Measurement of China's public health level: compilation and research of an index.

BACKGROUND: With the development of the economy, public health has become increasingly important. Therefore, it is important to establish a comprehensive and scientific the public health level index (PHL) system to measure public health level as a research priority. The current research has limitations in exploring the PHL system; therefore, the field still lacks a comprehensive indicator system to measure the level of public health. Therefore, this paper aims to develop a multi-level public health index system and utilizes China as a case study to evaluate its public health status. The objective is to offer insights and recommendations for the improvement of public health initiatives in China and other regions. METHODS: Utilizing data from 2011 to 2020, a comprehensive PHL was developed to encompass three vital indices: the Public Health Service Index (PHS), the Public Health Resource Index (PHR), and the Population Health Level Index (PHL). Subsequently, the PHL, PHS, PHR, and PH were meticulously calculated using a comprehensive evaluation method. Amid the current disparity between public health and economic progress, both the spatial Durbin model and the spatial lag model were finally employed to examine the influence of economic level (EL) on PHL, thus affirming the consistent reliability and accuracy of PHS. RESULTS: Our findings revealed the following: (i) the PHL, PHS, and PHR indices show increasing trends in China; (ii) both EL and PHL exhibit high-high clustering and low-low clustering states; (iii) the PHL in the area has a positive spatial spillover effect on the surrounding area; (iv) EL will result in the siphoning effect of PHL; and (v) EL can enhance PHL through urbanization, PH, and PHS. CONCLUSIONS: The PHL system constructed in this paper demonstrates multiple levels, pluralism, spatio-temporal comparability, and robustness. It can reflect not only the input and output of public health initiatives but also the interconnectedness and autonomy within the public health system. Therefore, it can be widely utilized in other areas of public health research.

Intestinal toxicity alleviation and efficacy potentiation through therapeutic administration of Lactobacillus paracasei GY-1 in the treatment of gout flares with colchicine.

Gout flares have emerged as a significant public health concern. Colchicine (COL) is a first-line and standard drug for treating gout flares. However, its clinical use is limited due to various adverse effects. Besides, COL fails to adequately meet the needs of patients, particularly young patients. In this study, we investigate the therapeutic administration of Lactobacillus paracasei GY-1 (GY-1) to overcome the limitations of COL. Our results demonstrate that GY-1 attenuates COL toxicity in terms of body weight loss, decreased feed intake, mortality, reduced locomotor activity, colon shortening, increased oxidative stress, histological damage, and impaired gut permeability. Meanwhile, we demonstrate that GY-1 enhances the therapeutic effect for gout flares when combined with COL, as evidenced by the reduction in paw swelling, decreased levels of proinflammatory cytokines including IL-1ß and TNF-α, and an increase in the anti-inflammatory cytokine IL-10. Additionally, the absolute quantification of the gut microbiota shows that GY-1 restores the gut microbiota imbalance caused by COL. Furthermore, GY-1 reduces the abundance of 4 Alistipes species and 6 Porphyromonadaceae species, which may be responsible for toxicity alleviation. At the same time, GY-1 increases the abundance of Bacteroides sartorii and Enterococcus sp., which may contribute to its therapeutic efficacy. This study demonstrates the feasibility of developing probiotic-based adjuvant therapy or bacteriotherapy for treating gout flares. To our knowledge, GY-1 is the first probiotic that could be used as an alternative synergetic agent with COL for the therapeutic treatment of gout flares.

The relationship between agricultural and animal husbandry economic development and carbon emissions in Henan Province, the analysis of factors affecting carbon emissions, and carbon emissions prediction.

This study aims to investigate the relationship between agricultural and animal husbandry economic development and carbon emissions and the influencing factors on carbon emissions. Here, we combine the Tapio decoupling model with the STIRPAT model by using the panel data of Henan province from 2000 to 2020 for it. Our results reveal that (i) the main relationship between agricultural and animal husbandry economic development and carbon emissions is strong decoupling and weak decoupling; (ii) the intensity of carbon emissions and labor effects can optimize their relationship; (iii) the urbanization rate and per capita consumption expenditure in rural areas have a negative impact on carbon emissions, while the carbon emission intensity and total power of agricultural machinery are opposite. Therefore, Henan province needs to optimize its industrial structure, improve the economic level of rural areas, and reduce the use of fertilizers.

Rationally Constructed De Novo Fluorescent Nanosensor for Nitric Oxide Detection and Imaging in Living Cells and Inflammatory Mice Models.

For the early diagnosis and effective evaluation of treatment effects of inflammation, a de novo bioanalytical method is urgently needed to monitor the metabolite nitric oxide (NO) associated with inflammatory diseases. However, developing a reliable detection method with excellent water solubility, biocompatibility, long retention time, and blood circulation is still challenging. In this work, we reported for the first time a de novo host-guest self-assembled nanosensor CTA for the quantitative detection and visualization of NO levels in inflammatory models. CTA mainly consists of two parts: (i) an adamantyl-labeled guest small-molecule RN-adH containing a classical response moiety o-phenylenediamine for a chemical-specific response toward NO and fluorophore rhodamine B with excellent optical properties as an internal reference for self-calibration and (ii) a remarkable water-soluble and biocompatible supramolecular ß-cyclodextrin polymer (Poly-ß-CD) host. In the presence of NO, the o-phenylenediamine unit was reacted with NO at a low pH value of ∼7.0, accompanied by changes in the intensity of the two emission peaks corrected for each other and the change in fluorescence color of the CTA solution from fuchsia to pink. Furthermore, CTA was an effective tool for NO detection with a fast response time (∼60 s), high selectivity, and sensitivity (LOD: 22.3 nM). Impressively, the CTA nanosensor has successfully achieved the targeted imaging of NO in living inflammatory RAW 264.7 cells and mice models with satisfactory results, which can provide a powerful molecular tool for the visualization and assessment of the occurrence and development of NO-related inflammatory diseases in complex biosystems.

Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking.

BACKGROUND: So far, a lot of binning approaches have been intensively developed for untangling metagenome-assembled genomes (MAGs) and evaluated by two main strategies. The strategy by comparison to known genomes prevails over the other strategy by using single-copy genes. However, there is still no dataset with all known genomes for a real (not simulated) bacterial consortium yet. RESULTS: Here, we continue investigating the real bacterial consortium F1RT enriched and sequenced by us previously, considering the high possibility to unearth all MAGs, due to its low complexity. The improved F1RT metagenome reassembled by metaSPAdes here utilizes about 98.62% of reads, and a series of analyses for the remaining reads suggests that the possibility of containing other low-abundance organisms in F1RT is greatly low, demonstrating that almost all MAGs are successfully assembled. Then, 4 isolates are obtained and individually sequenced. Based on the 4 isolate genomes and the entire metagenome, an elaborate pipeline is then in-house developed to construct all F1RT MAGs. A series of assessments extensively prove the high reliability of the herein reconstruction. Next, our findings further show that this dataset harbors several properties challenging for binning and thus is suitable to compare advanced binning tools available now or benchmark novel binners. Using this dataset, 8 advanced binning algorithms are assessed, giving useful insights for developing novel approaches. In addition, compared with our previous study, two novel MAGs termed FC8 and FC9 are discovered here, and 7 MAGs are solidly unearthed for species without any available genomes. CONCLUSION: To our knowledge, it is the first time to construct a dataset with almost all known MAGs for a not simulated consortium. We hope that this dataset will be used as a routine toolkit to complement mock datasets for evaluating binning methods to further facilitate binning and metagenomic studies in the future.

Activated Two-Photon Near-Infrared Ratiometric Fluorescent Nanoprobe for ONOO- Detection and Early Diagnosis and Assessment of Liver Injury.

Liver injury poses a serious threat to human health and growing evidence suggests that it is closely associated with a biomarker (peroxynitrite, ONOO-). Therefore, considering that the relationship of ONOO- levels with the occurrence and development of liver injury disease remains a challenge, an urgent need exists to develop a reliable and robust tool for its visual rapid diagnosis and assessment. Herein, a two-photon near-infrared (TP-NIR) ratiometric fluorescent nanoprobe (NTC) based on a fluorescence resonance energy transfer (FRET) strategy was designed, synthesized, and characterized, which had the advantages of good water solubility, low background interference, deep tissue penetration, and high imaging resolution. Specially, NTC was constructed by self-assembly of an alkynyl group of a small-molecule fluorescent probe (NR) via click chemistry grafting onto azide chitosan (natural polymeric nanomaterial). NR contained acceptor 1 (NIR fluorophore) and donor 3 (D-π-A structure of naphthalimide derivative fluorophore) with outstanding TP properties that could be activated by ONOO- for the ratiometric detection of ONOO-. Furthermore, in the presence of ONOO-, NTC exhibited a short response time (∼10 s) and high selectivity and sensitivity toward ONOO- with an excellent detection limit as low as 15.3 nM over other reactive oxygen/nitrogen species. Notably, NTC has been successfully employed for ONOO- detection and imaging in living HepG2 cells, liver injury mice tissues, and mice models with satisfactory results. Thus, the construction of this NTC nanoprobe can provide a robust molecule tool for enabling early diagnosis and assessment of liver injury in the future.

Rational construction of a fluorescent sensor for simultaneous detection and imaging of hypochlorous acid and peroxynitrite in living cells, tissues and inflammatory rat models.

Modern medical research indicates that hypochlorous acid (HClO) and peroxynitrite (ONOO-) are important biomarkers of oxidative stress. However, the up- or down-regulation of HClO or ONOO- has been closely associated with the occurrence and development of various diseases. In order to investigate the intrinsic entanglement relationship between HClO and ONOO- and their relationship with the occurrence and development of inflammation, it is very valuable to develop fluorescent sensors that are capable of displaying different signals towards HClO, ONOO- and HClO/ONOO-. In this work, we rationally design and construct a novel robust small organic molecule fluorescent sensor (RhNp-ClO-ONOO) towards ONOO-, HClO and HClO/ONOO- with green, red, and green-red three different fluorescent signal outputs, respectively. RhNp-ClO-ONOO has fast responsive time for HClO (∼60 s) and ONOO- (∼20 s). Also it has markedly low detection limits for HClO (∼25.3 nM) and ONOO- (12.4 nM) respectively. In addition, RhNp-ClO-ONOO could be further shown to detect endogenous HClO/ONOO- in living cells, inflammatory tissues and rat model successfully. Therefore, this novel fluorescent sensor with double responsive moiety can offer a powerful tool for studying the role of HClO and ONOO- and the occurrence and development of inflammatory diseases.

FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation.

We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50-60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes.

Molecular engineering for construction of a novel ONOO-- activated multicolor fluorescent nanoprobe for early diagnosis and assessing treatment of arthritis in vivo.

Early diagnosis and assessment of the therapeutic effect of arthritis requires a reliable bioanalytical method to quantitatively and selectively detect the biomarkers peroxynitrite (ONOO-) in inflammatory diseases. Compared with previously reported probes for the specific detection of ONOO-, molecular engineering based on ONOO--activated multicolor fluorescence nanoprobes will have the advantages of providing multi-channel information and be more suitable for bioimaging in multicomponent complex environments. Herein, for the first time, a fluorescent nanoprobe (CSU-FT) based on fluorescence resonance energy transfer (FRET), which can be activated by ONOO-, was constructed for multicolor fluorescence imaging, diagnosis and treatment of arthritis in inflammatory mice. Specifically, an energy transfer scaffold was constructed by conjugation of a near-infrared (NIR) xanthane fluorophore with a rhodamine B fluorophore and multicolor by ONOO--modulated, which was then grafted onto sodium chondroitin sulfate (CSNa) to form CSU-FT through self-assembly. This nanoprobe shows a fast response time (<20s), outstanding selectivity and excellent detection limits as low as 11.7 nM. Interestingly, CSU-FT has been successfully used for intracellular multichannel imaging of endogenous ONOO- production as well as for diagnosis and treatment in a mice model of arthritis with impressive results, revealing practical application in physiological and pathological connection between ONOO- and arthritis.

A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes.

BACKGROUND: Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are computationally intensive. To address this problem, a strategy consisting of sieving (pre-selecting closely related genomes) followed by alignment and calculation has been proposed. RESULTS: Here, we initially test a published approach called "genome-wide tetranucleotide frequency correlation coefficient" (TETRA), which is specially tailored for sieving. Our results show that sieving by TETRA requires > 40% completeness for both genomes of a pair to yield > 95% sensitivity, indicating that TETRA is completeness-dependent. Accordingly, we develop a novel algorithm called "fragment tetranucleotide frequency correlation coefficient" (FRAGTE), which uses fragments rather than whole genomes for sieving. Our results show that FRAGTE achieves ~ 100% sensitivity and high specificity on simulated genomes, real genomes and metagenome-assembled genomes, demonstrating that FRAGTE is completeness-independent. Additionally, FRAGTE sieved a reduced number of total genomes for subsequent alignment and calculation to greatly improve computational efficiency for the process after sieving. Aside from this computational improvement, FRAGTE also reduces the computational cost for the sieving process. Consequently, FRAGTE extremely improves run efficiency for both the processes of sieving and after sieving (subsequent alignment and calculation) to together accelerate genome-wide species delineation. CONCLUSIONS: FRAGTE is a completeness-independent algorithm for sieving. Due to its high sensitivity, high specificity, highly reduced number of sieved genomes and highly improved runtime, FRAGTE will be helpful for whole-genome approaches to facilitate taxonomic studies in prokaryotes.

A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms.

BACKGROUND: Genomic composition has been found to be species specific and is used to differentiate bacterial species. To date, almost no published composition-based approaches are able to distinguish between most closely related organisms, including intra-genus species and intra-species strains. Thus, it is necessary to develop a novel approach to address this problem. RESULTS: Here, we initially determine that the "tetranucleotide-derived z-value Pearson correlation coefficient" (TETRA) approach is representative of other published statistical methods. Then, we devise a novel method called "Tetranucleotide-derived Z-value Manhattan Distance" (TZMD) and compare it with the TETRA approach. Our results show that TZMD reflects the maximal genome difference, while TETRA does not in most conditions, demonstrating in theory that TZMD provides improved resolution. Additionally, our analysis of real data shows that TZMD improves species differentiation and clearly differentiates similar organisms, including similar species belonging to the same genospecies, subspecies and intraspecific strains, most of which cannot be distinguished by TETRA. Furthermore, TZMD is able to determine clonal strains with the TZMD = 0 criterion, which intrinsically encompasses identical composition, high average nucleotide identity and high percentage of shared genomes. CONCLUSIONS: Our extensive assessment demonstrates that TZMD has high resolution. This study is the first to propose a composition-based method for differentiating bacteria at the strain level and to demonstrate that composition is also strain specific. TZMD is a powerful tool and the first easy-to-use approach for differentiating clonal and non-clonal strains. Therefore, as the first composition-based algorithm for strain typing, TZMD will facilitate bacterial studies in the future.

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community.

Reaching a comprehensive understanding of how nature solves the problem of degrading recalcitrant biomass may eventually allow development of more efficient biorefining processes. Here we interpret genomic and proteomic information generated from a cellulolytic microbial consortium (termed F1RT) enriched from soil. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes. Support for cellulolytic inter-species cooperation came from the discovery of F1RT microbes that encode and express complimentary enzymatic inventories that include both extracellular cellulosomes and secreted free-enzyme systems. Metabolic reconstruction of the seven F1RT phylotypes predicted a wider genomic rationale as to how this particular community functions as well as possible reasons as to why biomass conversion in nature relies on a structured and cooperative microbial community.

Genomic evolution of 11 type strains within family Planctomycetaceae.

The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.

Comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification.

Campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire Campylobacter genus to study their underlying genetic diversification. Up to now, 34 Campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. In this study, we first conducted genomic characterization, which includes genome-wide alignments, pan-genome analysis, and phylogenetic identification, to depict the genetic diversity of Campylobacter genus. Afterward, we improved the tetranucleotide usage pattern-based naïve Bayesian classifier to identify the abnormal composition fragments (ACFs, fragments with significantly different tetranucleotide frequency profiles from its genomic tetranucleotide frequency profiles) including horizontal gene transfers (HGTs) to explore the mechanisms for the genetic diversity of this organism. Finally, we analyzed the HGTs transferred via bacteriophage transductions. To our knowledge, this study is the first to use single nucleotide polymorphism information to construct liable microevolution phylogeny of 21 Campylobacter jejuni strains. Combined with the phylogeny of all the collected Campylobacter species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 Campylobacter organisms was determined. It was found that C. jejuni harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other Campylobacter members possess numerous ACFs possibly via intragenus recombination. Furthermore, some Campylobacter strains have undergone significant ancient viral integration during their evolution process. The improved method is a powerful tool for bacterial genomic analysis. Moreover, the findings would provide useful information for future research on Campylobacter genus.

Cloning, expression, and antigenicity of 14 proteins from Campylobacter jejuni.

Fourteen Campylobacter jejuni genes--porA, cadF, omp18, dnaK, flaC, peb1, peb2, peb3, peb4, ahpC, groEL, tuF, hipO, and Cj0069--were cloned and expressed in Escherichia coli BL21. The recombinant proteins were purified on histidine (His) and glutathione S-transferase (GST) trap columns using the ÄKTA Explorer 100 System. Recombinant proteins were visualized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The antigenicities of these recombinant proteins were assessed by Western blotting and enzyme-linked immunosorbent assays with anti-C. jejuni immune rabbit sera. Four recombinant proteins, including rGST-PorA, rHis-CadF, rGST-GroEL, and rGST-TuF, demonstrated reactions with both anti-serum and preimmune serum, while rHis-DnaK, rGST-FlaC, rGST-PEB2, rGST-PEB3, rGST-PEB4, and rGST-HipO showed variable antigenicity characteristics to the anti-sera derived from different C. jejuni strains. rHis-Omp18, rHis-PEB1, and rGST-AhpC demonstrated universal and specific antigenities with the entire anti-sera panel tested in this present study, while recombinant rGST-Cj0069 and rHis-DnaK did not react with any of the anti-C. jejuni sera tested. In conclusion, rGST-AhpC may be useful as a potential serodiagnostic antigen for C. jejuni infection.