D-Limonene Inhibits Pichia kluyveri Y-11519 in Sichuan Pickles by Disrupting Metabolism.

The Pichia kluyveri, a proliferation commonly found in Sichuan pickles (SCPs), can accelerate the growth and reproduction of spoilage bacteria, causing off-odor development and decay. Although D-limonene, a common natural preservative, effectively restricts P. kluyveri, its inhibitory mechanism remains unclear. This study aimed to elucidate this molecular mechanism by investigating the impact on basic P. kluyveri metabolism. The findings revealed that D-limonene inhibited P. kluyveri growth and disrupted the transcription of the genes responsible for encoding the enzymes involved in cell wall and membrane synthesis, oxidative phosphorylation, glycolysis, and the tricarboxylic acid (TCA) cycle pathway. The results indicated that these events disrupted crucial metabolism such as cell wall and membrane integrity, adenosine triphosphate (ATP) synthesis, and reactive oxygen species (ROS) balance. These insights provided a comprehensive understanding of the inhibitory effect of D-limonene on the growth and reproduction of P. kluyveri while highlighting its potential application in the SCP industry.

Enhancing targeted tumor treatment: A novel fuzzy logic framework for precision drug delivery strategy selection.

OBJECTIVE: This study aims to address the challenge of selecting optimal drug delivery strategies for tumor patients by introducing a novel theoretical framework. METHODS: We propose a fuzzy logic-based framework for quantitatively assessing Health States (HS) in tumor patients. This framework integrates quantified HS assessments with causality strength analyses, offering a comprehensive understanding of various drug delivery schemes' effectiveness from pharmacokinetic and pharmacodynamic perspectives. RESULTS: The efficacy of our approach is demonstrated through a series of real-world patient case studies, highlighting its potential to enhance the evaluation and selection of targeted drug delivery strategies. CONCLUSION: Our work contributes to the field by showcasing practical applications of fuzzy logic in targeted drug delivery systems (TDDs) and establishing a new benchmark for precision in drug delivery strategy selection. SIGNIFICANCE: This study has significant implications for developing personalized medical treatments, potentially revolutionizing the field with a more nuanced and scientifically rigorous method for evaluating and selecting drug delivery protocols. CONTRIBUTIONS: Development of a fuzzy logic framework for precise quantification of health states in tumor patients. Innovative integration of a causal system for comprehensively evaluating targeted drug delivery strategies.

Anti-signal recognition particle antibodies induce cardiac diastolic dysfunction via oxidative stress injury.

Objectives: Anti-signal recognition particle (SRP) antibodies, markers of immune-mediated necrotising myopathy, are reportedly related to cardiac involvement; however, whether they are pathogenic to the myocardium remains unclear. We aimed, therefore, to explore the pathogenicity of anti-SRP antibodies against the myocardium through in vivo and in vitro studies. Methods: Total immunoglobulin G (IgG), purified from patients with positive anti-SRP antibodies, was passively transferred into C57BL/6 mice. Cardiac function was evaluated via echocardiography and the ventricular pressure-volume loop; cardiac histological changes were analysed using haematoxylin-eosin staining, picrosirius red staining, immunofluorescence and immunohistochemistry. Additionally, reactive oxygen species (ROS) formation was evaluated by dihydroethidium (DHE) staining; mitochondrial morphology and function were evaluated using transmission electron microscopy and seahorse mitochondrial respiration assay, respectively. The myositis cohort at our centre was subsequently reviewed in terms of cardiac assessments. Results: After the passive transfer of total IgG from patients with positive anti-SRP antibodies, C57BL/6 mice developed significant left ventricular diastolic dysfunction (LVDD). Transcriptomic analysis and corresponding experiments revealed increased oxidative stress and mitochondrial damage in the hearts of the experimental mice. Cardiomyocytes exposed to anti-SRP-specific IgG, however, recovered normal mitochondrial metabolism after treatment with N-acetylcysteine, an ROS scavenger. Moreover, patients positive for anti-SRP antibodies manifested worse diastolic but equivalent systolic function compared to their counterparts after propensity score matching. Conclusion: Anti-SRP antibodies may play a pathogenic role in the development of LVDD by promoting ROS production and subsequent myocardial mitochondrial impairment. The inhibition of oxidative stress was effective in reversing anti-SRP antibody-induced LVDD.

Carbon metabolism of a novel isolate from Lacticaseibacillus rhamnosus Probio-M9 derived through space mutant.

AIMS: Carbon source is a necessary nutrient for bacterial strain growth. In industrial production, the cost of using different carbon sources varies greatly. Moreover, the complex environment in space may cause metabolic a series of changes in the strain, and this method has been successfully applied in some basic research. To date, space mutagenesis is still limited number of studies, particularly in carbon metabolism of probiotics. METHODS AND RESULTS: HG-R7970-41 was isolated from bacterium suspension (Probio-M9) after space flight, which can produce capsular polysaccharide after space mutagenesis. Phenotype Microarray (PM) was used to evaluated the metabolism of HG-R7970-41 in 190 single carbon sources. RNA sequencing and total protein identification of two strains revealed their different carbon metabolism mechanisms. PM results demonstrated the metabolism of 10 carbon sources were different between Probio-M9 and HG-R7970-41. Transcriptomic and proteomic analyses revealed that this change in carbon metabolism of HG-R7970-41 mainly related to changes in phosphorylation and the glycolysis pathway. Based on the metabolic mechanism of different carbon sources and related gene cluster analysis, we found that the final metabolic activities of HG-R7970-41 and Probio-M9 were mainly regulated by PTS-specific membrane embedded permease (EII), carbohydrate kinase and two rate-limiting enzymes (phosphofructokinase (PFK) and pyruvate kinase (PYK)) in the glycolysis pathway. The expanded culture test also confirmed that HG-R7970-41 had different metabolic characteristics from original strain. CONCLUSIONS: These results suggested that space environment could change carbon metabolism of Probio-M9. The new isolate (HG-R7970-41) showed a different carbon metabolism pattern from the original strain mainly by the regulation of two rate-limiting enzymes.

Lipid-associated macrophages for osimertinib resistance and leptomeningeal metastases in NSCLC.

Leptomeningeal metastases (LMs) remain a devastating complication of non-small cell lung cancer (NSCLC), particularly following osimertinib resistance. We conducted single-cell RNA sequencing on cerebrospinal fluid (CSF) from EGFR-mutant NSCLC with central nervous system metastases. We found that macrophages of LMs displayed functional and phenotypic heterogeneity and enhanced immunosuppressive properties. A population of lipid-associated macrophages, namely RNASE1_M, were linked to osimertinib resistance and LM development, which was regulated by Midkine (MDK) from malignant epithelial cells. MDK exhibited significant elevation in both CSF and plasma among patients with LMs, with higher MDK levels correlating to poorer outcomes in an independent cohort. Moreover, MDK could promote macrophage M2 polarization with lipid metabolism and phagocytic function. Furthermore, malignant epithelial cells in CSF, particularly after resistance to osimertinib, potentially achieved immune evasion through CD47-SIRPA interactions with RNASE1_M. In conclusion, we revealed a specific subtype of macrophages linked to osimertinib resistance and LM development, providing a potential target to overcome LMs.

Renalase alleviates salt-induced kidney necroptosis and inflammation.

Recent evidence suggests that necroptosis may contribute to the development of kidney injury. Renalase is a novel secretory protein that exerts potent prosurvival and anti-inflammatory effects. We hypothesized that renalase could protect the kidney from salt-induced injury by modulating necroptosis. High salt and renalase treatments were administered to Dahl salt-sensitive (SS) rats, renalase knockout (KO) mice, and HK-2 cells. Furthermore, a cohort of 514 eligible participants was utilized to investigate the association between single nucleotide polymorphisms (SNPs) in the genes RIPK1, RIPK3, and MLKL, and the risk of subclinical renal damage (SRD) over 14 years. A high-salt diet significantly increased the expression of key components of necroptosis, namely RIPK1, RIPK3, and MLKL, as well as the release of inflammatory factors in SS rats. Treatment with recombinant renalase reduced both necroptosis and inflammation. In renalase KO mice, salt-induced kidney injury was more severe than in wild-type mice, but supplementation with renalase attenuated the kidney injury. In vitro experiments with HK-2 cells revealed high salt increased necroptosis and inflammation. Renalase exhibited a dose-dependent decrease in salt-induced necroptosis, and this cytoprotective effect was negated by the knockdown of PMCA4b, which is the receptor of renalase. Furthermore, the cohort study showed that SNP rs3736724 in RIPK1 and rs11640974 in MLKL were significantly associated with the risk of SRD over 14 years. Our analysis shows that necroptosis plays a significant role in the development of salt-induced kidney injury and that renalase confers its cytoprotective effects by inhibiting necroptosis and inflammation.

Colorimetric and Fluorometric Determination of Fluoride in Tetrahydrofuran and Dimethyl Sulfoxide Using a 4-Hydroxypyrene Probe.

F- ions (fluoride ions) are crucial in various chemical waste and environmental safety contexts. However, excessive fluoride exposure can pose a threat to human well-being. In this study, a simple 4-substituted pyrene derivative known as 4-hydroxypyrene (4-PyOH) was designed as a colorimetric probe for detecting F- through the formation of hydrogen bonds between F- and a hydroxyl group. The probe 4-PyOH exhibited exceptional sensitivity and selectivity towards F- ions and was successfully utilized as test strips for detecting F- ions in organic solvents. The detection limit reached an impressively low level of 3.06 × 10-7 M in the organic solvent. The recognition mechanism was confirmed through 1H NMR titration.

Acute nitrite exposure causes gut microbiota dysbacteriosis and proliferation of pathogenic Photobacterium in shrimp.

Nitrite exposure has become a significant concern in the aquaculture industry, posing a severe threat to aquatic animals such as shrimp. While studies have reported the adverse effects of nitrite on shrimp growth, the part played by the gut microbiota in shrimp mortality resulting from nitrite exposure is poorly understood. Here, the effects of nitrite on shrimp gut bacterial community were investigated using 16S rRNA amplicon sequencing, bacterial isolation, genomic analysis, and infection experiments. Compared to the control_healthy group, changes in the bacterial composition of the nitrite_dead group were associated with reduced abundance of specific beneficial bacteria and increased abundance of certain pathogenic bacteria. Notably, members of the Photobacterium genus were found to be significantly enriched in the nitrite_dead group. Genomic analysis of a representative Photobacterium strain (LvS-8n3) revealed a variety of genes encoding bacterial toxins, including hemolysin, adhesin, and phospholipase. Furthermore, it was also found that LvS-8n3 exhibits strong pathogenicity, probably due to its high production of pathogenic factors and the ability to utilize nitrite for proliferation. Therefore, the proliferation of pathogenic Photobacterium species appears pivotal for driving shrimp mortality caused by nitrite exposure. These findings provide novel insights into the disease mechanism in shrimp under conditions of environmental change.

Ubiquitin-Specific Protease 22 Plays a Key Role in Increasing Extracellular Vesicle Secretion and Regulating Cell Motility of Lung Adenocarcinoma.

Tumor-derived extracellular vesicles (EVs) are potential biomarkers for tumors, but their reliable molecular targets have not been identified. The previous study confirms that ubiquitin-specific protease 22 (USP22) promotes lung adenocarcinoma (LUAD) metastasis in vivo and in vitro. Moreover, USP22 regulates endocytosis of tumor cells and localizes to late endosomes. However, the role of USP22 in the secretion of tumor cell-derived EVs remains unknown. In this study, it demonstrates that USP22 increases the secretion of tumor cell-derived EVs and accelerates their migration and invasion, invadopodia formation, and angiogenesis via EV transfer. USP22 enhances EV secretion by upregulating myosin IB (MYO1B). This study further discovers that USP22 activated the SRC signaling pathway by upregulating the molecule KDEL endoplasmic reticulum protein retention receptor 1 (KDELR1), thereby contributing to LUAD cell progression. The study provides novel insights into the role of USP22 in EV secretion and cell motility regulation in LUAD.

PASTICCINO2 interacting with Golgi Anti-Apoptotic Proteins resists endoplasmic reticulum stress dependent on very long-chain fatty acids.

The endoplasmic reticulum (ER) is crucial for maintaining cell homeostasis because it is the primary site for synthesizing secreted and transmembrane proteins and lipids. The unfolded protein response (UPR) is activated to restore ER homeostasis under ER stress. However, the relationship between lipids and the ER stress response in plants is not well understood. Arabidopsis Golgi anti-apoptotic proteins (GAAPs) are involved in resisting ER stress. To elucidate the function of GAAPs, PASTICCINO2 (PAS2), involved in very long-chain fatty acid (VLCFA) synthesis, was found to interact with GAAPs and IRE1. Single pas2 and gaap1/gaap2pas2 double mutants exhibited increased seedling damage and impaired UPR response under chronic ER stress. Site mutation combined with genetic analysis revealed that the role of PAS2 in resisting ER stress depended on its VLCFA synthesis domain. VLCFA contents were upregulated under ER stress, which required GAAPs. Exogenous VLCFAs partially restored the defect in UPR upregulation caused by PAS2 or GAAP mutations under chronic ER stress. These findings demonstrate that the association of PAS2 with GAAPs confers plant resistance to ER stress by regulating VLCFA synthesis and the UPR. This provides a basis for further studies on the connection between lipids and cell fate decisions under stress.

3MT-Net: A Multi-modal Multi-task Model for Breast Cancer and Pathological Subtype Classification Based on a Multicenter Study.

Breast cancer significantly impacts women's health, with ultrasound being crucial for lesion assessment. To enhance diagnostic accuracy, computer-aided detection (CAD) systems have attracted considerable interest. This study introduces a prospective deep learning architecture called "Multi-modal Multi-task Network" (3MT-Net). 3MT-Net utilizes a combination of clinical data, B-mode, and color Doppler ultrasound. We have designed the AM-CapsNet network, specifically tailored to extract crucial tumor features from ultrasound. To combine clinical data in 3MT-Net, we have employed a cascaded cross-attention to fuse information from three distinct sources. To ensure the preservation of pertinent information during the fusion of high-dimensional and low-dimensional data, we adopt the idea of ensemble learning and design an optimization algorithm to assign weights to different modalities. Eventually, 3MT-Net performs binary classification of benign and malignant lesions as well as pathological subtype classification. In addition, we retrospectively collected data from nine medical centers. To ensure the broad applicability of the 3MT-Net, we created two separate testsets and conducted extensive experiments. Furthermore, a comparative analysis was conducted between 3MT-Net and the industrial-grade CAD product S-detect. The AUC of 3MT-Net surpasses S-Detect by 1.4% to 3.8%.

Hollow spherical nano-traps using pillararene-based polymer for efficient uranium extraction from seawater.

Herein, a hollow spherical pillar[5]arene-based polymer (P5-AO) adsorbent was synthesized. The P5-AO adsorbent was capable of effectively capturing uranium from simulated seawater (139.5 mg g-1) and real seawater (8.1 mg g-1). We also elucidated the uranium adsorption mechanism of P5-AOvia extended X-ray absorption fine structure (EXAFS). This study provides a novel direction for the development of uranium capture adsorbents.

GATIS score for predicting the prognosis of rectal neuroendocrine neoplasms: A Chinese multicenter study of 12-year experience.

BACKGROUND: There is currently a shortage of accurate, efficient, and precise predictive instruments for rectal neuroendocrine neoplasms (NENs). AIM: To develop a predictive model for individuals with rectal NENs (R-NENs) using data from a large cohort. METHODS: Data from patients with primary R-NENs were retrospectively collected from 17 large-scale referral medical centers in China. Random forest and Cox proportional hazard models were used to identify the risk factors for overall survival and progression-free survival, and two nomograms were constructed. RESULTS: A total of 1408 patients with R-NENs were included. Tumor grade, T stage, tumor size, age, and a prognostic nutritional index were important risk factors for prognosis. The GATIS score was calculated based on these five indicators. For overall survival prediction, the respective C-indexes in the training set were 0.915 (95% confidence interval: 0.866-0.964) for overall survival prediction and 0.908 (95% confidence interval: 0.872-0.944) for progression-free survival prediction. According to decision curve analysis, net benefit of the GATIS score was higher than that of a single factor. The time-dependent area under the receiver operating characteristic curve showed that the predictive power of the GATIS score was higher than that of the TNM stage and pathological grade at all time periods. CONCLUSION: The GATIS score had a good predictive effect on the prognosis of patients with R-NENs, with efficacy superior to that of the World Health Organization grade and TNM stage.

The dual role of microglia in intracerebral hemorrhage.

Intracerebral hemorrhage has the characteristics of high morbidity, disability and mortality, which has caused a heavy burden to families and society. Microglia are resident immune cells in the central nervous system, and their activation plays a dual role in tissue damage after intracerebral hemorrhage. The damage in cerebral hemorrhage is embodied in the following aspects: releasing inflammatory factors and inflammatory mediators, triggering programmed cell death, producing glutamate induced excitotoxicity, and destroying blood-brain barrier; The protective effect is reflected in the phagocytosis and clearance of harmful substances by microglia, and the secretion of anti-inflammatory and neurotrophic factors. This article summarizes the function of microglia and its dual regulatory mechanism in intracerebral hemorrhage. In the future, drugs, acupuncture and other clinical treatments can be used to intervene in the activation state of microglia, so as to reduce the harm of microglia.

Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.

Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.

Preparation and characterization of Baijiu Jiuzao cellulose nanofibers-kafirin composite bio-film with excellent physical properties.

Jiuzao is the main solid by-products of Baijiu industry, which contain a high amount of underutilized cellulose and proteins. In recent years, cellulose nanofibers mixed with proteins to prepare biodegradable bio-based film materials have received widespread attention. In this study, we propose a novel method to simultaneously extract kafirin and cellulose from strong-flavor type of Jiuzao, and modify cellulose to prepare cellulose nanofibers by the TEMPO (2,2,6,6-tetramethylpiperidine-1-oxide) oxidation-pressure homogenization technique, and finally mix kafirin with cellulose nanofibers to prepare a new biodegradable bio-based composite film. Based on the analysis of one-way and response surface experiments, the highest purity of cellulose was 82.04 %. During cellulose oxidation, when NaClO was added at 25 mmol/g, cellulose nanofibers have a particle size of 80-120 nm, a crystallinity of 65.8°. Finally, kafirin and cellulose nanofibers were mixed to prepare films. The results showed that when cellulose nanofibers were added at 1 %, the film surface was smooth, the light transmittance was 60.8 %, and the tensile strength was 9.17 MPa at maximum, which was 104 % higher than pure protein film. The contact angle was 34.3°. This paper provides new ideas and theoretical basis for preparing biodegradable bio-based composite film materials, and improves the added value of Jiuzao.

Ovarian steroid cell tumors, not otherwise specified: three case reports and literature review.

Objective: To provide a reference for the diagnosis and treatment of ovarian steroid cell tumors, not otherwise specified (SCTs-NOS). Methods: We retrospectively analyzed the clinicopathological data of three patients with SCTs-NOS admitted to the Tianjin Medical University General Hospital from 2012 to 2022 and reviewed literature reports related to this disease. Results: A total of 3 cases in our center and 70 cases searched in literature reports were included. The age at diagnosis ranged from 3 to 93 years (median, 34 years). The common clinical manifestations were hirsutism, acne, deepened voice, clitoromegaly, amenorrhea, and excessive weight gain. Tumor sizes ranged from 1.2 to 45 cm, with an average diameter of 6.5cm. Most of SCTs-NOS were benign, but some of them exhibited malignant behavior. Surgery was the main treatment and close follow-up was required. The follow up time of 73 cases ranged from 3 to 132 months (median, 21.3 months). Disease recurrence or progression occurred in 14 cases (19.2%). Three of the 73 patients had a successful pregnancy. Conclusion: SCTs-NOS usually occur in women of reproductive age, which are mainly manifested as androgen excess symptoms. Surgery is an appropriate treatment for SCTs-NOS and should be individualized. Final diagnosis depends on pathology. SCTs-NOS have malignant potential, and the treatments for patients with malignant tumors and disease recurrence or progression were cytoreductive surgery, adjuvant chemotherapy, and gonadotrophin-releasing hormone agonists (GnRHa) therapy.

An end-to-end infant brain parcellation pipeline.

Objective: Accurate infant brain parcellation is crucial for understanding early brain development; however, it is challenging due to the inherent low tissue contrast, high noise, and severe partial volume effects in infant magnetic resonance images (MRIs). The aim of this study was to develop an end-to-end pipeline that enabled accurate parcellation of infant brain MRIs. Methods: We proposed an end-to-end pipeline that employs a two-stage global-to-local approach for accurate parcellation of infant brain MRIs. Specifically, in the global regions of interest (ROIs) localization stage, a combination of transformer and convolution operations was employed to capture both global spatial features and fine texture features, enabling an approximate localization of the ROIs across the whole brain. In the local ROIs refinement stage, leveraging the position priors from the first stage along with the raw MRIs, the boundaries o the ROIs are refined for a more accurate parcellation. Results: We utilized the Dice ratio to evaluate the accuracy of parcellation results. Results on 263 subjects from National Database for Autism Research (NDAR), Baby Connectome Project (BCP) and Cross-site datasets demonstrated the better accuracy and robustness of our method than other competing methods. Conclusion: Our end-to-end pipeline may be capable of accurately parcellating 6-month-old infant brain MRIs.

[Functions and mechanisms of testicular descent in Apodemus agrarius based on transcriptomics and metabolomics].

This study aims to explore the functions and mechanisms of testicular descent in Apodemus agrarius, and analyze the changes in genes and metabolite levels in this process. Illumina NovaSeq and liquid chromatography-mass spectrometry were used for the transcriptomic analysis and metabolomic analysis, respectively, of the normal and descending testis of A. agrarius. Gene ontology (GO) enrichment of the transcriptomic results revealed 240 differentially expressed genes (DEGs), such as Spesp1, Izumo1, Hyal5, and Fabp9. Kyoto encyclopedia of genes and genomes (KEGG) enrichment showed 52 DEGs, including Pcyt1, Pla2g4e, Gpd1l, and Lypla3. The qRT-PCR results were consistent with the transcriptomic results in terms of the expression patterns of six randomly selected genes in the normal and descending testis. The metabolomic results revealed 28 differential metabolites associated with the testicular function, including 3-dehydroquinic acid, α-linolenic acid, dihydroxyacetone phosphate, and fructose 1,6-bisphosphate. The conjoint analysis showcased that glycerophospholipid metabolism, α-linolenic acid metabolism, and arachidonic acid metabolism may be the key metabolic pathways regulating testicular descent in A. agrarius. This study will help to understand the mechanism of testicular descent and lay a theoretical foundation for exploring the mechanisms of the population changes of A. agrarius and developing laboratory animal resources.

Indole-3-propionic acid regulates lateral root development by targeting auxin signaling in Arabidopsis.

Indole-3-propionic acid (IPA) is known to be a microbe-derived compound with a similar structure to the phytohormone auxin (indole-3-acetic acid, IAA). Previous studies reported that IPA exhibited auxin-like bioactivities in plants. However, the underlying molecular mechanism is not totally understood. Here, we revealed that IPA modulated lateral root (LR) development via auxin signaling in the model plant Arabidopsis thaliana. Genetic analysis indicated that deficiency of the TIR1/AFB-Aux/IAA-ARF auxin signaling pathway abolished the effects of IPA on regulating LR development. Further biochemical, transcriptomic profiling and cell biological analyses revealed that IPA directly bound to the TIR1/AFB-Aux/IAA coreceptor complex and thus activated downstream gene expression. Therefore, our work revealed that IPA is a potential signaling molecule that modulates plant growth and development by targeting the TIR1/AFB-Aux/IAA-mediated auxin signaling pathway, providing potential insights into root growth regulation in plants.