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PloS One 2024Combining data from experiments on multispecies studies provides invaluable contributions to the understanding of basic disease mechanisms and pathophysiology of...
Combining data from experiments on multispecies studies provides invaluable contributions to the understanding of basic disease mechanisms and pathophysiology of pathogens crossing species boundaries. The task of multispecies gene expression analysis, however, is often challenging given annotation inconsistencies and in cases of small sample sizes due to bias caused by batch effects. In this work we aim to demonstrate that an alternative approach to standard differential expression analysis in single cell RNA-sequencing (scRNA-seq) based on effect size profiles is suitable for the fusion of data from small samples and multiple organisms. The analysis pipeline is based on effect size metric profiles of samples in specific cell clusters. The effect size substitutes standard differentiation analyses based on p-values and profiles identified based on these effect size metrics serve as a tool to link cell type clusters between the studied organisms. The algorithms were tested on published scRNA-seq data sets derived from several species and subsequently validated on own data from human and bovine peripheral blood mononuclear cells stimulated with Mycobacterium tuberculosis. Correlation of the effect size profiles between clusters allowed for the linkage of human and bovine cell types. Moreover, effect size ratios were used to identify differentially regulated genes in control and stimulated samples. The genes identified through effect size profiling were confirmed experimentally using qPCR. We demonstrate that in situations where batch effects dominate cell type variation in single cell small sample size multispecies studies, effect size profiling is a valid alternative to traditional statistical inference techniques.
Topics: Single-Cell Analysis; Animals; Humans; Cattle; Mycobacterium tuberculosis; Gene Expression Profiling; Algorithms; Leukocytes, Mononuclear; Sequence Analysis, RNA
PubMed: 38917129
DOI: 10.1371/journal.pone.0305874 -
PloS One 2024Gulf War Illness (GWI) is a chronic condition characterized by multisystem symptoms that still affect up to one-third of veterans who engaged in combat in the Gulf War...
Gulf War Illness (GWI) is a chronic condition characterized by multisystem symptoms that still affect up to one-third of veterans who engaged in combat in the Gulf War three decades ago. The aetiology of GWI is mainly explained by exposure to multiple toxic agents, vaccines, and medications. As there is a significant overlap in symptoms between GWI and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), the objective of this study was to investigate a biomarker widely reported in Natural Killer (NK) cells from ME/CFS patients, the Transient Receptor Potential Melastatin 3 (TRPM3) ion channel. NK cells from 6 healthy controls (HC) and 6 GWI participants were isolated, and TRPM3 function was assessed through whole-cell patch-clamp. As demonstrated by prior studies, NK cells from HC expressed typical TRPM3 function after pharmacomodulation. In contrast, this pilot investigation demonstrates a dysfunctional TRPM3 in NK cells from GWI participants through application of a TRPM3 agonist and confirmed by a TRPM3 antagonist. There was a significant reduction in TRPM3 function from GWI than results measured in HC. This study provides an unprecedented research field to investigate the involvement of TRP ion channels in the pathomechanism and potential medical interventions to improve GWI quality of life.
Topics: Humans; TRPM Cation Channels; Persian Gulf Syndrome; Killer Cells, Natural; Male; Middle Aged; Adult; Female; Case-Control Studies; Patch-Clamp Techniques
PubMed: 38917121
DOI: 10.1371/journal.pone.0305704 -
PloS One 2024Known for its strong diuretic properties, the perennial herbaceous plant Orthosiphon stamineus Benth. is believed to preserve the kidney disease. This study compared the...
BACKGROUND
Known for its strong diuretic properties, the perennial herbaceous plant Orthosiphon stamineus Benth. is believed to preserve the kidney disease. This study compared the boiling water extract with powdered Orthosiphon stamineus Benth. and used a highly sensitive and high resolution UHPLC-Q-Exactive-Orbitrap-HRMS technology to evaluate its chemical composition.
RESULTS
Furthermore, by monitoring the absorption of prototype components in rat plasma following oral treatment, the beneficial ingredients of the Orthosiphon stamineus Benth. decoction was discovered. Approximately 92 substances underwent a preliminary identification utilizing relevant databases, relevant literature, and reference standards. As the compound differences between the powdered Orthosiphon stamineus Benth. and its water decoction were analyzed, it was found that boiling produced additional compounds, 48 of which were new. 45 blood absorption prototype components and 49 OS metabolites were discovered from rat serum, and a kidney tissue homogenate revealed an additional 28 prototype components. Early differences in the distribution of ferulic acid, cis 4 coumaric acid, and rosmarinic acid were shown using spatial metabolomics. It was elucidated that the renal cortex region is where rosmarinic acid largely acts, offering a theoretical foundation for further studies on the application of OS in the prevention and treatment of illness as well as the preservation of kidney function.
SIGNIFICANCE
In this study, UHPLC-Q Exactive Orbitrap-HRMS was employed to discern OS's chemical composition, and a rapid, sensitive, and broad-coverage AFADESI-MSI method was developed to visualize the spatial distribution of compounds in tissues.
Topics: Orthosiphon; Animals; Chromatography, High Pressure Liquid; Rats; Plant Extracts; Male; Rats, Sprague-Dawley; Mass Spectrometry; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Kidney
PubMed: 38917120
DOI: 10.1371/journal.pone.0304852 -
PloS One 2024The Arctic faces increasing exposure to environmental chemicals such as metals, posing health risks to humans and wildlife. Biomonitoring of polar bears (Ursus...
The Arctic faces increasing exposure to environmental chemicals such as metals, posing health risks to humans and wildlife. Biomonitoring of polar bears (Ursus maritimus) can be used to quantify chemicals in the environment and in traditional foods consumed by the Inuit. However, typically, these samples are collected through invasive or terminal methods. The biomonitoring of feces could be a useful alternative to the current metal monitoring method within the Arctic. Here, we aim to 1) quantify the relationship between concentrations of metals in the feces and tissues (muscle, liver, and fat) of polar bears using predictive modeling, 2) develop an easy-to-use conversion tool for use in community-based monitoring programs to non-invasively estimate contaminant concentrations in polar bears tissues and 3) demonstrate the application of these models by examining potential exposure risk for humans from consumption of polar bear muscle. Fecal, muscle, liver, and fat samples were harvested from 49 polar bears through a community-based monitoring program. The samples were analyzed for 32 metals. Exploratory analysis indicated that mean metal concentrations generally did not vary by age or sex, and many of the metals measured in feces were positively correlated with the internal tissue concentration. We developed predictive linear regression models between internal (muscle, liver, fat) and external (feces) metal concentrations and further explored the mercury and methylmercury relationships for utility risk screening. Using the cross-validated regression coefficients, we developed a conversion tool that contributes to the One Health approach by understanding the interrelated health of humans, wildlife, and the environment in the Arctic. The findings support using feces as a biomonitoring tool for assessing contaminants in polar bears. Further research is needed to validate the developed models for other regions in the Arctic and assess the impact of environmental weathering on fecal metal concentrations.
Topics: Ursidae; Feces; Animals; Female; Male; Arctic Regions; Metals; Biological Monitoring; Food Contamination; Humans; Environmental Monitoring; Environmental Pollutants; Liver
PubMed: 38917117
DOI: 10.1371/journal.pone.0305398 -
PloS One 2024This study evaluates the impact of dietary supplementation of the blue-green alga Arthrospira platensis NIOF17/003 nanoparticles (AN) on the growth performance,...
Arthrospira platensis nanoparticles dietary supplementation improves growth performance, steroid hormone balance, and reproductive productivity of Nile tilapia (Oreochromis niloticus) broodstock.
This study evaluates the impact of dietary supplementation of the blue-green alga Arthrospira platensis NIOF17/003 nanoparticles (AN) on the growth performance, whole-body biochemical compositions, blood biochemistry, steroid hormonal, and fry production efficiency of Nile tilapia (Oreochromis niloticus) broodstock, during the spawning season. After a 21-day preparation period to equip the females and ensure that their ovaries were filled with eggs, mating between the mature females and males took place in a 3:1 ratio during a 14-day spawning cycle. A total of 384 tilapia broodstock 288 females and 96 males with an initial body weight of 450.53±0.75, were divided into four groups; AN0: a basal diet as a control group with no supplementation of Arthrospira platensis, and the other three groups (AN2, AN4, and AN6) were diets supplemented with nanoparticles of A. platensis at levels of 2, 4, and 6 g kg─1 diet, respectively. The results found that fish-fed group AN6 showed the highest significant differences in weight gain (WG), final weight (FW), feed conversion ratio (FCR), protein efficiency ratio (PER), and feed efficiency ratio (FER). Females fed the AN6 diet showed the highest significant fat content. Compared to the AN0 group, fish fed on the supplemented diets showed significant improvement (p < 0.05) in triglyceride, glucose, and aspartate aminotransferase (AST). A gradual increase in AN inclusion level resulted in a gradual increase in the concentrations of luteinizing hormone (LH), and follicle-stimulating hormone (FSH), testosterone, progesterone, and prolactin. The rates (%) of increase in fry production for females fed supplemented diets were 10.5, 18.6, and 32.2% for AN2, AN4, and AN6, respectively, compared to the control group. This work concluded that the inclusion levels of 6 g kg─1 of A. platensis nanoparticles in the diet of Nile tilapia broodstock significantly improved the growth performances, steroid hormone concentrations, and increased the fry production efficiency by 32.2%, respectively. These findings revealed that A. platensis nanoparticles resulted in a significantly enhanced female' reproductive productivity of Nile tilapia broodstock.
Topics: Animals; Dietary Supplements; Nanoparticles; Female; Reproduction; Spirulina; Cichlids; Male; Animal Feed; Gonadal Steroid Hormones
PubMed: 38917116
DOI: 10.1371/journal.pone.0299480 -
PloS One 2024Human induced pluripotent stem cells (hiPSCs) derived into neurons offer a powerful in vitro model to study cellular processes. One method to characterize functional...
Human induced pluripotent stem cells (hiPSCs) derived into neurons offer a powerful in vitro model to study cellular processes. One method to characterize functional network properties of these cells is using multielectrode arrays (MEAs). MEAs can measure the electrophysiological activity of cellular cultures for extended periods of time without disruption. Here we used WTC11 hiPSCs with a doxycycline-inducible neurogenin 2 (NGN2) transgene differentiated into neurons co-cultured with primary human astrocytes. We achieved a synchrony index ∼0.9 in as little as six-weeks with a mean firing rate of ∼13 Hz. Previous reports show that derived 3D brain organoids can take several months to achieve similar strong network burst synchrony. We also used this co-culture to model aspects of blood-brain barrier breakdown by using human serum. Our fully human co-culture achieved strong network burst synchrony in a fraction of the time of previous reports, making it an excellent first pass, high-throughput method for studying network properties and neurodegenerative diseases.
Topics: Humans; Astrocytes; Induced Pluripotent Stem Cells; Coculture Techniques; Neurons; Cell Differentiation; Cells, Cultured; Nerve Tissue Proteins; Basic Helix-Loop-Helix Transcription Factors; Electrodes; Blood-Brain Barrier
PubMed: 38917115
DOI: 10.1371/journal.pone.0303901 -
PloS One 2024N-butylphthalide (NBP) is a monomeric compound extracted from natural plant celery seeds, whether intestinal microbiota alteration can modify its pharmacokinetics is...
OBJECTIVE
N-butylphthalide (NBP) is a monomeric compound extracted from natural plant celery seeds, whether intestinal microbiota alteration can modify its pharmacokinetics is still unclear. The purpose of this study is to investigate the effect of intestinal microbiota alteration on the pharmacokinetics of NBP and its related mechanisms.
METHODS
After treatment with antibiotics and probiotics, plasma NBP concentrations in SD rats were determined by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The effect of intestinal microbiota changes on NBP pharmacokinetics was compared. Intestinal microbiota changes after NBP treatment were analyzed by 16S rRNA sequencing. Expressions of CYP3A1 mRNA and protein in the liver and small intestine tissues under different intestinal flora conditions were determined by qRT-PCR and Western Blot. KEGG analysis was used to analyze the effect of intestinal microbiota changes on metabolic pathways.
RESULTS
Compared to the control group, the values of Cmax, AUC0-8, AUC0-∞, t1/2 in the antibiotic group increased by 56.1% (P<0.001), 56.4% (P<0.001), 53.2% (P<0.001), and 24.4% (P<0.05), respectively. In contrast, the CL and Tmax values decreased by 57.1% (P<0.001) and 28.6% (P<0.05), respectively. Treatment with antibiotics could reduce the richness and diversity of the intestinal microbiota. CYP3A1 mRNA and protein expressions in the small intestine of the antibiotic group were 61.2% and 66.1% of those of the control group, respectively. CYP3A1 mRNA and protein expressions in the liver were 44.6% and 63.9% of those in the control group, respectively. There was no significant change in the probiotic group. KEGG analysis showed that multiple metabolic pathways were significantly down-regulated in the antibiotic group. Among them, the pathways of drug metabolism, bile acid biosynthesis and decomposition, and fatty acid synthesis and decomposition were related to NBP biological metabolism.
CONCLUSION
Antibiotic treatment could affect the intestinal microbiota, decrease CYP3A1 mRNA and protein expressions and increase NBP exposure in vivo by inhibiting pathways related to NBP metabolism.
Topics: Animals; Gastrointestinal Microbiome; Anti-Bacterial Agents; Rats; Benzofurans; Rats, Sprague-Dawley; Male; Cytochrome P-450 CYP3A; Liver; Intestine, Small
PubMed: 38917098
DOI: 10.1371/journal.pone.0297713 -
PloS One 2024Increases in near-surface ozone (O3) concentrations is a global environmental problem. High-concentration O3 induces stress in plants, which can lead to visible damage... (Meta-Analysis)
Meta-Analysis
Increases in near-surface ozone (O3) concentrations is a global environmental problem. High-concentration O3 induces stress in plants, which can lead to visible damage to plants, reduced photosynthesis, accelerated aging, inhibited growth, and can even plant death. However, its impact has not been comprehensively evaluated because of the response differences between individual plant species, environmental O3 concentration, and duration of O3 stress in plants. We used a meta-analysis approach based on 31 studies 343 observations) to examine the effects of elevated O3 on malondialdehyde (MDA), superoxide dismutase (SOD), and peroxidase (POD) activities in herbaceous plants. Globally, important as they constitute the majority of the world's food crops. We partitioned the variation in effect size found in the meta-analysis according to the presence of plant species (ornamental herb, rice, and wheat), O3 concentration, and duration of O3 stress in plants. Our results showed that the effects of elevated O3 on plant membrane lipid peroxidation depending on plant species, O3 concentration, and duration of O3 stress in plants. The wheat SOD and POD activity was significantly lower compared to the herbs and rice (P<0.01). The SOD activity of all herbaceous plants increased by 34.6%, 10.5%, and 26.3% for exposure times to elevated O3 environments of 1-12, 13-30, and 31-60 days, respectively. When the exposure time was more than 60 days, SOD activity did not increase but significantly decreased by 12.1%. However, the POD activity of herbaceous plants increased by 30.4%, 57.3%, 21.9% and 5.81%, respectively, when exposure time of herbaceous plants in elevated O3 environment was 1-12, 13-30, 31-60 and more than 60 days. Our meta-analysis revealed that (1) rice is more resistant to elevated O3 than wheat and ornamental herbs likely because of the higher activity of antioxidant components (e.g., POD) in the symplasts, (2) exposure to elevated O3 concentrations for >60 days, may result in antioxidant SOD lose its regulatory ability, and the antioxidant component POD in the symplast is mainly used to resist O3 damage, and (3) the important factors affected the activity of SOD and POD in plants were not consistent: the duration of O3 stress in plants was more important than plant species and O3 concentration for SOD activity. However, for POD activity, plant species was the most important factor.
Topics: Superoxide Dismutase; Antioxidants; Ozone; Malondialdehyde; Lipid Peroxidation; Plants; Oxidative Stress; Oxidoreductases; Oryza; Peroxidase
PubMed: 38917096
DOI: 10.1371/journal.pone.0305688 -
PloS One 2024Climate variability has become one of the most pressing issues of our time, affecting various aspects of the environment, including the agriculture sector. This study...
Climate variability has become one of the most pressing issues of our time, affecting various aspects of the environment, including the agriculture sector. This study examines the impact of climate variability on Ghana's maize yield for all agro-ecological zones and administrative regions in Ghana using annual data from 1992 to 2019. The study also employs the stacking ensemble learning model (SELM) in predicting the maize yield in the different regions taking random forest (RF), support vector machine (SVM), gradient boosting (GB), decision tree (DT), and linear regression (LR) as base models. The findings of the study reveal that maize production in the regions of Ghana is inconsistent, with some regions having high variability. All the climate variables considered have positive impact on maize yield, with a lesser variability of temperature in the Guinea savanna zones and a higher temperature variability in the Volta Region. Carbon dioxide (CO2) also plays a significant role in predicting maize yield across all regions of Ghana. Among the machine learning models utilized, the stacking ensemble model consistently performed better in many regions such as in the Western, Upper East, Upper West, and Greater Accra regions. These findings are important in understanding the impact of climate variability on the yield of maize in Ghana, highlighting regional disparities in maize yield in the country, and highlighting the need for advanced techniques for forecasting, which are important for further investigation and interventions for agricultural planning and decision-making on food security in Ghana.
Topics: Zea mays; Ghana; Machine Learning; Climate Change; Support Vector Machine; Agriculture; Climate; Crops, Agricultural; Carbon Dioxide; Temperature
PubMed: 38917094
DOI: 10.1371/journal.pone.0305762 -
PloS One 2024Obesity is associated with concomitant chronic conditions. An early metabolic consequence of obesity is disruption of glucose and insulin homeostasis. One of the...
INTRODUCTION
Obesity is associated with concomitant chronic conditions. An early metabolic consequence of obesity is disruption of glucose and insulin homeostasis. One of the consequences is impaired fasting glucose (IFG). Visceral fat is metabolically more harmful than subcutaneous fat, but few information is available regarding the association between the risk of abnormal glucose in increased waist circumference.
METHODS
This study is based on a cross sectional of 1,381 population-based from Palembang, Indonesia. The eligibility requirements subject were to be older than 18 and consent to taking fasting glucose and lipid profile tests as well as physical exams measuring their body weight, height, blood pressure, abdominal circumference, and waist circumference.
RESULTS
The number of subjects consisting of 798 noncentral obesity with normoglycemia, 376 central obesity with normoglycemia, and 207 central obesity with concomitant IFG. The prevalence central obesity with concomitant IFG was 35.51%. In subjects with central obesity, there were significant differences in proportions based on sex, age, marital status, education, and occupation. In multivariate analysis show that the risk factors that contribute to having a significant association with central obesity with concomitant IFG are sex (female), age (>40 years), blood pressure (hypertension), and HDL-C <50 mg/dL (p<0.001). The analysis also founded that there was a significant difference in the dietary pattern of sweet foods (p = 0.018), sweet drinks (p = 0.002), soft drinks (p = 0.001) and smoking habit (p<0.001) between subjects with obesity central and concomitant IFG compared to subjects with noncentral obesity. The majority of subjects with obesity central and concomitant IFG had consuming these risky foods >6 times/week.
CONCLUSION
The prevalence of central obesity with IFG is quite high. There are significant differences in the characteristics, lipid profile, blood pressure, dietary pattern, and smoking habit of central obesity with concomitant IFG was confirmed in this population-based observational study.
Topics: Humans; Male; Female; Cross-Sectional Studies; Adult; Middle Aged; Risk Factors; Blood Glucose; Obesity, Abdominal; Fasting; Indonesia; Waist Circumference; Obesity; Prevalence
PubMed: 38917085
DOI: 10.1371/journal.pone.0305604