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1.
Cancer Med ; 13(13): e7409, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38967515

ABSTRACT

AIM: This study aimed to explore the association between patient-reported items at different time points after hematopoietic stem cell transplantation (HSCT) and long-term survival. METHODS: We conducted a study with 144 allogeneic HSCT patients, following them for 5 years post-transplantation. Data from the Functional Assessment of Cancer Therapy-Bone Marrow Transplant (FACT-BMT) questionnaire were collected before transplantation and at 1, 3, 6, 12, 18, 36, and 60 months after transplantation. Demographic characteristics and survival status were also assessed. RESULTS: Among the 144 cases, the 5-year overall survival (OS), progression-free survival (PFS), non-relapse mortality (NRM), and graft-versus-host disease-free (GRFS) rates were 65%, 48%, 17%, and 36% respectively. Health-related quality of life (HRQOL) showed a fluctuating pattern over 5 years. Using a latent class mixed model, patients were classified into two groups based on their physical well-being (PWB) scores during the 60-month follow-up. Class 1 had initially lower PWB scores, which gradually increased over time. In contrast, Class 2 maintained higher PWB scores with slight increases over time. Kaplan-Meier survival analysis revealed that Class 1 had better OS (70.9% vs. 52.9%, p = 0.021), PFS (60.5% vs. 41.2%, p = 0.039), and GRFS (35.1% vs. 29.3%, p = 0.035) compared to Class 2. CONCLUSIONS: Patients who had higher initial PWB scores after HSCT demonstrated improved long-term survival outcomes. The PWB score could serve as a valuable predictor for the prognosis of HSCT.


Subject(s)
Hematopoietic Stem Cell Transplantation , Patient Reported Outcome Measures , Quality of Life , Humans , Male , Female , Adult , Middle Aged , Young Adult , Graft vs Host Disease/etiology , Adolescent , Surveys and Questionnaires
2.
BMC Cardiovasc Disord ; 24(1): 324, 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38918738

ABSTRACT

BACKGROUND: With advancements in chronic total coronary occlusion (CTO) recanalization techniques and concepts, the success rate of recanalization has been steadily increasing. However, the current data are too limited to draw any reliable conclusions about the efficacy and safety of drug-coated balloons (DCBs) in CTO percutaneous coronary intervention (PCI). Herein, we conducted a meta-analysis to confirm the efficacy of DCB in CTO PCI. METHODS: We systematically searched PubMed, Web of Science and Embase from inception to July 25, 2023. The primary outcome was major advent cardiovascular events (MACE), including cardiac death, nonfatal myocardial infarction (MI), target lesion revascularization (TLR), and target vessel revascularization (TVR). The follow-up angiographic endpoints were late lumen enlargement (LLE), reocclusion and restenosis. RESULTS: Five studies with a total of 511 patients were included in the meta-analysis. Across studies, patients were predominantly male (72.9-85.7%) and over fifty years old. The summary estimate rate of MACE was 13.0% (95% CI 10.1%-15.9%, I2 = 0%, p = 0.428). The summary estimate rates of cardiac death and MI were 2.2% (95% CI 0.7%-3.7%, I2 = 0%, p = 0.873) and 1.2% (95% CI -0.2-2.6%, I2 = 13.7%, p = 0.314), respectively. Finally, the pooled incidences of TLR and TVR were 10.1% (95% CI 5.7%-14.5%, I2 = 51.7%, p = 0.082) and 7.1% (95% CI 3.0%-11.2%, I2 = 57.6%, p = 0.070), respectively. Finally, the summary estimate rates of LLE, reocclusion and restenosis were 59.4% (95% CI 53.5-65.3%, I2 = 0%, p = 0.742), 3.3% (95% CI 1.1-5.4%, I2 = 0%, p = 0.865) and 17.5% (95% CI 12.9-22.0%, I2 = 0%, p = 0.623), respectively. CONCLUSION: Accordingly, DCB has the potential to be used as a treatment for CTO in suitable patients.


Subject(s)
Angioplasty, Balloon, Coronary , Cardiac Catheters , Coated Materials, Biocompatible , Coronary Occlusion , Humans , Coronary Occlusion/diagnostic imaging , Coronary Occlusion/mortality , Coronary Occlusion/therapy , Treatment Outcome , Chronic Disease , Angioplasty, Balloon, Coronary/instrumentation , Angioplasty, Balloon, Coronary/adverse effects , Angioplasty, Balloon, Coronary/mortality , Risk Factors , Aged , Female , Middle Aged , Male , Cardiovascular Agents/administration & dosage , Cardiovascular Agents/adverse effects , Aged, 80 and over , Risk Assessment , Time Factors , Equipment Design , Coronary Restenosis/etiology , Coronary Restenosis/diagnostic imaging , Coronary Restenosis/mortality
3.
Br J Pharmacol ; 2024 Jun 23.
Article in English | MEDLINE | ID: mdl-38922702

ABSTRACT

BACKGROUND AND PURPOSE: Traditional Chinese medicine (TCM) played an important role in controlling the COVID-19 pandemic, but the scientific basis and its active ingredients are still weakly studied. This study aims to decipher the underlying anti-SARS-CoV-2 mechanisms of glycyrrhetinic acid (GA). EXPERIMENTAL APPROACH: GA's anti-SARS-CoV-2 effect was verified both in vitro and in vivo. Homogeneous time-resolved fluorescence assays, biolayer interferometry technology, and molecular docking were employed to examine interactions of GA with human stimulator of interferon genes (hSTING). Immunofluorescence staining, western blot, and RT-qPCR were used to investigate nuclear translocation of interferon regulatory factor 3 (IRF3) and levels of STING target genes. Pharmacokinetics of GA was studied in mice. KEY RESULTS: GA could directly bind to Ser162 and Tyr240 residues of hSTING, thus up-regulating downstream targets and activation of the STING signalling pathway. Such activation is crucial for limiting the replication of SARS-CoV-2 Omicron in Calu-3 cells and protecting against lung injury induced by SARS-CoV-2 Omicron infection in K18-ACE2 transgenic mice. Immunofluorescence staining and western blot indicated that GA increased levels of phosphorylated STING, phosphorylated TANK-binding kinase-1, and cyclic GMP-AMP synthase (cGAS). Importantly, GA increased nuclear translocation of IRF3. Pharmacokinetic analysis of GA in mice indicated it can be absorbed into circulation and detected in the lung at a stable level. CONCLUSION AND IMPLICATIONS: Activation of the cGAS-STING pathway through the GA-STING-IRF3 axis is essential for the antiviral activity of GA in mice, providing new insights into the potential translation of GA for treating SARS-CoV-2 in patients.

4.
Ying Yong Sheng Tai Xue Bao ; 35(4): 909-916, 2024 Apr 18.
Article in Chinese | MEDLINE | ID: mdl-38884225

ABSTRACT

The stoichiometric characteristics of leaves can reflect environmental adaptation of plants, and thus the study of the relationship between them is helpful for exploring plant adaptation strategies. In this study, taking the national second-level key protection species, Ammopiptanthus mongolicus, as the research object, we set up 26 plots to collect samples, and measured the content of carbon (C), nitrogen (N), phosphorus (P) and water use efficiency (WUE) of leaves. We analyzed the relationship between leaf stoichiometric characteristics and WUE, and quantified the contributions of soil, climate, and water use efficiency to the variations of leaf stoichiometry. The results showed that C, N, and P contents in the leaves were (583.99±27.93), (24.31±2.09), and (1.83±0.06) mg·g-1, respectively. The coefficients of variation were 4.8%, 8.6%, and 3.2%, respectively, all belonging to weak variability, indicating that foliar contents of C, N and P tended to a certain stable value. The average value of N:P was 13.3, indicating that the growth of A. mongolicus was mainly limited by N. WUE was not correlated with leaf C content, but was significantly positively correlated with leaf N and P contents and N:P, and significantly negatively correlated with C:N and C:P, indicating that there was a linear synergistic trend between WUE and leaf nutrient content. The main factors influencing leaf C content and C:P were climatic factors, the leaf N content and N:P were mainly affected by soil factors, and the water use efficiency mainly affected leaf P content and C:N, indicating that the driving factors of different stoichiometric characteristics were different. The results could help eva-luate the habitat adaptation of desert plants, which would provide a theoretical basis for the conservation and management of A. mongolicus.


Subject(s)
Carbon , Nitrogen , Phosphorus , Plant Leaves , Plant Leaves/chemistry , Plant Leaves/metabolism , Plant Leaves/growth & development , China , Nitrogen/analysis , Nitrogen/metabolism , Phosphorus/analysis , Phosphorus/metabolism , Carbon/analysis , Carbon/metabolism , Ecosystem , Water/analysis , Water/metabolism , Water/chemistry , Adaptation, Physiological , Soil/chemistry
5.
BMC Plant Biol ; 24(1): 565, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38879490

ABSTRACT

BACKGROUND: AP2/ERF is a large family of plant transcription factor proteins that play essential roles in signal transduction, plant growth and development, and responses to various stresses. The AP2/ERF family has been identified and verified by functional analysis in various plants, but so far there has been no comprehensive study of these factors in Chinese prickly ash. Phylogenetic, motif, and functional analyses combined with transcriptome analysis of Chinese prickly ash fruits at different developmental stages (30, 60, and 90 days after anthesis) were conducted in this study. RESULTS: The analysis identified 146 ZbAP2/ERF genes that could be classified into 15 subgroups. The motif analysis revealed the presence of different motifs or elements in each group that may explain the functional differences between the groups. ZbERF13.2, ZbRAP2-12, and ZbERF2.1 showed high levels of expression in the early stages of fruit development. ZbRAP2-4, and ZbERF3.1 were significantly expressed at the fruit coloring stage (R2 and G2). ZbERF16 were significantly expressed at fruit ripening and expression level increased as the fruit continued to develop. Relative gene expression levels of 6 representative ZbAP2/ERFs assessed by RT-qPCR agreed with transcriptome analysis results. CONCLUSIONS: These genes identified by screening can be used as candidate genes that affect fruit development. The results of the analysis can help guide future genetic improvement of Chinese prickly ash and enrich our understanding of AP2/ERF transcription factors and their regulatory functions in plants.


Subject(s)
Fruit , Gene Expression Regulation, Plant , Phylogeny , Plant Proteins , Transcription Factors , Fruit/genetics , Fruit/growth & development , Plant Proteins/genetics , Plant Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Gene Expression Profiling , Genome, Plant , Genes, Plant , East Asian People
6.
RSC Adv ; 14(27): 19581-19585, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38895521

ABSTRACT

A facile and efficient strategy for modular access to furo[3,2-c]chromen-4-ones using 4-hydroxycoumarin and ß-nitroalkenes via Lewis acid-catalyzed formal [3 + 2] annulation protocol is described. This reaction proceeds via cascade Michael addition/nucleophilic addition/elimination in the presence of Yb(OTf)3, which involves the formation of two new σ (C-C and C-O) bonds for the construction of a novel furan ring in a single operation. This protocol affords a variety of functional groups, thereby providing a practical and efficient method for the fabrication of a furo[3,2-c]chromen-4-one framework.

7.
Cancer Res Commun ; 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38904265

ABSTRACT

Tumor hypoxia has been shown to predict poor patient outcomes in several cancer types, partially because it reduces radiation's ability to kill cells. We hypothesized that some of the clinical effects of hypoxia could also be due to its impact on the tumor microbiome. Therefore, we examined the RNA-seq data from the Oncology Research Information Exchange Network (ORIEN) database of colorectal cancer (CRC) patients treated with radiotherapy. We identified microbial RNAs for each tumor and related them to the hypoxic gene expression scores calculated from host mRNA. Our analysis showed that the hypoxia expression score predicted poor patient outcomes and identified tumors enriched with certain microbes such as Fusobacterium nucleatum. The presence of other microbes, such as Fusobacterium canifelinum, predicted poor patient outcomes, suggesting a potential interaction between hypoxia, the microbiome, and radiation response. To experimentally investigate this concept, we implanted CT26 CRC cells into immune-competent BALB/c and immune-deficient athymic nude mice. After growth, where tumors passively acquired microbes from the gastrointestinal tract, we harvested tumors, extracted nucleic acids, and sequenced host and microbial RNAs. We stratified tumors based on their hypoxia score and performed a metatranscriptomic analysis of microbial gene expression. In addition to hypoxia-trophic and -phobic microbial populations, analysis of microbial gene expression at the strain level showed expression differences based on the hypoxia score. Thus, hypoxia appears to associate with different microbial populations and elicit an adaptive transcriptional response in intratumoral microbes, potentially influencing clinical outcomes.

8.
Biomed Eng Online ; 23(1): 53, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38858706

ABSTRACT

BACKGROUND: Metastasis is one of the main factors leading to the high mortality rate of gastric cancer. The current monitoring methods are not able to accurately monitor gastric cancer metastasis. METHODS: In this paper, we constructed a new type of hollow Mn 3 O 4 nanocomposites, Mn 3 O 4 @HMSN-Cy7.5-FA, which had a size distribution of approximately 100 nm and showed good stability in different liquid environments. The in vitro magnetic resonance imaging (MRI) results show that the nanocomposite has good response effects to the acidic microenvironment of tumors. The acidic environment can significantly enhance the contrast of T 1 -weighted MRI. The cellular uptake and endocytosis results show that the nanocomposite has good targeting capabilities and exhibits good biosafety, both in vivo and in vitro. In a gastric cancer nude mouse orthotopic metastatic tumor model, with bioluminescence imaging's tumor location information, we realized in vivo MRI/fluorescence imaging (FLI) guided precise monitoring of the gastric cancer orthotopic and metastatic tumors with this nanocomposite. RESULTS: This report demonstrates that Mn 3 O 4 @HMSN-Cy7.5-FA nanocomposites is a promising nano-diagnostic platform for the precision diagnosis and therapy of gastric cancer metastasis in the future. CONCLUSIONS: In vivo MRI/FLI imaging results show that the nanocomposites can achieve accurate monitoring of gastric cancer tumors in situ and metastases. BLI's tumor location information further supports the good accuracy of MRI/FLI dual-modality imaging. The above results show that the MHCF NPs can serve as a good nano-diagnostic platform for precise in vivo monitoring of tumor metastasis. This nanocomposite provides more possibilities for the diagnosis and therapy of gastric cancer metastases.


Subject(s)
Folic Acid , Magnetic Resonance Imaging , Nanocomposites , Neoplasm Metastasis , Stomach Neoplasms , Stomach Neoplasms/diagnostic imaging , Stomach Neoplasms/pathology , Animals , Nanocomposites/chemistry , Mice , Cell Line, Tumor , Humans , Folic Acid/chemistry , Manganese Compounds/chemistry , Optical Imaging , Mice, Nude , Oxides
9.
Microbiol Res ; 285: 127782, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38833832

ABSTRACT

As a major human and animal pathogen, Staphylococcus aureus can attach to medical implants (abiotic surface) or host tissues (biotic surface), and further establish robust biofilms which enhances resistance and persistence to host immune system and antibiotics. Cell-wall-anchored proteins (CWAPs) covalently link to peptidoglycan, and largely facilitate the colonization of S. aureus on various surfaces (including adhesion and biofilm formation) and invasion into host cells (including adhesion, immune evasion, iron acquisition and biofilm formation). During biofilm formation, CWAPs function in adhesion, aggregation, collagen-like fiber network formation, and consortia formation. In this review, we firstly focus on the structural features of CWAPs, including their intracellular function and interactions with host cells, as well as the functions and ligand binding of CWAPs in different stages of S. aureus biofilm formation. Then, the roles of CWAPs in different biofilm processes with regards in development of therapeutic approaches are clarified, followed by the association between CWAPs genes and clonal lineages. By touching upon these aspects, we hope to provide comprehensive knowledge and clearer understanding on the CWAPs of S. aureus and their roles in biofilm formation, which may further aid in prevention and treatment infection and vaccine development.


Subject(s)
Bacterial Adhesion , Bacterial Proteins , Biofilms , Cell Wall , Staphylococcal Infections , Staphylococcus aureus , Biofilms/growth & development , Staphylococcus aureus/physiology , Staphylococcus aureus/genetics , Humans , Staphylococcal Infections/microbiology , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Cell Wall/metabolism , Animals , Peptidoglycan/metabolism
10.
Spectrochim Acta A Mol Biomol Spectrosc ; 319: 124550, 2024 Oct 15.
Article in English | MEDLINE | ID: mdl-38823240

ABSTRACT

Near-infrared organic fluorescent probes have great need in biological sciences and medicine but most of them are still largely unable to meet demand. In this work, a delicate multipurpose organic fluorescent probe (DPPM-TPA) with aggregation-induced emission performances is designed and prepared by facile method to reflect fluorescence labeling, two-photon imaging, and long-term fluorescent tracking. Specifically, DPPM-TPA NPs was constructed from 4-(diphenylamino)phenylboronic acid and DPPM-Br by classical Suzuki coupling reaction and then coated with F127. Such nanoprobe possessed high stability in diverse medium under ambient temperatures, low cytotoxicity, and brilliant fluorescence performance. More importantly, DPPM-TPA NPs showed excellent two-photon imaging and extraordinary long-term fluorescence tracing capacity to malignant tumor, and it can last up to 9 days. These results indicated that DPPM-TPA NPs is expected to serve as a fluorescent probe for photodiagnostic and providing a new idea for the development of long-term fluorescent tracker.


Subject(s)
Fluorescent Dyes , Fluorescent Dyes/chemistry , Humans , Animals , Neoplasms , Mice , Spectrometry, Fluorescence , Nanoparticles/chemistry , Cell Line, Tumor , Boronic Acids/chemistry
11.
Nat Commun ; 15(1): 4710, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38844475

ABSTRACT

Alzheimer's Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-cell and spatial RNA-seq database for Alzheimer's disease (ssREAD). It offers a broader spectrum of AD-related datasets, an optimized analytical pipeline, and improved usability. The database encompasses 1,053 samples (277 integrated datasets) from 67 AD-related scRNA-seq & snRNA-seq studies, totaling 7,332,202 cells. Additionally, it archives 381 ST datasets from 18 human and mouse brain studies. Each dataset is annotated with details such as species, gender, brain region, disease/control status, age, and AD Braak stages. ssREAD also provides an analysis suite for cell clustering, identification of differentially expressed and spatially variable genes, cell-type-specific marker genes and regulons, and spot deconvolution for integrative analysis. ssREAD is freely available at https://bmblx.bmi.osumc.edu/ssread/ .


Subject(s)
Alzheimer Disease , RNA-Seq , Single-Cell Analysis , Alzheimer Disease/genetics , Humans , Single-Cell Analysis/methods , Animals , Mice , RNA-Seq/methods , Brain/metabolism , Brain/pathology , Databases, Genetic , Transcriptome , Sequence Analysis, RNA/methods , Gene Expression Profiling/methods , Male
13.
J Acupunct Meridian Stud ; 17(3): 100-109, 2024 06 30.
Article in English | MEDLINE | ID: mdl-38898647

ABSTRACT

Importance: Post-stroke sialorrhea (PSS) refers to excessive saliva flowing out the lip border after a stroke. PSS negatively affects patient self-image and social communication and may lead to depression. Limited evidence supports the link between excessive salivation and PSS. No large-scale, strictly controlled randomized controlled trials have shown the effectiveness of acupuncture in treating PSS patients. Objective: We aim to compare the effects of intraoral and sham acupuncture in PSS patients and explore relationships among salivation and drooling severity and frequency and swallowing function in stroke patients. Design: Clinical study protocol, SPIRIT compliant. Setting: Prospective, single-center, randomized, and sham-controlled trial. Population: We will recruit 106 PSS patients to receive 4-week intraoral or sham acupuncture. Additionally, 53 stroke patients without PSS will undergo a conventional 4-week treatment program to compare salivation between PSS and non-PSS patients. Exposures: Intraoral or sham acupuncture. Main Outcomes and Measures: The main evaluation index will be the 3-minute saliva weight (3MSW), comparing changes in 3MSW from baseline to weeks 4 and 8. Secondary assessment indices will include the "Drooling Severity and Frequency Scale" and "Functional Oral Intake Scale." Results: The results from this study will be published in peer-reviewed journals. Conclusion: Comparing effects of intraoral and sham acupuncture in PSS patients, this study may contribute important evidence for future PSS treatment and provide valuable insights into whether salivation issues in stroke patients are attributed to heightened salivary secretion or dysphagia.


Subject(s)
Acupuncture Therapy , Sialorrhea , Stroke , Humans , Sialorrhea/therapy , Sialorrhea/etiology , Acupuncture Therapy/methods , Stroke/complications , Stroke/therapy , Stroke/physiopathology , Male , Prospective Studies , Female , Salivation , Adult , Middle Aged , Randomized Controlled Trials as Topic
14.
Clin Nutr ; 43(6): 1475-1487, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38723301

ABSTRACT

BACKGROUND & AIMS: The past few decades have witnessed a rapid growth in the prevalence of nonalcoholic fatty liver disease (NAFLD). While the ketogenic diet (KD) is considered for managing NAFLD, the safety and efficacy of the KD on NAFLD has been a controversial topic. Here, we aimed to investigate the effect of KD of different durations on metabolic endpoints in mice with NAFLD and explore the underlying mechanisms. METHODS: NAFLD mice were fed with KD for 1, 2, 4 and 6 weeks, respectively. The blood biochemical indexes (blood lipids, AST, ALT and etc.) and liver fat were measured. The LC-MS/MS based proteomic analysis was performed on liver tissues. Metallothionein-2 (MT2) was knocked down with adeno-associated virus (AAV) or small interfering RNA (siRNA) in NAFLD mice and AML-12 cells, respectively. H&E, BODIPY and ROS staining were performed to examine lipid deposition and oxidative stress. Furthermore, MT2 protein levels, nucleus/cytoplasm distribution and DNA binding activity of peroxisome proliferators-activated receptors α (PPARα) were evaluated. RESULTS: KD feeding for 2 weeks showed the best improvement on NAFLD phenotype. Proteomic analysis revealed that MT2 was a key candidate for different metabolic endpoints of NAFLD affected by different durations of KD feeding. MT2 knockdown in NAFLD mice blocked the effects of 2 weeks of KD feeding on HFD-induced steatosis. In mouse primary hepatocytes and AML-12 cells, MT2 protein levels were induced by ß-hydroxybutyric acid (ß-OHB). MT2 Knockdown blunted the effects of ß-OHB on alleviating PA-induced lipid deposition. Mechanistically, 2 weeks of KD or ß-OHB treatment reduced oxidative stress and upregulated the protein levels of MT2 in nucleus, which subsequently increased its DNA binding activity and PPARα protein expression. CONCLUSIONS: Collectively, these findings indicated that KD feeding prevented NAFLD in a time dependent manner and MT2 is a potential target contributing to KD improvement on steatosis.


Subject(s)
Diet, Ketogenic , Metallothionein , Mice, Inbred C57BL , Non-alcoholic Fatty Liver Disease , Oxidative Stress , Up-Regulation , Animals , Non-alcoholic Fatty Liver Disease/metabolism , Non-alcoholic Fatty Liver Disease/prevention & control , Non-alcoholic Fatty Liver Disease/genetics , Metallothionein/genetics , Metallothionein/metabolism , Diet, Ketogenic/methods , Mice , Male , Liver/metabolism , Antioxidants/metabolism , PPAR alpha/metabolism , PPAR alpha/genetics , Disease Models, Animal , Lipid Metabolism , Time Factors
15.
Microbiol Spectr ; 12(6): e0035324, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38717160

ABSTRACT

Candida albicans (C. albicans) and Lactiplantibacillus plantarum subsp. plantarum (L. plantarum) are frequently identified in various niches, but their dual-species interaction, especially with C. albicans in yeast form, remains unclear. This study aimed to investigate the dual-species interaction of L. plantarum and C. albicans, including proliferation, morphology, and transcriptomes examined by selective agar plate counting, microscopy, and polymicrobial RNA-seq, respectively. Maintaining a stable and unchanged growth rate, L. plantarum inhibited C. albicans yeast cell proliferation but not hyphal growth. Combining optical microscopy and atomic force microscopy, cell-to-cell direct contact and co-aggregation with L. plantarum cells surrounding C. albicans yeast cells were observed during dual-species interaction. Reduced C. albicans yeast cell proliferation in mixed culture was partially due to L. plantarum cell-free culture supernatant but not the acidic environment. Upon polymicrobial transcriptomics analysis, interesting changes were identified in both L. plantarum and C. albicans gene expression. First, two L. plantarum quorum-sensing systems showed contrary changes, with the activation of lamBDCA and repression of luxS. Second, the upregulation of stress response-related genes and downregulation of cell cycle, cell survival, and cell integrity-related pathways were identified in C. albicans, possibly connected to the stress posed by L. plantarum and the reduced yeast cell proliferation. Third, a large scale of pathogenesis and virulence factors were downregulated in C. albicans, indicating the potential interruption of pathogenic activities by L. plantarum. Fourth, partial metabolism and transport pathways were changed in L. plantarum and C. albicans. The information in this study might aid in understanding the behavior of L. plantarum and C. albicans in dual-species interaction.IMPORTANCEThe anti-Candida albicans activity of Lactiplantibacillus plantarum has been explored in the past decades. However, the importance of C. albicans yeast form and the effect of C. albicans on L. plantarum had also been omitted. In this study, the dual-species interaction of L. plantarum and C. albicans was investigated with a focus on the transcriptomes. Cell-to-cell direct contact and co-aggregation with L. plantarum cells surrounding C. albicans yeast cells were observed. Upon polymicrobial transcriptomics analysis, interesting changes were identified, including contrary changes in two L. plantarum quorum-sensing systems and reduced cell survival-related pathways and pathogenesis determinants in C. albicans.


Subject(s)
Candida albicans , Microbial Interactions , Quorum Sensing , Candida albicans/genetics , Candida albicans/pathogenicity , Candida albicans/physiology , Candida albicans/metabolism , Candida albicans/growth & development , Quorum Sensing/genetics , Virulence/genetics , Lactobacillus plantarum/genetics , Lactobacillus plantarum/metabolism , Lactobacillus plantarum/physiology , Gene Expression Regulation, Fungal , Transcriptome , Virulence Factors/genetics , Virulence Factors/metabolism
16.
bioRxiv ; 2024 May 08.
Article in English | MEDLINE | ID: mdl-38765956

ABSTRACT

Spatially resolved transcriptomics have enabled the inference of gene expression patterns within two and three-dimensional space, while introducing computational challenges due to growing spatial resolutions and sparse expressions. Here, we introduce scBSP, an open-source, versatile, and user-friendly package designed for identifying spatially variable genes in large-scale spatial transcriptomics. scBSP implements sparse matrix operation to significantly increase the computational efficiency in both computational time and memory usage, processing the high-definition spatial transcriptomics data for 19,950 genes on 181,367 spots within 10 seconds. Applied to diverse sequencing data and simulations, scBSP efficiently identifies spatially variable genes, demonstrating fast computational speed and consistency across various sequencing techniques and spatial resolutions for both two and three-dimensional data with up to millions of cells. On a sample with hundreds of thousands of sports, scBSP identifies SVGs accurately in seconds to on a typical desktop computer.

17.
Comput Struct Biotechnol J ; 23: 1786-1795, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38707535

ABSTRACT

The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, we present ConGcR, a contrastive learning-based model for integrating gene expression, spatial location, and tissue morphology for data representation and spatial tissue architecture identification. Graph convolution and ResNet were used as encoders for gene expression with spatial location and histological image inputs, respectively. We further enhanced ConGcR with a graph auto-encoder as ConGaR to better model spatially embedded representations. We validated our models using 16 human brains, four chicken hearts, eight breast tumors, and 30 human lung spatial transcriptomics samples. The results showed that our models generated more effective embeddings for obtaining tissue architectures closer to the ground truth than other methods. Overall, our models not only can improve tissue architecture identification's accuracy but also may provide valuable insights and effective data representation for other tasks in spatial transcriptome analyses.

19.
World J Clin Cases ; 12(14): 2457-2462, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38765744

ABSTRACT

BACKGROUND: Acute lower gastrointestinal bleeding (LGIB) is a common occurrence in clinical practice. However, appendiceal bleeding is an extremely rare condition that can easily be overlooked and misdiagnosed. The preoperative detection of appendiceal bleeding often poses challenges due to the lack of related guidelines and consensus, resulting in controversial treatment approaches. CASE SUMMARY: We presented a case of a 33-year-old female who complained of hematochezia that had lasted for 1 d. Colonoscopy revealed continuous bleeding in the appendiceal orifice. A laparoscopic appendectomy was performed immediately, and a pulsating blood vessel was observed in the mesangium of the appendix, accordingly, active bleeding into the appendicular lumen was considered. Pathological examination revealed numerous hyperplastic vessels in the appendiceal mucosa and dilated capillary vessels. CONCLUSION: The preoperative detection of appendiceal bleeding is often challenging, colonoscopy is extremely important, bowel preparation is not routinely recommended for patients with acute LGIB or only low-dose bowel preparation is recommended. Laparoscopic appendectomy is the most appropriate treatment for appendiceal bleeding.

20.
J Chromatogr A ; 1726: 464963, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38723493

ABSTRACT

The monitoring of organic compounds in aquatic matrices poses challenges due to its complexity and time-intensive nature. To address these challenges, we introduce a novel approach utilizing a dual-channel mono (1D) and comprehensive two-dimensional (2D) gas chromatography coupled with time-of-flight mass spectrometry (GC × GC-TOFMS) system, integrated with a robotic pretreatment platform, for online monitoring of both volatile organic compounds (VOCs) and semivolatile organic compounds (SVOCs) in water matrices. Employing the robotic platform, we establish a suite of online liquid-liquid extraction (LLE) pretreatment processes for water samples, marking the first instance of such procedures. Leveraging the automatic headspace (HS) module, dual robotic preparations of HS and LLE are sequentially executed to extract VOCs and SVOCs from water matrices. The GC × GC-TOFMS system is distinguished by its dual-channel analytical column configuration, facilitating sequential analysis of VOCs in GC-TOFMS mode and SVOCs in GC × GC-TOFMS mode. Quantitative detection of 55 target VOCs and 104 SVOCs is achieved in a water sample using the instrument system. Our method demonstrates excellent correlation coefficients ranging from 0.990 to 1.000, method detection limits ranging from 0.08 to 4.78 µg L-1, relative standard deviations below 19.3 %, and recovery rates ranging from 50.0 % to 124.0 %. To validate the online monitoring capabilities of our system, we assess target SVOCs at three different concentration levels over a 3-day period. Most compounds exhibit recovery rates ranging from 70.0 % to 130.0 %. Furthermore, we apply our method to analyze a real water sample, successfully identifying over 100 target and nontarget VOCs/SVOCs, including alcohols, aldehydes, ketones, acids, esters, and phenols. These results highlight the efficacy of the proposed analysis system, capable of conducting two distinct analyses in automatic sequence, thereby enhancing the efficiency and accuracy of organic compound analysis in water matrices.


Subject(s)
Gas Chromatography-Mass Spectrometry , Liquid-Liquid Extraction , Robotics , Volatile Organic Compounds , Volatile Organic Compounds/analysis , Volatile Organic Compounds/isolation & purification , Gas Chromatography-Mass Spectrometry/methods , Liquid-Liquid Extraction/methods , Water Pollutants, Chemical/analysis , Water Pollutants, Chemical/isolation & purification , Limit of Detection
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