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1.
Nat Commun ; 15(1): 5602, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38961108

ABSTRACT

Abnormal trophoblast self-renewal and differentiation during early gestation is the major cause of miscarriage, yet the underlying regulatory mechanisms remain elusive. Here, we show that trophoblast specific deletion of Kat8, a MYST family histone acetyltransferase, leads to extraembryonic ectoderm abnormalities and embryonic lethality. Employing RNA-seq and CUT&Tag analyses on trophoblast stem cells (TSCs), we further discover that KAT8 regulates the transcriptional activation of the trophoblast stemness marker, CDX2, via acetylating H4K16. Remarkably, CDX2 overexpression partially rescues the defects arising from Kat8 knockout. Moreover, increasing H4K16ac via using deacetylase SIRT1 inhibitor, EX527, restores CDX2 levels and promoted placental development. Clinical analysis shows reduced KAT8, CDX2 and H4K16ac expression are associated with recurrent pregnancy loss (RPL). Trophoblast organoids derived from these patients exhibit impaired TSC self-renewal and growth, which are significantly ameliorated with EX527 treatment. These findings suggest the therapeutic potential of targeting the KAT8-H4K16ac-CDX2 axis for mitigating RPL, shedding light on early gestational abnormalities.


Subject(s)
CDX2 Transcription Factor , Cell Proliferation , Cell Self Renewal , Histone Acetyltransferases , Trophoblasts , Trophoblasts/metabolism , CDX2 Transcription Factor/metabolism , CDX2 Transcription Factor/genetics , Animals , Female , Humans , Mice , Pregnancy , Cell Self Renewal/genetics , Histone Acetyltransferases/metabolism , Histone Acetyltransferases/genetics , Abortion, Habitual/metabolism , Abortion, Habitual/genetics , Mice, Knockout , Histones/metabolism , Cell Differentiation , Placentation/genetics
2.
FEMS Microbiol Ecol ; 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38955391

ABSTRACT

Drought is a major stressor to soil microbial communities, and the intensification of climate change is predicted to increase hydric stress worldwide in the coming decades. As a possible mitigating factor for the consequences of prolonged drought periods, above and belowground biodiversity can increase ecosystem resistance and resilience by improving metabolic redundancy and complementarity as biodiversity increases. Here, we investigated the interaction effect between plant richness and successive, simulated summer drought on soil microbial communities during a period of 9 years.To do that, we made use of a well-established biodiversity experiment (The Jena Experiment) to investigate the response of microbial richness and community composition to successive drought periods alongside a plant richness gradient, which covers 1-, 2-, 4-, 8-, 16- and 60-species plant communities. Plots were covered from natural precipitation by installing rain shelters 6 weeks every summer. Bulk soil samples were collected 1 year after the last summer drought was simulated. Our data indicate that bacterial richness increased after successive exposure to drought, with the increase being stable along the plant richness gradient. We identified a significant effect of plant species richness on the soil microbial community composition and determined the taxa significantly impacted by drought at each plant richness level. Our data successfully demonstrates that summer drought might have a legacy effect on soil bacterial communities.

3.
Front Endocrinol (Lausanne) ; 15: 1378293, 2024.
Article in English | MEDLINE | ID: mdl-38887264

ABSTRACT

Objective: This study aimed to distinguish between healthy controls and patients with OSAHS regarding homocysteine (HCY) levels and investigate how individuals with OSAHS respond to continuous positive airway pressure ventilation (CPAP) in terms of serum and plasma HCY levels. Methods: To ascertain published articles about OSAHS, an exhaustive search was performed across medical databases, encompassing PubMed, Web of Science, EMBASE, CNKI, and Cochrane Library, until January 2, 2024. This study reviewed the literature regarding HCY levels in individuals with OSAHS and control groups, HCY levels under pre- and post-CPAP treatment, the Pearson/Spearman correlation coefficients between HCY levels and apnea-hypopnea index (AHI), and the hazard ratio (HR) of HCY levels concerning the occurrence of major adverse cerebrocardiovascular events (MACCEs) in patients with OSAHS. Meta-analyses were performed using weighted mean difference (WMD), correlation coefficients, and HR as effect variables. The statistical analysis was conducted using the R 4.1.2 and STATA 11.0 software packages. Results: In total, 33 articles were selected for the final analysis. The OSAHS group exhibited significantly higher serum/plasma HCY levels than the control group (WMD = 4.25 µmol/L, 95% CI: 2.60-5.91, P< 0.001), particularly among individuals with moderate and severe OSAHS. Additionally, subgroup analysis using mean age, ethnicity, mean body mass index, and study design type unveiled significantly elevated levels of HCY in the serum/plasma of the OSAHS group compared to the control group. CPAP treatment can significantly decrease serum/plasma HCY levels in patients with OSAHS. Moreover, elevated HCY levels in individuals with OSAHS could be one of the risk factors for MACCEs (adjusted HR = 1.68, 95% CI = 1.10-2.58, P = 0.017). AHI scores show a positive correlation with serum/plasma HCY levels. Conclusion: Patients with OSAHS had elevated serum/plasma HCY levels compared to healthy controls; however, CPAP therapy dramatically decreased HCY levels in patients with OSAHS. In patients with OSAHS, elevated HCY levels were linked with an increased risk of MACCEs, and HCY was positively connected with AHI values. HCY levels may serve as a useful clinical indicator for determining the severity and efficacy of OSAHS treatments. Systematic review registration: https://www.crd.york.ac.uk/prospero/, identifier CRD42024498806.


Subject(s)
Continuous Positive Airway Pressure , Homocysteine , Sleep Apnea, Obstructive , Humans , Sleep Apnea, Obstructive/therapy , Sleep Apnea, Obstructive/blood , Homocysteine/blood
4.
Nat Commun ; 15(1): 4826, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38844502

ABSTRACT

During extensive periods without rain, known as dry-downs, decreasing soil moisture (SM) induces plant water stress at the point when it limits evapotranspiration, defining a critical SM threshold (θcrit). Better quantification of θcrit is needed for improving future projections of climate and water resources, food production, and ecosystem vulnerability. Here, we combine systematic satellite observations of the diurnal amplitude of land surface temperature (dLST) and SM during dry-downs, corroborated by in-situ data from flux towers, to generate the observation-based global map of θcrit. We find an average global θcrit of 0.19 m3/m3, varying from 0.12 m3/m3 in arid ecosystems to 0.26 m3/m3 in humid ecosystems. θcrit simulated by Earth System Models is overestimated in dry areas and underestimated in wet areas. The global observed pattern of θcrit reflects plant adaptation to soil available water and atmospheric demand. Using explainable machine learning, we show that aridity index, leaf area and soil texture are the most influential drivers. Moreover, we show that the annual fraction of days with water stress, when SM stays below θcrit, has increased in the past four decades. Our results have important implications for understanding the inception of water stress in models and identifying SM tipping points.


Subject(s)
Ecosystem , Soil , Water , Soil/chemistry , Water/metabolism , Temperature , Plant Transpiration/physiology , Plants/metabolism , Dehydration , Plant Leaves/physiology , Climate , Rain , Machine Learning
5.
Front Psychiatry ; 15: 1397706, 2024.
Article in English | MEDLINE | ID: mdl-38938464

ABSTRACT

Objectives: This study aims to evaluate the efficacy of repeated transcranial magnetic stimulation (rTMS) combined with fluoxetine in enhancing the early antidepressant response in first-episode adolescent depression cases, providing insights for patient diagnosis and treatment. Methods: One hundred and thirty-five adolescents experiencing their first depressive episode were randomly assigned to either a sham group treated with fluoxetine or to low or high repetitive transcranial magnetic stimulation (rTMS) groups receiving both rTMS and fluoxetine. Therapeutic effects were assessed by comparing changes in Hamilton Depression Scale (HAMD-17) scores, cognitive function scores from the Wisconsin Card Sorting Test (WCST), and Clinical Global Impression-improvement (CGI-I) scores, along with recording adverse reactions. Results: The total effectiveness rate in the rTMS groups (Low, 95.56%; High, 97.78%) was significantly higher than in the Sham rTMS group (80%) (F = 11.15, P<0.0001). Post-treatment, not only the Low but also the High rTMS group exhibited more significant reductions in HAMD-17 (Low, 21.05; High, 21.45) and CGI-I scores (Low, 3.44; High, 3.60) compared to the Sham rTMS group (HAMD-17, 16.05; CGI-I, 2.57) (two weeks: F = 7.889, P = 0.0006; four weeks: F = 15.900, P<0.0001). Additionally, the two rTMS groups exhibited fewer erroneous responses and persistent errors in the WCST and completed more WCST categorizations than the Sham rTMS group. There was no significant difference in adverse reaction rates between the groups (F=4.421, P=0.0794). Conclusions: The combination of fluoxetine with rTMS demonstrates enhanced therapeutic effectiveness in treating adolescent depression, effectively controlling disease progression, reducing depressive symptoms, and improving cognitive function, making it a valuable clinical approach.

6.
Neurotherapeutics ; : e00392, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38944636

ABSTRACT

Repetitive transcranial magnetic stimulation (rTMS) is a non-invasive brain stimulation technique for modulating cortical activities and improving neural plasticity. Several studies investigated the effects of rTMS, etc., but the results are inconsistent. This study was designed to examine whether rTMS applied on the left dorsolateral prefrontal cortex (l-DLPFC) showed an effect on improving cognitive deficits in SZ and whether the early efficacy could predict efficacy at subsequent follow-ups. Cognitive ability was assessed using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) scale at baseline, weeks 2, 6, and 24. We found a significant interaction between time (weeks 0, 2, 6, and 24) and intervention on immediate memory and RBANS total scores (p â€‹= â€‹0.02 and p â€‹= â€‹0.04), indicating that both 10-Hz and 20-Hz rTMS stimulations had a delayed beneficial effect on immediate memory in SZ. Moreover, we found that 20-Hz rTMS stimulation, but not 10-Hz rTMS improved immediate memory at week 6 compared to the sham group (p â€‹= â€‹0.029). More importantly, improvements in immediate memory at week 2 were positively correlated with improvements at week 24 (ߠ​= â€‹0.461, t â€‹= â€‹3.322, p â€‹= â€‹0.002). Our study suggests that active rTMS was beneficial for cognitive deficits in patients with SZ. Furthermore, efficacy at week 2 could predict the subsequent efficacy at 24-week follow-up.

7.
New Phytol ; 243(3): 1205-1219, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38855965

ABSTRACT

Decades of studies have demonstrated links between biodiversity and ecosystem functioning, yet the generality of the relationships and the underlying mechanisms remain unclear, especially for forest ecosystems. Using 11 tree-diversity experiments, we tested tree species richness-community productivity relationships and the role of arbuscular (AM) or ectomycorrhizal (ECM) fungal-associated tree species in these relationships. Tree species richness had a positive effect on community productivity across experiments, modified by the diversity of tree mycorrhizal associations. In communities with both AM and ECM trees, species richness showed positive effects on community productivity, which could have resulted from complementarity between AM and ECM trees. Moreover, both AM and ECM trees were more productive in mixed communities with both AM and ECM trees than in communities assembled by their own mycorrhizal type of trees. In communities containing only ECM trees, species richness had a significant positive effect on productivity, whereas species richness did not show any significant effects on productivity in communities containing only AM trees. Our study provides novel explanations for variations in diversity-productivity relationships by suggesting that tree-mycorrhiza interactions can shape productivity in mixed-species forest ecosystems.


Subject(s)
Biodiversity , Mycorrhizae , Trees , Mycorrhizae/physiology , Trees/microbiology , Species Specificity
8.
Antimicrob Agents Chemother ; 68(7): e0052424, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38899917

ABSTRACT

HRS9432(A) is a long-acting echinocandin antifungal medication primarily used to treat invasive fungal infections, particularly invasive candidiasis. The safety, tolerability, and pharmacokinetic characteristics of HRS9432(A) injection were investigated in a randomized, double-blind, placebo-controlled, single- and multiple-ascending-dose Phase I study involving 56 healthy adult subjects. Doses ranging from 200 to 1200 mg were administered. Safety was continually monitored, including adverse events, clinical laboratory examinations, vital signs, 12-lead electrocardiograms, and physical examinations, while the pharmacokinetic profile within the body was evaluated. The results indicated that concentrations of HRS9432 peaked immediately after infusion, demonstrating essentially linear pharmacokinetic characteristics within the dosage range of 200-1,200 mg. It exhibited a low clearance rate and an extended half-life, with a clearance of approximately 0.2 L/h, a volume of distribution of around 40 L, and a half-life of approximately 140h following a single dose. The accumulation index for AUC0-τ after multiple doses ranged from 1.41 to 1.75. No severe adverse events occurred during the study, and the severity of all adverse events was mild or moderate. Therefore, the intravenous administration of HRS9432(A) in healthy Chinese adult subjects, either as multiple infusions of 200 to 600 mg (once a week, four doses) or as a single infusion of 900-1,200 mg, demonstrated overall good safety and tolerability. The pharmacokinetic exhibited essentially linear characteristics in the body, supporting a weekly dosing frequency for clinical applications and providing additional options for the treatment or prevention of invasive fungal infections. CLINICAL TRIALS: This study is registered with the International Clinical Trials Registry Platform as ChiCTR2300073525.


Subject(s)
Antifungal Agents , Healthy Volunteers , Humans , Double-Blind Method , Adult , Male , Antifungal Agents/pharmacokinetics , Antifungal Agents/administration & dosage , Antifungal Agents/adverse effects , Female , Young Adult , Half-Life , Area Under Curve , Micafungin/pharmacokinetics , Micafungin/administration & dosage , Micafungin/adverse effects , Middle Aged , Asian People , East Asian People
9.
Res Vet Sci ; 174: 105291, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38729095

ABSTRACT

Avian pathogenic Escherichia coli (APEC) is a widespread bacterium that causes significant economic losses to the poultry industry. APEC biofilm formation may result in chronic, persistent, and recurrent infections in clinics, making treatment challenging. Baicalein is a natural product that exhibits antimicrobial and antibiofilm activities. This study investigates the inhibitory effect of baicalein on APEC biofilm formation at different stages. The minimum inhibitory concentration (MIC) of baicalein on APEC was determined, and the growth curve of APEC biofilm formation was determined. The effects of baicalein on APEC biofilm adhesion, accumulation, and maturation were observed using optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy. The biofilm inhibition rate of baicalein was calculated at different stages. The MIC of baicalein against APEC was 256 µg/mL. The process of APEC biofilm maturation takes approximately 48 h after incubation, with initial adhesion completed at 12 h, and cell accumulation finished at 24 h. Baicalein had a significant inhibitory effect on APEC biofilm formation at concentrations above 1 µg/mL (p < 0.01). Notably, baicalein had the highest rate of biofilm formation inhibition when added at the adhesion stage. Therefore, it can be concluded that baicalein is a potent inhibitor of APEC biofilm formation in vitro and acts, primarily by inhibiting cell adhesion. These findings suggests that baicalein has a potential application for inhibiting APEC biofilm formation and provides a novel approach for the prevention and control APEC-related diseases.


Subject(s)
Bacterial Adhesion , Biofilms , Escherichia coli , Flavanones , Microbial Sensitivity Tests , Flavanones/pharmacology , Biofilms/drug effects , Biofilms/growth & development , Escherichia coli/drug effects , Escherichia coli/physiology , Bacterial Adhesion/drug effects , Animals , Anti-Bacterial Agents/pharmacology , Poultry Diseases/microbiology , Poultry Diseases/drug therapy , Chickens , Escherichia coli Infections/veterinary , Escherichia coli Infections/microbiology , Escherichia coli Infections/drug therapy , Microscopy, Electron, Scanning
10.
J Food Sci ; 89(6): 3455-3468, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38700315

ABSTRACT

Excessive accumulation of advanced glycation end products (AGEs) in the body is associated with diabetes and its complications. In this study, we aimed to explore the potential and mechanism of coffee leaf extract (CLE) in inhibiting the generation of AGEs and their precursors in an in vitro glycation model using bovine serum albumin and glucose (BSA-Glu) for the first time. High-performance liquid chromatography analysis revealed that CLE prepared with ultrasound pretreatment (CLE-U) contained higher levels of trigonelline, mangiferin, 3,5-dicaffeoylquinic acid, and γ-aminobutyric acid than CLE without ultrasound pretreatment (CLE-NU). The concentrations of these components, along with caffeine and rutin, were dramatically decreased when CLE-U or CLE-NU was incubated with BSA-Glu reaction mixture. Both CLE-U and CLE-NU exhibited a dose-dependent inhibition of fluorescent AGEs, carboxymethyllysine, fructosamine, 5-hydroxymethylfurfural, 3-deoxyglucosone, glyoxal, as well as protein oxidation products. Notably, CLE-U exhibited a higher inhibitory capacity compared to CLE-NU. CLE-U effectively quenched fluorescence intensity and increased the α-helix structure of the BSA-Glu complex. Molecular docking results suggested that the key bioactive compounds present in CLE-U interacted with the arginine residues of BSA, thereby preventing its glycation. Overall, this research sheds light on the possible application of CLE as a functional ingredient in combating diabetes by inhibiting the generation of AGEs.


Subject(s)
Glycation End Products, Advanced , Plant Extracts , Plant Leaves , Serum Albumin, Bovine , Plant Extracts/pharmacology , Plant Extracts/chemistry , Plant Leaves/chemistry , Serum Albumin, Bovine/chemistry , Coffea/chemistry , Alkaloids/pharmacology , Furaldehyde/analogs & derivatives , Furaldehyde/pharmacology , Fructosamine , Chromatography, High Pressure Liquid , Glyoxal , Glucose/metabolism , Molecular Docking Simulation , Glycosylation/drug effects , Quinic Acid/analogs & derivatives , Quinic Acid/pharmacology , Rutin/pharmacology , Lysine/analogs & derivatives , Caffeine/pharmacology , Deoxyglucose/analogs & derivatives , Deoxyglucose/pharmacology , Xanthones
11.
Molecules ; 29(10)2024 May 16.
Article in English | MEDLINE | ID: mdl-38792200

ABSTRACT

Electrochemical oxidation of ammonia is an attractive process for wastewater treatment, hydrogen production, and ammonia fuel cells. However, the sluggish kinetics of the anode reaction has limited its applications, leading to a high demand for novel electrocatalysts. Herein, the electrode with the in situ growth of NiCu(OH)2 was partially transformed into the NiCuOOH phase by a pre-treatment using highly oxidative solutions. As revealed by SEM, XPS, and electrochemical analysis, such a strategy maintained the 3D structure, while inducing more active sites before the in situ generation of oxyhydroxide sites during the electrochemical reaction. The optimized NiCuOOH-1 sample exhibited the current density of 6.06 mA cm-2 at 0.5 V, which is 1.67 times higher than that of NiCu(OH)2 (3.63 mA cm-2). Moreover, the sample with a higher crystalline degree of the NiCuOOH phase exhibited lower performance, demonstrating the importance of a moderate treatment condition. In addition, the NiCuOOH-1 sample presented low selectivity (<20%) towards NO2- and stable activity during the long-term operation. The findings of this study would provide valuable insights into the development of transition metal electrocatalysts for ammonia oxidation.

12.
Polymers (Basel) ; 16(10)2024 May 16.
Article in English | MEDLINE | ID: mdl-38794602

ABSTRACT

Interest in the development of eco-friendly, sustainable, and convenient bio-based coatings to enhance flame retardancy and antibacterial properties in cotton fabrics is growing. In this work, chitosan was protonated at its amino groups using a method with a high atom economy using an equimolar amount of amino trimethylene phosphonic acid (ATMP), resulting in the fabrication of a single-component chitosan-based multifunctional coating (ATMP-CS), thereby avoiding any additional neutralization or purification steps. Cotton fabrics coated with various loads of ATMP-CS were prepared through a padding-drying-curing process. The morphology, thermal stability, mechanical properties, antibacterial properties, flame-retardant behavior, and flame-retardant mechanism of these fabrics were investigated. The coating exhibited excellent film-forming properties, and it imparted a uniform protective layer onto the surfaces of the cotton fabrics. When the load capacity reached 11.5%, the coated fabrics achieved a limiting oxygen index of 29.7% and successfully passed the VFT test. Moreover, the ATMP-CS coating demonstrated antibacterial rates against Escherichia coli and Staphylococcus aureus reaching 95.1% and 99.9%, respectively. This work presents a straightforward and gentle approach to fabricating colorless, environmentally friendly, and highly efficient fabric coatings that have potential applications in promoting the use of bio-based materials.

13.
Front Microbiol ; 15: 1384991, 2024.
Article in English | MEDLINE | ID: mdl-38800755

ABSTRACT

Introduction: Rapid identification of infected individuals through viral RNA or antigen detection followed by effective personal isolation is usually the most effective way to prevent the spread of a newly emerging virus. Large-scale detection involves mass specimen collection and transportation. For biosafety reasons, denaturing viral transport medium has been extensively used during the SARS-CoV-2 pandemic. However, the high concentrations of guanidinium isothiocyanate (GITC) in such media have raised issues around sufficient GITC supply and laboratory safety. Moreover, there is a lack of denaturing transport media compatible with SARS-CoV-2 RNA and antigen detection. Methods: Here, we tested whether supplementing media containing low concentrations of GITC with ammonium sulfate (AS) would affect the throat-swab detection of SARS-CoV-2 or a viral inactivation assay targeting coronavirus and other enveloped and non-enveloped viruses. The effect of adding AS to the media on RNA stability and its compatibility with SARS-CoV-2 antigen detection were also tested. Results and discussion: We found that adding AS to the denaturing transport media reduced the need for high levels of GITC, improved SARS-COV-2 RNA detection without compromising virus inactivation, and enabled the denaturing transport media compatible with SARS-CoV-2 antigen detection.

14.
Schizophr Res ; 2024 May 09.
Article in English | MEDLINE | ID: mdl-38729789

ABSTRACT

BACKGROUND: Schizophrenia (SZ) is characterized by disconnected cerebral networks. Recent studies have shown that functional connectivity between the cerebellar dorsal dentate nucleus (dDN) and cerebrum is correlated with psychotic symptoms, and processing speed in SZ patients. Dynamic effective connectivity (dEC) is a reliable indicator of brain functional status. However, the dEC between the dDN and cerebrum in patients with SZ remains largely unknown. METHODS: Resting-state functional MRI data, symptom severity, and cognitive performance were collected from 74 SZ patients and 53 healthy controls (HC). Granger causality analysis and sliding time window methods were used to calculate dDN-based dEC maps for all subjects, and k-means clustering was performed to obtain several dEC states. Finally, between-group differences in dynamic effective connectivity variability (dECV) and clinical correlations were obtained using two-sample t-tests and correlation analysis. RESULTS: We detected four dEC states from the cerebrum to the right dDN (IN states) and three dEC states from the right dDN to the cerebrum (OUT states), with SZ group having fewer transitions in the OUT states. SZ group had increased dECV from the right dDN to the right middle frontal gyrus (MFG) and left lingual gyrus (LG). Correlations were found between the dECV from the right dDN to the right MFG and symptom severity and between the dECV from the right dDN to the left LG and working memory performance. CONCLUSIONS: This study reveals a dynamic causal relationship between cerebellar dDN and the cerebrum in SZ and provides new evidence for the involvement of cerebellar neural circuits in neurocognitive functions in SZ.

15.
Int J Mol Sci ; 25(9)2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38732022

ABSTRACT

The molecular weight (MW) of an enzyme is a critical parameter in enzyme-constrained models (ecModels). It is determined by two factors: the presence of subunits and the abundance of each subunit. Although the number of subunits (NS) can potentially be obtained from UniProt, this information is not readily available for most proteins. In this study, we addressed this gap by extracting and curating subunit information from the UniProt database to establish a robust benchmark dataset. Subsequently, we propose a novel model named DeepSub, which leverages the protein language model and Bi-directional Gated Recurrent Unit (GRU), to predict NS in homo-oligomers solely based on protein sequences. DeepSub demonstrates remarkable accuracy, achieving an accuracy rate as high as 0.967, surpassing the performance of QUEEN. To validate the effectiveness of DeepSub, we performed predictions for protein homo-oligomers that have been reported in the literature but are not documented in the UniProt database. Examples include homoserine dehydrogenase from Corynebacterium glutamicum, Matrilin-4 from Mus musculus and Homo sapiens, and the Multimerins protein family from M. musculus and H. sapiens. The predicted results align closely with the reported findings in the literature, underscoring the reliability and utility of DeepSub.


Subject(s)
Databases, Protein , Deep Learning , Protein Subunits , Protein Subunits/chemistry , Protein Subunits/metabolism , Animals , Humans , Protein Multimerization , Mice , Computational Biology/methods
16.
Glob Chang Biol ; 30(5): e17297, 2024 May.
Article in English | MEDLINE | ID: mdl-38738805

ABSTRACT

Current biogeochemical models produce carbon-climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first-order or Michaelis-Menten kinetics at the global scale. Nevertheless, a wider range of data with high-quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics-function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.


Subject(s)
Carbon Cycle , Carbon , Soil , Soil/chemistry , Carbon/analysis , Models, Theoretical , Computer Simulation
17.
PLoS One ; 19(5): e0303184, 2024.
Article in English | MEDLINE | ID: mdl-38739608

ABSTRACT

Community-supported agriculture (CSA) represents a collaborative model where local farms and community members form partnerships to facilitate the direct delivery of fresh produce from farms to consumers. This study primarily investigates the experiences of current CSA members, focusing on the key factors influencing their retention intentions. Employing a convergent parallel mixed methods approach, this study gathers and analyzes both quantitative data (such as factors affecting members' retention intentions) and qualitative data (derived from interviews reflecting members' perceptions of their CSA experiences). The integration of these datasets provides a comprehensive understanding of the factors that shape CSA membership dynamics. The research findings underscore that Convenience, Product Quality, and Positive Interactions are pivotal factors that contribute to members' Intentions to continue their CSA memberships. These insights are crucial for enhancing the services provided to CSA members and hold significant implications for the broader scope of CSA membership research. This study not only fills a critical gap in understanding the Chinese CSA context but also contributes to the global discourse on sustainable agriculture practices and community engagement.


Subject(s)
Agriculture , Humans , Consumer Behavior , Community Participation , Female , Male , Farms , China
18.
Front Public Health ; 12: 1384510, 2024.
Article in English | MEDLINE | ID: mdl-38807999

ABSTRACT

Background: The timely diagnosis of tuberculosis through innovative biomarkers that do not rely on sputum samples is a primary focus for strategies aimed at eradicating tuberculosis. miR-29 is an important regulator of tuberculosis pathogenesis. Its differential expression pattern in healthy, latent, and active people who develop tuberculosis has revealed its potential as a biomarker in recent studies. Therefore, a systematic review and meta-analysis were performed for the role of miR-29 in the diagnosis of tuberculosis. Methods: EMBASE, PubMed, CNKI, Web of Science, and Cochrane Library databases were searched utilizing predefined keywords for literature published from 2000 to February 2024.Included in the analysis were studies reporting on the accuracy of miR-29 in the diagnosis of tuberculosis, while articles assessing other small RNAs were not considered. All types of study designs, including case-control, cross-sectional, and cohort studies, were included, whether prospectively or retrospectively sampled, and the quality of included studies was determined utilizing the QUADAS-2 tool. Publication bias was analyzed via the construction of funnel plots. Heterogeneity among studies and summary results for specificity, sensitivity, and diagnostic odds ratio (DOR) are depicted in forest plots. Results: A total of 227 studies were acquired from the various databases, and 18 articles were selected for quantitative analysis. These articles encompassed a total of 2,825 subjects, primarily sourced from the Asian region. Patient specimens, including sputum, peripheral blood mononuclear cells, cerebrospinal fluid and serum/plasma samples, were collected upon admission and during hospitalization for tuberculosis testing. miR-29a had an overall sensitivity of 82% (95% CI 77, 85%) and an overall specificity of 82% (95% CI 78, 86%) for detecting tuberculosis. DOR was 21 (95% CI 16-28), and the area under the curve was 0.89 (95% CI 0.86, 0.91). miR-29a had slightly different diagnostic efficacy in different specimens. miR-29a showed good performance in both the diagnosis of pulmonary tuberculosis and extrapulmonary tuberculosis. miR-29b and miR-29c also had a good performance in diagnosis of tuberculosis. Conclusion: As can be seen from the diagnostic performance of miR-29, miR-29 can be used as a potential biomarker for the rapid detection of tuberculosis. Systematic Review Registration: https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=461107.


Subject(s)
Biomarkers , MicroRNAs , Tuberculosis , Humans , MicroRNAs/genetics , Biomarkers/analysis , Tuberculosis/diagnosis , Sensitivity and Specificity
19.
J Insect Sci ; 24(3)2024 May 01.
Article in English | MEDLINE | ID: mdl-38809687

ABSTRACT

Huanglongbing (HLB), a devastating citrus disease caused by Candidatus Liberibacter asiaticus, is efficiently vectored by the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae). Tamarixia radiata (Waterston) plays a crucial role as an ectoparasitoid, preying on D. citri nymphs. By collecting and identifying headspace volatiles from fifth instar nymphs of D. citri using a gas chromatograph-mass spectrometer (GC-MS), we obtained a collection of 9 volatile compounds. These compounds were subsequently chosen to investigate the electrophysiological and behavioral responses of female T. radiata. At a concentration of 10 µg/µl, 9 compounds were compared with cis-3-hexen-1-ol (control), resulting in trans-2-nonenal inducing the highest relative electroantennogram (EAG) value, followed by hexanal, heptanal, n-heptadecane, tetradecanal, n-tetradecane, n-pentadecane, 1-tetradecanol, and 1-dodecanol. The top 5 EAG responses of female T. radiata to these compounds were further investigated through EAG dose-response experiments. The results showed positive dose-responses as concentrations increased from 0.01 to 10 µg/µl. In Y-tube olfactometer bioassays, female T. radiata exhibited a preference for specific compounds. They were significantly attracted to tetradecanal at a concentration of 10 µg/µl and trans-2-nonenal at 0.01 µg/µl, while no significant attraction was observed toward hexanal, heptanal, or n-heptadecane. Our report is the first to demonstrate that volatiles produced by D. citri nymphs attract T. radiata, which suggests that this parasitoid may utilize nymph volatiles to locate its host.


Subject(s)
Hemiptera , Nymph , Volatile Organic Compounds , Animals , Nymph/growth & development , Nymph/physiology , Hemiptera/physiology , Female , Wasps/physiology , Electrophysiological Phenomena , Behavior, Animal/drug effects , Arthropod Antennae/physiology , Arthropod Antennae/drug effects
20.
Front Vet Sci ; 11: 1388173, 2024.
Article in English | MEDLINE | ID: mdl-38812557

ABSTRACT

The purpose of the present study was to investigate the effects of different levels of a Chinese herbal medicine formulation combined with JM113 (CHM-JM113) on growth performance, antioxidant capacity, organ index, and intestinal health of AA broilers. The AA broiler chicks were randomly allocated to 5 treatments as follows: a basic diet for the control group, the basic diet supplemented with 0.25% CHM-JM113, 0.5% CHM-JM113, 1% CHM-JM113 and 2% CHM-JM113 for the treatment group, respectively. The results showed that the addition of CHM-JM113 to the diet significantly reduced the mortality (p < 0.01) and improved the European Broiler Index (EBI) (p < 0.05), whereas it had no significance on growth performance of AA broilers (p > 0.05). Comparing the control group, 0.5 and 1% CHM-JM113 group significantly improved the organ index of liver, spleen and bursa (p < 0.05). In terms of intestinal morphology and structure, the addition of different levels of CHM-JM113 increased VH and VH/CD ratio, decreased CD in the small intestine compared to the control group, with 1 and 2% of the additive dose being more effective (p < 0.05). Chinese herbal medicine and probiotics as natural antioxidants also significantly increased the content of SOD in serum of 21-day-old broilers (p < 0.01), and significantly decreased the content of MDA in serum (p < 0.01). At 42 days of age, the addition of 1 and 2% CHM-JM113 significantly increased the content of SOD (p < 0.01) and significantly decreased the content of MDA in the organism (p < 0.01), accompanied by a significant increase in T-AOC and CAT content. In the study of the effect of CHM-JM113 on intestinal immunity, compared with the control group, we found that 1% or 2% CHM-JM113 had a better effect on the expression of occludin and claudin-1 in the intestinal segments of broilers (p < 0.05). For the expression of GATA-3, 0.5% CHM-JM113 may have a better effect (p < 0.05). CHM-JM113 may be used as an antibiotic alternative in broiler production.

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