Acid Species Research Articles

Untargeted Lipidomic Profiling of Amniotic Fluid Reveals Dysregulated Lipid Metabolism in Healthy Normal-Weight Mothers with Fetal Macrosomia

Background: Alterations in maternal lipid metabolism have been elucidated by several studies in relation to macrosomia. However, the lipidome of the intrauterine compartment associated with macrosomia, particularly in early pregnancy, remains largely unknown. Objectives: (1) To compare the lipidomic profile of early 2nd trimester amniotic fluid (AF) of healthy mothers with normal body mass index who gave birth to large-for-gestational age (LGA) versus appropriate-for-gestational age (AGA) infants; and (2) to examine if insulin and glucose concentrations in AF were associated with the AF lipidomic profile. Methods: In this nested case–control study, bio-banked AF samples were collected from pregnant women undergoing routine amniocentesis at 12–22 weeks of gestation. A subsample of 15 LGA infants (cases) were contrasted with 15 AGA infants (controls). An untargeted lipidomics analysis using liquid chromatography quadrupole time-of-flight mass spectrometry was conducted. Univariate and multivariate statistical analyses (principal component analysis and partial least-squares discriminant analysis) were used to extract differentially abundant (DA) features with high variable importance in projection (VIP) scores. Results: LGA AF was characterized by elevations of 30 phosphatidic acid species. Among other DA features, sphingomyelin (SM 14:0;O2/20:1) had the highest VIP score and was markedly elevated in LGA AF. Neither insulin nor glucose was associated with 2nd trimester AF lipidomic profiles in these healthy, normal-weight mothers. Conclusion: These findings provide evidence of early dysregulated lipid metabolism in healthy, normal-weight mothers with LGA infants.

Modulating structure of Ce-UiO-66 by introducing fluorinated terephthalic acid for enhanced removal efficiency of antibiotics: Insights into degradation kinetics and pathways

In this work, the 2-fluoroterephthalic acid with asymmetric structure and high electronegative F species was introduced in the assembly of Ce-UiO-66 catalysts to increase the defect density and enlarge pore structure for enhancement in removal efficiency of sulfamethoxazole. Owing to the strong coordination ability from high electronegative F species of 2-fluoroterephthalic acid with Ce-oxo nodes, the designed CUF exhibited improved interfacial properties (accelerated electron transfer rate, available active sites and enhanced interaction with PMS), which was favorable for the exploration and accessibility of active sites with sulfamethoxazole and PMS to decrease the adsorption barrier and accelerate PMS activation. As a result, the CUF catalysts exhibited higher adsorption capacity (173.4 mg/g) than that of CUH (117.8 mg/g), the enhanced degradation efficiency of sulfamethoxazole with a rate constant higher than 2.3 times CUH, good elimination (>95 %) of methylene blue, tetracycline and ibuprofen. In addition, the CUF/PMS system possessed satisfactory stability in wide solution pH, recycling and real water and good potential application in continuous wastewater treatment based on the designed dynamic catalytic reactor. This work provided deep insight into the design of catalysts with high adsorption performance and degradation efficiency based on the structure–activity relationship.

Gentle Skepticism to the Degeneracy Nature of “First Genetic Code UUU”

This study reports our discoveries about the serious defects of the genetic topic “UUU’s degeneracy”, as • Matthaei-Nirenberg poly-U experiment in 1961 never mentioned the degeneracy nature of first genetic code UUU. • Ochoa’s experimental conclusion “3U:phe, 2U1C:phe” was lack of the chemical transforming process between “20 groups of 3 nucleotides (or 20 species of amino acids)” and “64 linear nucleotide triplets( or 64 times of amino acids frequency), the mathematical transformation of three consecutive nucleotides on Watson-Crick model of DNA from 64 linear triplets to 20 triangles (in Gamow’s observation of diamond code) could never be the chemical relations to make “20 species of amino acids” repeated to “64 times of amino acids” , and Ochoa’s UUU was neither a group of three U, nor linear triplet UUU. • Many concepts involved in UUU’s degeneracy seriously violates Matthaei-Nirenberg poly-U experiment in 1961. • In mathematics, the parameters array of (1:1, 1:1, 1:1, 1:1, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:3, 1:6, 1:6, 1:6, 1:6) is not only the “degeneracy value” of each triplet, but also the “expansion value” of each amino acid, therefore, each amino acid can be chosen to correspond any value of triplets in Gamow - Crick “coding” proposals. • Wobble Hypothesis only changes anticodon and doesn’t change the species of amino acids on tRNA. • In chemistry, Poly-(U,C) producing poly-phe in non-Nirenberg experiments serious violates Poly-U producing poly-phe in Matthaie-Nirenberg experiments. • No biochemists find the model protein in which the phenylalanine has only 2 shares, nor the total proportion among different amino acids are as “(1:1:2 :2,:2 :2:2 :2 :2 :2:2 :3:4 :4:4:4:4:6:6:6) “, and in which the model nucleic acid has 64 triplet (each triplet codon displays once in the model nucleic acids). In the end, we suggest to cancel the concept of UUU’s degeneracy, i.e.: “UUU degenerate to UUC” cannot be established in biochemical sciences.

Boosted 1,2-Dichloroethane Deep Destruction over CoRu/Al2O3 Bifunctional Catalysts via Surface Oxygen and Water Molecule Synergistic Activation.

Developing efficacious catalysts with superior Cl resistance and polychlorinated byproduct inhibition capability is crucial for realizing the environmentally friendly purification of chlorinated volatile organic compounds (CVOCs). Activating CVOC molecules and desorbing Cl species by modulating the metal-oxygen property is a promising strategy to fulfill these. Herein, a bifunctional CoRu/Al2O3 catalyst with synergistic Co and Ru interactions (Ru-O-Co species) was rationally fabricated, which possesses abundant surface Co2+ and Ruδ+ sites and collaboratively facilitates the activation of lattice oxygen (O2-) and molecular oxygen (O2 → O2- → O-), accelerating 1,2-dichloroethane (1,2-DCE) decomposition via the reaction route of enolic species → aldehydes → carboxylate/carbonate. Furthermore, CoRu/Al2O3 stimulates 1,2-DCE oxidation under humid conditions as H2O molecules can be easily activated to active *OH (potential oxidizing agent) over Ru species, accelerating C-Cl dissociation and Cl desorption and promoting the transformation of catecholate-type (C═O) species to easily oxidizable carboxylic acid (COOH) species, remarkably suppressing the formation of hazardous CCl4 and CHCl2CH2Cl. This study provides critical insights into the development of bifunctional catalysts to synergistically activate surface oxygen species and H2O molecules for industrial CVOC stable and efficient elimination.

A Mix of Probiotic Strains Prevents Hepatic Steatosis, and Improves Oxidative Stress Status and Gut Microbiota Composition in Obese Mice.

The gut microbiota plays a role in fat accumulation and energy homeostasis. Therefore, probiotic supplementation may improve metabolic parameters and control body weight. In this study, mice are fed either a high-fat diet (HFD) or an HFD supplemented with oral gavage of a mixture of three probiotic strains, Bifidobacterium lactis Lafti B94, Lactobacillus plantarum HA-119, and Lactobacillus helveticus Lafti L10 for 7 weeks. It finds that probiotic supplementation modulates body weight gain, food energy efficiency, and fat accumulation caused by the HFD. This probiotic mix prevents liver damage and lipid metabolic disorders in HFD-fed obese mice. The probiotic supplementation significantly downregulates the expression of the proinflammatory cytokines interleukin-1β, tumor necrosis factor-α, and malondialdehyde (MDA) in the liver and upregulated catalase (CAT), superoxide dismutase (SOD), and nuclear respiratory factor 1 (Nrf1) expression. Mice supplemented with the probiotic mix also show different microbiota compositions, with an increase in Clostridia_UCG-014 and Lachnospiraceae_nk4a136_group and a decrease in the Dubosiella genus compared with those in mice fed only an HFD. Finally, the amounts of fecal pentanoic acid and the three bile acid species increase in mice with probiotic supplementation. Treatment with a combination of a mixture of three probiotic strains, B. lactis Lafti B94, L. plantarum HA-119, and L. helveticus Lafti L10 for 7 weeks, ameliorates the effects of HFD induced obesity in mice.

RICE LONG GRAIN 3 delays dark-induced senescence by downregulating abscisic acid signaling and upregulating reactive oxygen species scavenging activity.

Leaf senescence is a complex developmental process influenced by abscisic acid (ABA) and reactive oxygen species (ROS), both of which increase during senescence. Understanding the regulatory mechanisms of leaf senescence can provide insights into enhancing crop yield and stress tolerance. In this study, we aimed to elucidate the role and mechanisms of rice (Oryza sativa) LONG GRAIN 3 (OsLG3), an APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factor, in orchestrating dark-induced leaf senescence. The transcript levels of OsLG3 gradually increased during dark-induced and natural senescence. Transgenic plants overexpressing OsLG3 exhibited delayed senescence, whereas CRISPR/Cas9-mediated oslg3 mutants exhibited accelerated leaf senescence. OsLG3 overexpression suppressed senescence-induced ABA signaling by downregulating OsABF4 (an ABA-signaling-related gene) and reduced ROS accumulation by enhancing catalase activity through upregulation of OsCATC. In vivo and in vitro binding assays demonstrated that OsLG3 downregulated OsABF4 and upregulated OsCATC by binding directly to their promoter regions. These results demonstrate the critical role of OsLG3 in fine-tuning leaf senescence progression by suppressing ABA-mediated signaling while simultaneously activating ROS-scavenging mechanisms. These findings suggest that OsLG3 could be targeted to enhance crop resilience and longevity.

Hepatic bile acid accretion correlates with cholestatic liver injury and therapeutic response in Cyp2c70 knockout mice with a humanized bile acid composition.

Cyp2c70 knockout (KO) mice lack the liver enzyme responsible for synthesis of 6-hydroxylated muricholate bile acid species and possess a more hydrophobic human-like bile acid composition. Cyp2c70 KO mice develop cholestatic liver injury that can be prevented by administration of an ileal bile acid transporter (IBAT) inhibitor. In this study, we investigated the potential of an ileal bile acid transporter (IBAT) inhibitor (SC-435) and steroidal FXR agonist (cilofexor) to modulate established hepatobiliary injury and the consequent relationship of intrahepatic bile acid content and hydrophobicity to the cholestatic liver injury phenotype. Oral administration of SC-435, cilofexor, or combined treatment for 2 weeks markedly reduced serum markers of liver injury and improved histological and gene expression markers of fibrosis, liver inflammation, and ductular reaction in male and female Cyp2c70 KO mice, with greatest benefit in the combination treatment group. The IBAT inhibitor and FXR agonist significantly reduced intrahepatic bile acid content but not hepatic bile acid pool hydrophobicity, and markers of liver injury were strongly correlated with intrahepatic total bile acid and taurochenodeoxycholic acid accretion. Biomarkers of liver injury increased linearly with similar hepatic thresholds for pathological accretion of hydrophobic bile acids in male and female Cyp2c70 KO mice. These findings further support targeting intrahepatic bile acid retention as a component of treatments for cholestatic liver disease.

Lipid droplets sequester palmitic acid to disrupt endothelial ciliation and exacerbate atherosclerosis in male mice

Disruption of ciliary homeostasis in vascular endothelial cells has been implicated in the development of atherosclerosis. However, the molecular basis for the regulation of endothelial cilia during atherosclerosis remains poorly understood. Herein, we provide evidence in male mice that the accumulation of lipid droplets in vascular endothelial cells induces ciliary loss and contributes to atherosclerosis. Triglyceride accumulation in vascular endothelial cells differentially affects the abundance of free fatty acid species in the cytosol, leading to stimulated lipid droplet formation and suppressed protein S-palmitoylation. Reduced S-palmitoylation of ciliary proteins, including ADP ribosylation factor like GTPase 13B, results in the loss of cilia. Restoring palmitic acid availability, either through pharmacological inhibition of stearoyl-CoA desaturase 1 or a palmitic acid-enriched diet, significantly restores endothelial cilia and mitigates the progression of atherosclerosis. These findings thus uncover a previously unrecognized role of lipid droplets in regulating ciliary homeostasis and provide a feasible intervention strategy for preventing and treating atherosclerosis.

Systemic deficits in lipid homeostasis promote aging-associated impairments in B cell progenitor development.

Organismal aging has been associated with diverse metabolic and functional changes across tissues. Within the immune system, key features of physiological hematopoietic cell aging include increased fat deposition in the bone marrow, impaired hematopoietic stem and progenitor cell (HSPC) function, and a propensity towards myeloid differentiation. This shift in lineage bias can lead to pre-malignant bone marrow conditions such as clonal hematopoiesis of indeterminate potential (CHIP) or clonal cytopenias of undetermined significance (CCUS), frequently setting the stage for subsequent development of age-related cancers in myeloid or lymphoid lineages. At the systemic as well as sub-cellular level, human aging has also been associated with diverse lipid alterations, such as decreased phospholipid membrane fluidity that arises as a result of increased saturated fatty acid (FA) accumulation and a decay in n-3 polyunsaturated fatty acid (PUFA) species by the age of 80 years, however the extent to which impaired FA metabolism contributes to hematopoietic aging is less clear. Here, we performed comprehensive multi-omics analyses and uncovered a role for a key PUFA biosynthesis gene, ELOVL2 , in mouse and human immune cell aging. Whole transcriptome RNA-sequencing studies of bone marrow from aged Elovl2 mutant (enzyme-deficient) mice compared with age-matched controls revealed global down-regulation in lymphoid cell markers and expression of genes involved specifically in B cell development. Flow cytometric analyses of immune cell markers confirmed an aging-associated loss of B cell markers that was exacerbated in the bone marrow of Elovl2 mutant mice and unveiled CD79B, a vital molecular regulator of lymphoid progenitor development from the pro-B to pre-B cell stage, as a putative surface biomarker of accelerated immune aging. Complementary lipidomic studies extended these findings to reveal select alterations in lipid species in aged and Elovl2 mutant mouse bone marrow samples, suggesting significant changes in the biophysical properties of cellular membranes. Furthermore, single cell RNA-seq analysis of human HSPCs across the spectrum of human development and aging uncovered a rare subpopulation (<7%) of CD34 + HSPCs that expresses ELOVL2 in healthy adult bone marrow. This HSPC subset, along with CD79B -expressing lymphoid-committed cells, were almost completely absent in CD34 + cells isolated from elderly (>60 years old) bone marrow samples. Together, these findings uncover new roles for lipid metabolism enzymes in the molecular regulation of cellular aging and immune cell function in mouse and human hematopoiesis. In addition, because systemic loss of ELOVL2 enzymatic activity resulted in down-regulation of B cell genes that are also associated with lymphoproliferative neoplasms, this study sheds light on an intriguing metabolic pathway that could be leveraged in future studies as a novel therapeutic modality to target blood cancers or other age-related conditions involving the B cell lineage.

Thioctic Acid-Based Solvent-Free and Recoverable Adhesive for Dry/Wet Environments.

Metal adhesive synthesis typically involves heating and solvents, and the resultant adhesives lack degradability and suffer from recycling and sustainable problems. Herein, we developed a solvent-free and chemically degradable biobased adhesive (p(Elp-TA)+PVP) from thioctic acid (TA), its derivative (Elp), and polyvinylpyrrolidone (PVP). Through a rapid acid-triggered cationic ring-opening polymerization of dithiolane at ambient conditions, p(Elp-TA)+PVP adhesive could build up a strong lap shear strength of 1123 kPa in air and an underwater lap shear strength of 534 kPa to the copper plate. Molecular dynamics simulations show that compared to p(Elp-TA), the presence of an appropriate amount of PVP can significantly enhance the binding energy of the adhesive molecules to the metal substrate, and the rapid adhesion of p(Elp-TA)+PVP molecules to metal substrates was achieved through a synergistically dynamic adaptive network enhanced by hydrogen bonding, reversible dynamic bonding, and metal coordination bonding at 40 ps. More importantly, the applied p(Elp-TA)+PVP adhesive could be easily degraded and reverted to its small-molecular-weight lipoic acid species. Upon exposure to dithiothreitol, a green reducing agent, the average molecular weight of the adhesive could quickly decrease from 1603 kDa to 274 Da. This green adhesive constructed by a simple method provides a promising general strategy for developing a controlled degradable and recoverable adhesive from natural resources.

Liraglutide and Colesevelam Changes Serum and Fecal Bile Acid Levels in a Randomized Trial with Patients with Bile Acid Diarrhea.

Both liraglutide and colesevelam improve bile acid diarrhea (BAD) symptoms. Colesevelam binds excess amounts of diarrhea-causing bile acids in the colon whereas the mode of action for liraglutide remains elusive. Here, we examined the impact of colesevelam and liraglutide treatment on the concentrations of bile acids in serum and feces and the fecal microbiota composition to better understand the two drugs' modes of action. Bile acid species were analyzed in serum and fecal samples from a randomized, double-blind, double-dummy trial at baseline and after three and six weeks of orally administered colesevelam (1,875 mg twice daily, n = 26) or subcutaneously administered liraglutide (uptitrated by weekly increments of 0.6 mg from 0.6 to 1.8 mg daily, n = 26) in patients with 75selenium-homotaurocholic acid test-verified, idiopathic, or post-cholecystectomy BAD. Fecal microbiota composition was analyzed by 16S rRNA gene amplicon sequencing at the same time points. Colesevelam increased the fecal concentrations of all bile acid species while it decreased serum concentrations of secondary bile acids. Liraglutide induced a small increase in serum unconjugated bile acid concentrations without affecting fecal bile acid concentrations. No changes in fecal microbiota composition were observed with either treatment. Colesevelam and liraglutide exhibit distinct effects on serum and fecal bile acid concentrations with colesevelam reducing serum concentrations of secondary bile acids and promoting fecal bile acid excretion while liraglutide enhances serum concentrations of unconjugated bile acids, potentially through deceleration of small intestinal transit time allowing more time for passive absorption of bile acids.

An Improved Method and Device for Nucleic Acid Isolation Using a High-Salt Gel Electroelution Trap.

The success of DNA analytical methods, including long-read sequencing, depends on the availability of high-quality, purified DNA. Previously, we developed a method and device for isolating high-molecular-weight (HMW) DNA for long-read sequencing using a high-salt gel electroelution trap. Here, we present an improved version of this method for purifying nucleic acids with high yield and purity from even the most challenging biological samples. The proposed method is a significant improvement over the previously published procedure, offering a simple, fast, and efficient solution for isolating HMW DNA and smaller DNA and RNA molecules. The method utilizes vertical gel electrophoresis in two nested, partially overlapping electrophoretic columns. The upper, smaller-diameter column has a thin layer of agarose gel at the bottom, which separates nucleic acids from impurities, and an electrophoresis buffer on top. After the target nucleic acid has been gel-purified on the upper column, a larger-diameter column with a layer of high-salt gel overlaid with electrophoresis buffer is inserted from below. The purified nucleic acid is then electroeluted into the buffer-filled gap between the separating gel and the high-salt gel, where excess counterions from the high-salt gel slow its migration and cause it to accumulate. The proposed vertical purification system outperforms the previously described horizontal system in terms of ease of use, speed, scalability, and compatibility with high-throughput workflows. Furthermore, the vertical system allows for the sequential purification of several nucleic acid species from the same sample using interchangeable salt-gel columns.

Maternal Docosahexaenoic Acid Supplementation Alters Maternal and Fetal Docosahexaenoic Acid Status and Placenta Phospholipids in Pregnancies Complicated by High Body Mass Index.

An optimal fetal supply of docosahexaenoic acid (DHA) is critical for normal brain development. The relationship between maternal DHA intake and DHA delivery to the fetus is complex and is dependent on placental handling of DHA. Little data exist on placental DHA levels in pregnancies supplemented with the recommended dose of 200 mg/d. Our objective was to determine how prenatal DHA at the recommended 200 mg/d impacts maternal, placental, and fetal DHA status in both normal-weight and high-BMI women compared to women taking no supplements. Maternal blood, placenta, and cord blood were collected from 30 healthy pregnant women (BMI 18.9-43.26 kg/m2) giving birth at term. Red blood cells (RBCs) and villous tissue were isolated, and lipids were extracted to determine DHA content by LC-MS/MS. Data were analyzed by supplement group (0 vs. 200 mg/d) and maternal BMI (normal weight or high BMI) using two-way ANOVA. We measured maternal choline levels in maternal and cord plasma samples. Supplementation with 200 mg/d DHA significantly increased (p < 0.05) maternal and cord RBC DHA content only in pregnancies complicated by high BMI. We did not find any impact of choline levels on maternal or cord RBC phospholipids. There were no significant differences in total placental DHA content by supplementation or maternal BMI (p > 0.05). Placental levels of phosphatidylinositol (PI) and phosphatidic acid containing DHA species were higher (p < 0.05) in high-BMI women without DHA supplementation compared to both normal-BMI and high-BMI women taking DHA supplements. Maternal DHA supplementation at recommended doses cord increased RBC DHA content only in pregnancies complicated by higher BMI. Surprisingly, we found that obesity was related to an increase in placental PI and phosphatidic acid species, which was ameliorated by DHA supplementation. Phosphatidic acid activates placental mTOR, which regulates amino acid transport and may explain previous findings of the impact of DHA on placental function. Current recommendations for DHA supplementation may not be achieving the goal of improving fetal DHA levels in normal-weight women.

Unravelling the therapeutic landscape of bile acid-based therapies in gastrointestinal disorders.

Bile acids serve as endogenous ligands for nuclear and cell membrane receptors and play a crucial role in bile acid and lipid metabolism. These detergent-like compounds promote bile flow and aid in the absorption of dietary fats and fat-soluble vitamins in the intestine. Synthesized in the liver as end products of cholesterol catabolism, bile acids exhibit a chemical structure comprising a nucleus and a side chain featuring a carboxyl group, with diverse steric arrangements and potential polar substituents. Critical interactions occur between bile acid species and various nuclear and cell membrane receptors, including the farnesoid X receptor and G-protein-coupled bile acid receptor 1. This research aimed to review the literature on bile acids and their roles in treating different diseases. Currently, numerous investigations are concentrating on specific bile acid species that target nuclear receptors in the gastrointestinal system, aiming to improve the treatment of conditions such as nonalcoholic fatty liver disease. Given the global attention this topic has garnered from research groups, it is considered relatively new, thus anticipating some gaps or incomplete data. Bile acid species have a significant therapeutic promise, especially in their ability to activate or inhibit nuclear receptors, such as farnesoid X receptor. This research provides to offer essential information for scientists and medical practitioners interested in discovering new studies that underscore the importance of bile acids in ameliorating and impeding the progression of disorders. Furthermore, it opens avenues for previously overlooked bile acid-based therapies.

Determination of solid-state acidity of lyophilized trehalose containing citrate, phosphate, and histidine buffers using UV/VIS diffuse reflectance and solid-state NMR spectroscopy

Changes in the protonation state of lyophilized proteins can impact structural integrity, chemical stability, and propensity to aggregate upon reconstitution. When a buffer is chosen, the freezing/drying process may result in dramatic changes in the protonation state of the protein due to ionization shift of the buffer. In order to determine whether protonation shifts are occurring, ionizable probes can be added to the formulation. Optical probes (dyes) have shown dramatic ionization changes in lyophilized products, but it is unclear whether the pH indicator is uniform throughout the matrix and whether the change in the pH indicator actually mirrors drug ionization changes. In solid-state NMR (SSNMR) spectroscopy, the chemical shift of the carbonyl carbon in carboxylic acids is very sensitive to the ionization state of the acid. Therefore, SSNMR can be used to measure ionization changes in a lyophilized matrix by employing a small quantity of an isotopically-labeled carboxylic acid species in the formulation. This paper compares the apparent pH of six trehalose-containing lyophilized buffer systems using SSNMR and UV-Vis diffuse reflectance spectroscopy (UVDRS). Both SSNMR and UVDRS results using two different ionization probes (butyric acid and bromocresol purple, respectively) showed little change in apparent acidity compared to the pre-lyophilized solution in a sodium citrate buffer, but a greater change was observed in potassium phosphate, sodium phosphate, and histidine buffers. While the trends between the two methods were similar, there were differences in the numerical values of equivalent pH (pHeq) observed between the two methods. The potential causes contributing to the differences are discussed.

Mechanisms and Effects of Activation of Innate Immunity by Mitochondrial Nucleic Acids.

In recent years, a growing number of roles have been identified for mitochondria in innate immunity. One principal mechanism is that translocation of mitochondrial nucleic acid species from the mitochondrial matrix to the cytosol and endolysosomal lumen in response to an array of microbial and non-microbial environmental stressors has been found to serve as a second messenger event in the cell signaling of the innate immune response. Thus, mitochondrial DNA and RNA have been shown to access the cytosol through several regulated mechanisms involving remodeling of the mitochondrial inner and outer membranes and to access lysosomes via vesicular transport, thereby activating cytosolic (e.g., cyclic GMP-AMP synthase [cGAS]; retinoic acid-inducible gene-I [RIG-I]-like receptors) and endolysosomal (Toll-like Receptor [TLR]7, -9) nucleic acid receptors that induce type I interferons and pro-inflammatory cytokines. In this mini-review, we discuss these molecular mechanisms of mitochondrial nucleic acid mislocalization and their roles in host defense, autoimmunity, and auto-inflammatory disorders. The emergent paradigm is one in which host-derived DNA interestingly serves as a signal amplifier in the innate immune response and also as an alarm signal for disturbances in organellar homeostasis. The apparent vast excess of mitochondria and mitochondrial DNA nucleoids per cell may thus serve to sensitize the cell response to stressors while ensuring an underlying reserve of intact mitochondria to sustain cellular metabolism. An improved understanding of these molecular mechanisms will hopefully afford future opportunities for therapeutic intervention in human disease.

Accelerating Toluene Oxidation over Boron-Titanium-Oxygen Interface: Steric Hindrance of the Methyl Group Induced by the Plane-Adsorption Configuration.

Elimination of dilute gaseous toluene is one of the critical concerns within the field of indoor air remediation. The typical degradation route on titanium-based catalysts, "toluene-benzaldehyde-carbon dioxide", necessitates the oxidation of the methyl group as a prerequisite for photocatalytic toluene oxidation. However, the inherent planar adsorption configuration of toluene molecules, dominated by the benzene rings, leads to significant steric hindrance for the methyl group. This steric hindrance prevents the methyl group from contacting the active species on the catalyst surface, thereby limiting the removal of toluene under indoor conditions. To date, no effective strategy to control the steric hindrance of the methyl group has been identified. Herein, we showed a B-Ti-O interface that exhibits significantly enhanced toluene removal efficiency under indoor conditions. In-depth investigations revealed that, compared to typical Ti-based photocatalysts, the steric hindrance between the methyl group and the catalyst surface decreased from 3.42 to 3.03 Å on the designed interface. This reduction originates from the matching of orbital energy levels between Ti 3dz2 and C 2pz of the benzene ring. The decreased steric hindrance improved the efficiency of toluene being attacked by surface active species, allowing for rapid conversion into benzaldehyde and benzoic acid species for subsequent reactions. Our work provides novel insights into the steric hindrance effect in the elimination of aromatic volatile organic compounds.

Improved functions for nonlinear sequence comparison using SEEKR.

SEquence Evaluation through k-mer Representation (SEEKR) is a method of sequence comparison that uses sequence substrings called k-mers to quantify the nonlinear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate P-values that ascribe statistical significance to SEEKR-derived similarities, as well as visualize different aspects of k-mer similarity. We apply the new functions to identify chromatin-enriched lncRNAs that contain XIST-like sequence features, and we demonstrate the utility of applying SEEKR on lncRNA fragments to identify potential RNA-protein interaction domains. We also highlight ways in which SEEKR can be applied to augment studies of lncRNA conservation, and we outline the best practice of visualizing RNA-seq read density to evaluate support for lncRNA annotations before their in-depth study in cell types of interest.

Effect of temperature and relative humidity on the moisture recovery and specific resistance of yak hair fiber

This study measured the moisture regain and specific resistance values of yak hair fiber in a humidified environment to provide a theoretical basis for the development and utilization of yak hair fiber in the fields of textile, electronics and manufacturing. The effects of temperature and relative humidity on moisture absorption and electrical resistance of yak hair fiber were measured, and the effects of ambient temperature and humidity on the moisture regain and specific resistance of yak hair fiber were evaluated when using a new type of water-cooled textile air conditioner as a humidifying device, and the amino acid structure and crystallinity were compared between yak hair fiber and wool fiber. The experimental results show that temperature and relative humidity have a greater effect on the moisture regain rate and specific resistance value of the fiber, and the higher the temperature and relative humidity, the higher the moisture regain rate of yak hair fiber and the lower the specific resistance. When the temperature was 30 °C and the relative humidity was 85%, the fiber had the lowest specific resistance value and the highest moisture return rate. In terms of amino acid species, there is not much difference in chemical structure between yak hair fiber and wool fiber. The crystallinity of yak hair fiber is lower than that of wool fiber.

High-fat feeding drives the intestinal production and assembly of C16:0 ceramides in chylomicrons.

Consumption of a diet rich in saturated fat increases lipid absorption from the intestine, assembly into chylomicrons, and delivery to metabolic tissues via the lymphatic and circulatory systems. Accumulation of ceramide lipids, composed of sphingosine and a fatty acid, in metabolic tissues contributes to the pathogenesis of cardiovascular diseases, type 2 diabetes mellitus and cancer. Using a mesenteric lymph duct cannulated rat model, we showed that ceramides are generated by the intestine and assembled into chylomicrons, which are transported via the mesenteric lymphatic system. A lipidomic screen of intestinal-derived chylomicrons identified a diverse range of fatty acid, sphingolipid, and glycerolipid species that have not been previously detected in chylomicrons, including the metabolically deleterious C16:0 ceramide that increased in response to high-fat feeding in rats and human high-lipid meal replacement enteral feeding. In conclusion, high-fat feeding increases the export of intestinal-derived C16:0 ceramide in chylomicrons, identifying a potentially unknown mechanism through which ceramides are transported systemically to contribute to metabolic dysfunction.