-
Molecular Cell Jun 2024The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its...
The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.
PubMed: 38955181
DOI: 10.1016/j.molcel.2024.06.006 -
Computers in Biology and Medicine Jul 2024Missing data is a common challenge in mass spectrometry-based metabolomics, which can lead to biased and incomplete analyses. The integration of whole-genome sequencing...
BACKGROUND
Missing data is a common challenge in mass spectrometry-based metabolomics, which can lead to biased and incomplete analyses. The integration of whole-genome sequencing (WGS) data with metabolomics data has emerged as a promising approach to enhance the accuracy of data imputation in metabolomics studies.
METHOD
In this study, we propose a novel method that leverages the information from WGS data and reference metabolites to impute unknown metabolites. Our approach utilizes a multi-scale variational autoencoder to jointly model the burden score, polygenetic risk score (PGS), and linkage disequilibrium (LD) pruned single nucleotide polymorphisms (SNPs) for feature extraction and missing metabolomics data imputation. By learning the latent representations of both omics data, our method can effectively impute missing metabolomics values based on genomic information.
RESULTS
We evaluate the performance of our method on empirical metabolomics datasets with missing values and demonstrate its superiority compared to conventional imputation techniques. Using 35 template metabolites derived burden scores, PGS and LD-pruned SNPs, the proposed methods achieved R-scores > 0.01 for 71.55 % of metabolites.
CONCLUSION
The integration of WGS data in metabolomics imputation not only improves data completeness but also enhances downstream analyses, paving the way for more comprehensive and accurate investigations of metabolic pathways and disease associations. Our findings offer valuable insights into the potential benefits of utilizing WGS data for metabolomics data imputation and underscore the importance of leveraging multi-modal data integration in precision medicine research.
PubMed: 38955127
DOI: 10.1016/j.compbiomed.2024.108813 -
Water Research Jun 2024Biological activated carbon filter (BAC) is one of the most effective technologies for removing disinfection by-product (DBP) precursors from water. Biochar is a...
Biological activated carbon filter (BAC) is one of the most effective technologies for removing disinfection by-product (DBP) precursors from water. Biochar is a lower-cost medium that has the potential to replace granular activated carbon in BAC applications, thus leading to the development of biological biochar filter (BCF). This study compared BCF with BAC for the removal of DBP precursors using column experiments. Both BCF and BAC achieved the removal of DBP precursors, resulting in concentrations of all DBP formation potential below the World Health Organization guideline values for drinking water. Bromodichloromethane and unknown DBP precursor removal by BCF was comparable to that by BAC. However, BAC removed more chloroform and dichloroacetontrile precursors than BCF. For microbial community analysis, cell numbers in a bottom layer (inlet) of BCF and BAC columns were higher than those in the top layer. The abundances of Nordella and a microbial genus from Burkholderiaceae at the bottom layer showed a strong correlation to the number of DBP precursors removed and were comparable in BCF and BAC. This finding likely contributes to the similarities between DBPs species removed and the removal performances of some known and unknown DBP precursors by BCF and BAC. Overall results from this study revealed that biochar can be served as a low-cost and sustainable replacement of activated carbon in water filter for DBP precursor removal.
PubMed: 38955037
DOI: 10.1016/j.watres.2024.121994 -
International Journal of Food... Jun 2024Sterigmatocystin (STC) is an emerging mycotoxin that poses a significant threat to the food security of cereal crops. To mitigate STC contamination in maize, this study...
Sterigmatocystin (STC) is an emerging mycotoxin that poses a significant threat to the food security of cereal crops. To mitigate STC contamination in maize, this study employed selected lactic acid bacteria as biocontrol agents against Aspergillus versicolor, evaluating their biocontrol potential and analyzing the underlying mechanisms. Lactiplantibacillus plantarum HJ10, isolated from pickle, exhibited substantial in vitro antifungal activity and passed safety assessments, including antibiotic resistance and hemolysis tests. In vivo experiments demonstrated that L. plantarum HJ10 significantly reduced the contents of A. versicolor and STC in maize (both >84 %). The impact of heat, enzymes, alkali, and other treatments on the antifungal activity of cell-free supernatant (CFS) was investigated. Integrated ultra-high-performance liquid chromatography (UPLC) and gas chromatography-mass spectrometry (GC-MS) analysis revealed that lactic acid, acetic acid, and formic acid are the key substances responsible for the in vitro antifungal activity of L. plantarum HJ10. These metabolites induced mold apoptosis by disrupting cell wall structure, increasing cell membrane fluidity, reducing enzyme activities, and disrupting energy metabolism. However, in vivo antagonism by L. plantarum HJ10 primarily occurs through organic acid production and competition for growth space and nutrients. This study highlights the potential of L. plantarum HJ10 in reducing A. versicolor and STC contamination in maize.
PubMed: 38955023
DOI: 10.1016/j.ijfoodmicro.2024.110809 -
Biochemical and Biophysical Research... Jun 2024Sepsis, a life-threatening condition resulting in multiple organ dysfunction, is characterized by a dysregulated immune response to infection. Current treatment options...
Sepsis, a life-threatening condition resulting in multiple organ dysfunction, is characterized by a dysregulated immune response to infection. Current treatment options are limited, leading to unsatisfactory outcomes for septic patients. Here, we present a series of studies utilizing compact bone mesenchymal stem cells (CB-MSCs) and their derived paracrine mediators, especially exosome (CB-MSCs-Exo), to treat mice with cecal ligation and puncture-induced sepsis. Our results demonstrate that CB-MSCs treatment significantly improves the survival rate of septic mice by mitigating excessive inflammatory response and attenuating sepsis-induced organ injuries. Furthermore, CB-MSCs-conditioned medium, CB-MSCs secretome (CB-MSCs-Sec), and CB-MSCs-Exo exhibit potent anti-inflammatory effects in lipopolysaccharide (LPS)-stimulated murine macrophage (RAW264.7). Intriguingly, intravenous administration of CB-MSCs-Exo confers superior protection against inflammation and organ damage in septic mice compared to CB-MSCs in certain aspects. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomic analysis, we identify a range of characterized proteins derived from the paracrine activity of CB-MSCs, involved in critical biological processes such as immunomodulation and apoptosis. Our findings highlight that the paracrine products of CB-MSCs could serve as a promising cell-free therapeutic agent for sepsis.
PubMed: 38954981
DOI: 10.1016/j.bbrc.2024.150313 -
Food Chemistry Jun 2024In this study, a simple, sensitive, and rapid method was developed for the simultaneous determination of 99 kinds of pesticides in fatty milk samples. This novel...
Determination of multi-residue pesticides in dairy products using single-step emulsification/demulsification clean-up strategy combined with low-pressure gas chromatography-tandem mass spectrometry.
In this study, a simple, sensitive, and rapid method was developed for the simultaneous determination of 99 kinds of pesticides in fatty milk samples. This novel emulsification-demulsification clean-up approach, coupled with an automatic demulsification-dehydration cartridge, allowed rapid single-step clean-up operation and high throughput. It also achieved effective and selective removal of lipids. The analysis was performed using low-pressure gas chromatography-tandem mass spectrometry (LPGC-MS/MS). Based on the optimal conditions, the targeted pesticides showed good linearity in the range of 5-250 μg/kg, with recoveries of 70-120% at spiking levels of 5, 10, and 20 μg/kg in cow milk, goat milk, and almond milk, respectively. The limit of quantification for most pesticides was 5 μg/kg, and the RSDs were lower than 20%. Analysis of real dairy products obtained from local markets revealed a potential risk in plant-derived almond milk, but no significant risks were found for cow and goat milk.
PubMed: 38954952
DOI: 10.1016/j.foodchem.2024.140246 -
Prostaglandins, Leukotrienes, and... May 2024Epoxyeicosatrienoic acids (EpETrEs) are bioactive lipid mediators of arachidonic acid cytochrome P450 oxidation. In vivo, the free (unbound) form of EpETrEs regulate...
Epoxyeicosatrienoic acids (EpETrEs) are bioactive lipid mediators of arachidonic acid cytochrome P450 oxidation. In vivo, the free (unbound) form of EpETrEs regulate multiple processes including blood flow, angiogenesis and inflammation resolution. Free EpETrEs are thought to rapidly degrade via soluble epoxide hydrolase (sEH); yet, in many tissues, the majority of EpETrEs are esterified to complex lipids (e.g. phospholipids) suggesting that esterification may play a major role in regulating free, bioactive EpETrE levels. This hypothesis was tested by quantifying the metabolism of intraperitoneally injected free d11-11(12)-Epoxyeicosatrienoic acid (d11-11(12)-EpETrE) in male and female rats. Plasma and tissues (liver, adipose and brain) were obtained 3 to 4 min later and assayed for d11-11(12)-EpETrE and its sEH metabolite, d11-11,12-dihydroxyeicosatrienoic acid (d11-11,12-diHETrE) in both the free and esterified lipid fractions. In both males and females, the majority of injected tracer was recovered in liver followed by plasma and adipose. No tracer was detected in the brain, indicating that brain levels are maintained by endogenous synthesis from precursor fatty acids. In plasma, liver, and adipose, the majority (>54 %) of d11-11(12)-EpETrE was found esterified to phospholipids or neutral lipids (triglycerides and cholesteryl esters). sEH-derived d11-11,12-diHETrE was not detected in plasma or tissues, suggesting negligible conversion within the 3-4 min period post tracer injection. This study shows that esterification is the main pathway regulating free 11(12)-EpETrE levels in vivo.
PubMed: 38954932
DOI: 10.1016/j.plefa.2024.102622 -
Forensic Science International Jul 2024To summarize recent cases of fatal insulin poisoning both domestically and internationally, thereby offering valuable insights for the forensic identification of insulin...
PURPOSE
To summarize recent cases of fatal insulin poisoning both domestically and internationally, thereby offering valuable insights for the forensic identification of insulin overdose cases.
METHODS
Literature published since 2000 on fatal insulin overdose were systematically searched and screened. Data encompassing variables such as year, age, sex, cause of death, scene conditions, occupations, medical histories of victims and perpetrators, autopsy timing, dosage and administration methods, forensic pathology, and toxicological analysis, were compiled for rigorous statistical analysis.
RESULTS
Among the 29 fatal cases of insulin poisoning, suicides and homicides accounted for 55.2 % and 41.4 %, respectively. Precisely 34.5 % of victims or perpetrators were associated with the medical industry, 27.6 % had diabetes, and 24.1 % had mental illnesses such as depression. Intravenous injection resulted in quicker death than did subcutaneous injection. In some cases, immunohistochemical staining of insulin and protamine at injection sites yielded positive results. The average molar ratio of insulin to C-peptide in post-mortem blood was 13.76 ± 5.167, indicating a significant diagnostic value for insulin poisoning.
CONCLUSION
Assessment of cases of fatal insulin overdose should be thorough, incorporating case investigation, scene examination, medical records review, autopsy findings, pathological examinations, and laboratory tests, alongside considering the condition of the body and timing of death autopsy. Using mass spectrometry to detect insulin proves valuable, particularly in cases of poor body preservation.
PubMed: 38954875
DOI: 10.1016/j.forsciint.2024.112126 -
Journal of the American Society For... Jul 2024We have recently developed a charge inversion ion/ion reaction to selectively derivatize phosphatidylserine lipids via gas-phase Schiff base formation. This tandem mass...
We have recently developed a charge inversion ion/ion reaction to selectively derivatize phosphatidylserine lipids via gas-phase Schiff base formation. This tandem mass spectrometry (MS/MS) workflow enables the separation and detection of isobaric lipids in imaging mass spectrometry, but the images acquired using this workflow are limited to relatively poor spatial resolutions due to the current time and limit of detection requirements for these ion/ion reaction imaging mass spectrometry experiments. This trade-off between chemical specificity and spatial resolution can be overcome by using computational image fusion, which combines complementary information from multiple images. Herein, we demonstrate a proof-of-concept workflow that fuses a low spatial resolution (i.e., 125 μm) ion/ion reaction product ion image with higher spatial resolution (i.e., 25 μm) ion images from a full scan experiment performed using the same tissue section, which results in a predicted ion/ion reaction product ion image with a 5-fold improvement in spatial resolution. Linear regression, random forest regression, and two-dimensional convolutional neural network (2-D CNN) predictive models were tested for this workflow. Linear regression and 2D CNN models proved optimal for predicted ion/ion images of PS 40:6 and SHexCer d38:1, respectively.
PubMed: 38954826
DOI: 10.1021/jasms.4c00144 -
Journal of Agricultural and Food... Jul 2024Squalene has been proven to possess various bioactive functions that are widely present in vegetable oils. A more comprehensive understanding of the reaction behavior of...
Squalene has been proven to possess various bioactive functions that are widely present in vegetable oils. A more comprehensive understanding of the reaction behavior of squalene under oxidative conditions was achieved by studying its antioxidant capacity and thermal degradation products. The total singlet oxygen quenching rate constant ( ) of squalene was 3.8 × 10 M s, and both physical and chemical quenching mechanisms equally contribute to the overall singlet oxygen quenching. Fourteen degradation products of squalene were identified at 180 °C by using gas chromatography-mass spectrometry (GC-MS). Combining with DFT calculations, the thermal degradation pathway of squalene was proposed: the aldehydes, ketones, and alcohols, and epoxy compounds were formed by the homolytic cleavage of squalene hydroperoxides to form alkoxy radicals, followed by β-scission of the alkoxyl radicals at adjacent C-C bonds or intramolecular cyclization.
PubMed: 38954802
DOI: 10.1021/acs.jafc.4c03329