments, respectively. This suggests that biochar application at a rate of 30 t·ha−1, nitrogen fertilizer usage can be reduced by 10% and 20% to achieve optimal and sustainable tobacco production