Open and Closed Cage Silsesquioxane Dimers.

Polyhedral oligomeric silsesquioxane (POSS) is an organic-inorganic hybrid molecule with two structural variations, closed- and open-cage configurations, referred to as completely condensed POSS (CC-POSS) and corner-opened POSS (CO-POSS), respectively. In this study, we synthesized 12 dimers by combining CC- and CO-POSS variants decorated with isobutyl or phenyl substituents to explore their structure-property relationships. The choice of substituents, both at the cage vertices and open sites, significantly affected the thermal and optical properties of the materials. Modifying the substituents on CO- and CC-POSS, which are isomers, led to significant alterations in the material properties. Notably, isomer-bearing carbazole substituents exhibited a substantially higher quantum yield (0.32) than its counterpart isomer (0.13), underscoring the crucial role of structural nuances in determining material performance. These results offer valuable insights for the design of novel silsesquioxane-based materials.

Determination of 16 ultraviolet-absorbing compounds in marine invertebrates by using LC-USI-MS/MS coupled with QuEChERS.

In this study, we examined multiple endocrine-disrupting ultraviolet-absorbing compounds (UVACs) in marine invertebrates used in personal care products and packaging. Modified QuEChERS and liquid chromatography UniSpray ionization tandem mass spectrometry were used to identify 16 UVACs in marine invertebrates. Matrix-matched calibration curves revealed high linearity (r ≥ 0.9929), with limits of detection and quantification of 0.006-1.000 and 0.020-3.000 ng/g w.w., respectively. In oysters, intraday and interday analyses revealed acceptable accuracy (93%-120%) and precision (≤18%), except for benzophenone (BP) and ethylhexyl 4-(dimethylamino) benzoate. Analysis of 100 marine invertebrate samples revealed detection frequencies of 100%, 98%, 89%, 64%, and 100% for BP, 4-hydroxybenzophenone, 4-methylbenzophenone, 4-methylbenzylidene camphor, and benzophenone-3 (BP-3), respectively. BP and BP-3 were detected at concentrations of 4.40-27.39 and < 0.020-0.560 ng/g w.w., respectively, indicating their widespread presence. Overall, our proposed method successfully detected UVACs in marine invertebrates, raising concerns regarding their potential environmental and health effects.

Spectral and HPLC Analyses of Synthesized Butin and Butein.

Butin and butein are significant bioactive flavanones derived from plants, existing as tautomers of each other. However, their physicochemical attributes, such as their spectral profiles under varying experimental conditions in aqueous solutions and established chromatographic methods for distinguishing between them, remain undetermined. In this study, we determined the basic properties of butin and butein using conventional spectroscopic, reversed-phase, and chiral HPLC analyses. The spectra of the synthesized butin and butein were analyzed using a UV-Vis spectrophotometer in several solvents with different polarities as well as in aqueous solutions at various pH values. Furthermore, the behavior of the measured spectra was reproduced by calculations to reveal the effects of the solvent and pH on the spectra of butin and butein in organic and aqueous solutions. Subsequently, we assessed the structural stability of butin and butein using reversed-phase HPLC, which revealed that butein is unstable compared with butin in a general culture medium. The synthesized butin was effectively separated into R- and S-isomers with positive and negative Cotton effects, respectively, via HPLC using a chiral column. These findings will aid in uncovering the individual properties of both butin and butein that may have been concealed by their tautomerism and enable the synthesis of S-butin, which is typically challenging and time-consuming to isolate.

Linear isomer but not branched isomers of perfluorooctane sulfonate in plasma is associated with eicosapentaenoic acid, a seafood consumption biomarker.

BACKGROUND: Per- and polyfluoroalkyl substances (PFAS) are global contaminants. Seafood consumption is a possible PFAS exposure route to humans while the isomer specific analysis has not been conducted. METHODS: Perfluorooctane sulfonate (PFOS), perfluoroheptane sulfonate (PFHpS) and perfluorohexane sulfonate (PFHxS) were investigated in residents of Kyoto, Japan (n = 51). The relationship between plasma PFAS and seafood consumption biomarker, the ratio of eicosapentaenoic acid to arachidonic acid (EPA/AA) was examined by multiple regression analysis. RESULTS: Linear PFOS concentrations showed a significant positive correlation with the EPA/AA ratio in plasma samples (ß = 6.80, p = 0.0014). Linear PFHpS was marginally associated with EPA/AA ratio (ß = 0.178, p = 0.0874). Branched PFOS isomers and PFHxS had no associations with EPA/AA ratios. CONCLUSION: Seafood intake may be a significant exposure pathway for PFAS, such as PFOS but the isomers differ.

Filling the gaps in peptide maps with a platform assay for top-down characterization of purified protein samples.

Liquid chromatography-mass spectrometry (LC-MS) intact mass analysis and LC-MS/MS peptide mapping are decisional assays for developing biological drugs and other commercial protein products. Certain PTM types, such as truncation and oxidation, increase the difficulty of precise proteoform characterization owing to inherent limitations in peptide and intact protein analyses. Top-down MS (TDMS) can resolve this ambiguity via fragmentation of specific proteoforms. We leveraged the strengths of flow-programmed (fp) denaturing online buffer exchange (dOBE) chromatography, including robust automation, relatively high ESI sensitivity, and long MS/MS window time, to support a TDMS platform for industrial protein characterization. We tested data-dependent (DDA) and targeted strategies using 14 different MS/MS scan types featuring combinations of collisional- and electron-based fragmentation as well as proton transfer charge reduction. This large, focused dataset was processed using a new software platform, named TDAcquireX, that improves proteoform characterization through TDMS data aggregation. A DDA-based workflow provided objective identification of αLac truncation proteoforms with a two-termini clipping search. A targeted TDMS workflow facilitated the characterization of αLac oxidation positional isomers. This strategy relied on using sliding window-based fragment ion deconvolution to generate composite proteoform spectral match (cPrSM) results amenable to fragment noise filtering, which is a fundamental enhancement relevant to TDMS applications generally.

In vitro metabolic studies and machine learning analysis of mass spectrometry data: A dual strategy for differentiating alpha-pyrrolidinohexiophenone (α-PHP) and alpha-pyrrolidinoisohexanophenone (α-PiHP) in urine analysis.

Synthetic cathinones are some of the most prevalent new psychoactive substances (NPSs) globally, with alpha-pyrrolidinoisohexanophenone (α-PiHP) being particularly noted for its widespread use in the United States, Europe, and Taiwan. However, the analysis of isomeric NPSs such as α-PiHP and alpha-pyrrolidinohexiophenone (α-PHP) is challenging owing to similarities in their retention times and mass spectra. This study proposes a dual strategy based on in vitro metabolic experiments and machine learning-based classification modelling for differentiating α-PHP and α-PiHP in urine samples: (1) in vitro metabolic experiments using pooled human liver microsomes and liquid chromatography tandem quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) were conducted to identify the key metabolites of α-PHP and α-PiHP from the high-resolution MS/MS spectra. After 5 h incubation, 71.4 % of α-PHP and 64.7 % of α-PiHP remained unmetabolised. Nine phase I metabolites were identified for each compound, including primary ß-ketone reduction (M1) metabolites. Comparing the metabolites and retention times confirmed the efficacy of in vitro metabolic experiments for differentiating NPS isomers. Subsequently, analysis of seven real urine samples revealed the presence for various metabolites, including M1, that could be used as suitable detection markers at low concentrations. The aliphatic hydroxylation (M2) metabolite peak counts and metabolite retention times were used to determine α-PiHP use. (2) Classification models for the parent compounds and M1 metabolites were developed using principal component analysis for feature extraction and logistic regression for classification. The training and test sets were devised from the spectra of standard samples or supernatants from in vitro metabolism experiments with different incubation times. Both models had classification accuracies of 100 % and accurately identified α-PiHP and its M1 metabolite in seven real urine samples. The proposed methodology effectively distinguished between such isomers and confirmed their presence at low concentrations. Overall, this study introduces a novel concept that addresses the complexities in analysing isomeric NPSs and suggests a path towards enhancing the accuracy and reliability of NPS detection.

Serum Mac-2 binding protein glycosylation isomer dynamics in patients achieving sustained virologic response for hepatitis C virus.

BACKGROUND AND AIM: Understanding the dynamics of serum Mac-2 binding protein glycosylation isomer (M2BPGi) remains pivotal for hepatitis C virus (HCV) patients' post-sustained virologic response (SVR12) through direct-acting antivirals (DAAs). METHODS: We compared areas under receiver operating characteristic curves (AUROCs) of M2BPGi, FIB-4, and APRI and assess M2BPGi cutoff levels in predicting fibrosis stages of ≥F3 and F4 utilizing transient elastography in 638 patients. Variations in M2BPGi levels from pretreatment to SVR12 and their association with pretreatment alanine transaminase (ALT) levels and fibrosis stage were investigated. RESULTS: The AUROCs of M2BPGi were comparable to FIB-4 in predicting ≥F3 (0.914 vs 0.902, P = 0.48) and F4 (0.947 vs 0.915, P = 0.05) but were superior to APRI in predicting ≥F3 (0.914 vs 0.851, P = 0.001) and F4 (0.947 vs 0.857, P < 0.001). Using M2BPGi cutoff values of 2.83 and 3.98, fibrosis stages of ≥F3 and F4 were confirmed with a positive likelihood ratio ≥10. The median M2BPGi change was -0.55. Patients with ALT levels ≥5 times ULN or ≥F3 demonstrated more pronounced median decreases in M2BPGi level compared to those with ALT levels 2-5 times ULN and <2 times ULN (-0.97 vs -0.68 and -0.44; P < 0.001) or with < F3 (-1.52 vs -0.44; P < 0.001). CONCLUSIONS: Serum M2BPGi is a reliable marker for advanced hepatic fibrosis. Following viral clearance, there is a notable M2BPGi decrease, with the extent of reduction influenced by ALT levels and fibrosis stage.

Accumulation of Per- and Polyfluoroalkyl Substances (PFAS) in Coastal Sharks from Contrasting Marine Environments: The New York Bight and The Bahamas.

Per- and polyfluoroalkyl substances (PFAS) enter the marine food web, accumulate in organisms, and potentially have adverse effects on predators and consumers of seafood. However, evaluations of PFAS in meso-to-apex predators, like sharks, are scarce. This study investigated PFAS occurrence in five shark species from two marine ecosystems with contrasting relative human population densities, the New York Bight (NYB) and the coastal waters of The Bahamas archipelago. The total detected PFAS (∑PFAS) concentrations in muscle tissue ranged from 1.10 to 58.5 ng g-1 wet weight, and perfluorocarboxylic acids (PFCAs) were dominant. Fewer PFAS were detected in Caribbean reef sharks (Carcharhinus perezi) from The Bahamas, and concentrations of those detected were, on average, ∼79% lower than in the NYB sharks. In the NYB, ∑PFAS concentrations followed: common thresher (Alopias vulpinus) > shortfin mako (Isurus oxyrinchus) > sandbar (Carcharhinus plumbeus) > smooth dogfish (Mustelus canis). PFAS precursors/intermediates, such as 2H,2H,3H,3H-perfluorodecanoic acid and perfluorooctanesulfonamide, were only detected in the NYB sharks, suggesting higher ambient concentrations and diversity of PFAS sources in this region. Ultralong-chain PFAS (C ≥ 10) were positively correlated with nitrogen isotope values (δ15N) and total mercury in some species. Our results provide some of the first baseline information on PFAS concentrations in shark species from the northwest Atlantic Ocean, and correlations between PFAS, stable isotopes, and mercury further contextualize the drivers of PFAS occurrence.

Identifying isomers in Chinese traditional medicine via density functional theory and ion fragmentation simulation software QCxMS.

In the realm of electrospray ionization mass spectrometry (ESI-MS), distinguishing among isomers poses a significant challenge due to the minimal spectral differences that often arise from their subtle structural differences. This makes the accurate identification of these compounds through solely experimental spectra a daunting task. Computational chemistry has emerged as a pivotal tool in bridging the gap between experimental observations and theoretical understanding. This study used the MS fragmentation simulation software, QCxMS, to model the spectra of five groups of isomers, encompassing 11 compounds, found in the traditional Chinese medicine, Zhishi Xiebai Guizhi Decoction. By comparing the spectra predicted through computational methods with those derived from Ultra-high performance liquid chromatography-quadrupole-time of flight-mass spectrometry (UPLC-Q-TOF-MS) experiments, it was observed that, following the optimization of simulation parameters, QCxMS was capable of generating reliable spectra for all examined compounds. Notably, the data calculated under both GFN1-xTB and GFN2-xTB levels exhibited no significant discrepancies. Further analysis enabled the identification of the principal fragments of the 11 compounds from the theoretical data, facilitating the deduction of their fragmentation pathways. The Density Functional Theory (DFT) method was subsequently applied to compute the primary fragmentation energies of these compounds. The findings revealed a congruence between the energy data calculated using both thermodynamic and kinetic approaches and the observed fragment abundance of the isomers. This alignment providing a more precise theoretical framework for understanding the mechanisms underlying the generation of fragment ion differences among isomers.

Mac-2 binding protein glycosylation isomer as a novel predictor of early recurrence after resection for hepatocellular carcinoma.

PURPOSE: Hepatocellular carcinoma (HCC) frequently recurs after radical resection, resulting in a poor prognosis. This study assessed the prognostic value of Mac-2 binding protein glycosylation isomer (M2BPGi) for early recurrence (ER) in patients with HCC. METHODS: Patients who underwent radical resection for HCC between 2015 and 2021. HCC recurrence within one year after curative resection was defined as ER. RESULTS: The 150 patients were divided into two groups: non-ER (116, 77.3%) and ER (34, 22.7%). The ER group had a lower overall survival rate (p < 0.0001) and significantly higher levels of M2BPGi (1.06 vs. 2.74 COI, p < 0.0001) than the non-ER group. High M2BPGi levels (odds ratio [OR] 1.78, 95% confidence interval [CI] 1.31-2.41, p < 0.0001) and a large tumor size (OR 1.31, 95% CI, 1.05-1.63; p = 0.0184) were identified as independent predictors of ER. M2BPGi was the best predictor of ER according to a receiver operating characteristic (ROC) analysis (area under the ROC curve 0.82, p < 0.0001). CONCLUSIONS: M2BPGi can predict ER after surgery and is useful for risk stratification in patients with HCC.

PEPICO analysis of catalytic reactor effluents towards quantitative isomer discrimination: DME conversion over a ZSM-5 zeolite.

The methanol-to-hydrocarbons (MTH) process involves the conversion of methanol, a C1 feedstock that can be produced from green sources, into hydrocarbons using shape-selective microporous acidic catalysts - zeolite and zeotypes. This reaction yields a complex mixture of species, some of which are highly reactive and/or present in several isomeric forms, posing significant challenges for effluent analysis. Conventional gas-phase chromatography (GC) is typically employed for the analysis of reaction products in laboratory flow reactors. However, GC is not suitable for the detection of highly reactive intermediates such as ketene or formaldehyde and is not suitable for kinetic studies under well defined low pressure conditions. Photoelectron-photoion coincidence (PEPICO) spectroscopy has emerged as a powerful analytical tool for unraveling complex compositions of catalytic effluents, but its availability is limited to a handful of facilities worldwide. Herein, PEPICO analysis of catalytic reactor effluents has been implemented at the FinEstBeAMS beamline of MAX IV Laboratory. The conversion of dimethyl ether (DME) on a zeolite catalyst (ZSM-5-MFI27) is used as a prototypical model reaction producing a wide distribution of hydrocarbon products. Since in zeolites methanol is quickly equilibrated with DME, this reaction can be used to probe vast sub-networks of the full MTH process, while eliminating or at least slowing down methanol-induced secondary reactions and catalyst deactivation. Quantitative discrimination of xylene isomers in the effluent stream is achieved by deconvoluting the coincidence photoelectron spectra.

Binding characteristics of the doxepin E/Z-isomers to the histamine H1 receptor revealed by receptor-bound ligand analysis and molecular dynamics study.

Doxepin is an antihistamine and tricyclic antidepressant that binds to the histamine H1 receptor (H1R) with high affinity. Doxepin is an 85:15 mixture of the E- and Z-isomers. The Z-isomer is well known to be more effective than the E-isomer, whereas based on the crystal structure of the H1R/doxepin complex, the hydroxyl group of Thr1123.37 is close enough to form a hydrogen bond with the oxygen atom of the E-isomer. The detailed binding characteristics and reasons for the differences remain unclear. In this study, we analyzed doxepin isomers bound to the receptor following extraction from a purified H1R protein complexed with doxepin. The ratio of the E- and Z-isomers bound to wild-type (WT) H1R was 55:45, indicating that the Z-isomer was bound to WT H1R with an approximately 5.2-fold higher affinity than the E-isomer. For the T1123.37V mutant, the E/Z ratio was 89:11, indicating that both isomers have similar affinities. Free energy calculations using molecular dynamics (MD) simulations also reproduced the experimental results of the relative binding free energy differences between the isomers for WT and T1123.37V. Furthermore, MD simulations revealed that the hydroxyl group of T1123.37 did not form hydrogen bonds with the E-isomer, but with the adjacent residues in the binding pocket. Analysis of the receptor-bound doxepin and MD simulations suggested that the hydroxyl group of T1123.37 contributes to the formation of a chemical environment in the binding pocket, which is slightly more favorable for the Z-isomer without hydrogen bonding with doxepin.

MicroRNA-223-3p levels in serum-derived extracellular vesicles predict regression of M2BPGi-based liver fibrosis after hepatitis C virus eradication by direct-acting antiviral agents.

BACKGROUND: We retrospectively investigated microRNA (miRNA) levels in serum-derived extracellular vesicles (EVs) as predictive indicators for regression of liver fibrosis, after achievement of a sustained virological response (SVR) by direct-acting antiviral (DAA) therapy for chronic hepatitis C (CHC). METHODS: The study subjects were recruited from a historical cohort of 108 CHC patients whose pretreatment serum Mac-2-binding protein glycosylation isomer (M2BPGi) levels were ≥ 2.0 cut-off index (COI). We classified patients with M2BPGi levels < 1.76 and ≥ 1.76 COI at 2 years after the end of treatment (EOT) into the regression and non-regression groups, respectively. Eleven of the patients were assigned to the discovery set, and we comprehensively investigated the miRNAs contained in serum-derived EVs at 24 weeks after the EOT (EOT24W), using RNA sequencing. The remaining 97 patients were assigned to the validation set, and reproducibility was verified by quantitative real-time PCR. RESULTS: Through analysis of the discovery and validation sets, we identified miR-223-3p and miR-1290 as candidate predictors. Subsequently, we analyzed various clinical data, including these candidate miRNAs. Multivariate analyses revealed that the levels of miR-223-3p at EOT24W were significantly associated with regression of M2BPGi-based liver fibrosis (Odds ratio: 1.380; P = 0.024). Consistent results were obtained, even when the serum M2BPGi levels were aligned by propensity score matching and in patients with advanced M2BPGi-based liver fibrosis (pretreatment M2BPGi levels ≥ 3.3 COI). CONCLUSIONS: The miR-223-3p level in serum-derived EVs at EOT24W is a feasible predictor of regression of M2BPGi-based liver fibrosis after achievement of an SVR by DAA therapy.

Serum Mac-2 binding protein glycosylation isomer and galectin-3 levels in adult-onset Still's disease and their association with cytokines.

Background: Autoinflammation with cytokine dysregulation may be implicated in the pathophysiology of adult-onset Still's disease (AOSD); however, the relationship between galectins and cytokines in patients with active AOSD remains unknown. We aimed to examine the relationship between circulating cytokines/chemokines and galectin-3 (Gal-3) or its ligand, Mac-2 binding protein glycosylation isomer (M2BPGi), in Japanese patients with AOSD. Methods: We recruited 44 consecutive patients diagnosed with AOSD according to the Yamaguchi criteria, 50 patients with rheumatoid arthritis (RA) as disease controls, and 27 healthy participants. Serum M2BPGi levels were directly measured using a HISCL M2BPGi reagent kit and an automatic immunoanalyzer (HISCL-5000). Serum Gal-3 concentrations were measured by enzyme-linked immunosorbent assay. The serum levels of 69 cytokines were analyzed in patients with AOSD using a multi-suspension cytokine array. We performed a cluster analysis of each cytokine expressed in patients with AOSD to identify specific molecular networks. Results: Significant increases in the serum concentrations of Gal-3 and M2BPGi were found in the serum of patients with AOSD compared with patients with RA and healthy participants (both p <0.001). There were significant positive correlations between serum Gal-3 levels and AOSD disease activity score (Pouchot score, r=0.66, p <0.001) and serum ferritin levels. However, no significant correlations were observed between serum M2BPGi levels and AOSD disease activity scores (Pouchot score, r = 0.32, p = 0.06) or serum ferritin levels. Furthermore, significant correlations were observed between the serum levels of Gal-3 and various inflammatory cytokines, including interleukin-18, in patients with AOSD. Immunosuppressive treatment in patients with AOSD significantly reduced serum Gal-3 and M2BPGi levels (p = 0.03 and 0.004, respectively). Conclusions: Although both Gal-3 and M2BPGi were elevated in patients with AOSD, only Gal-3 was a useful biomarker for predicting disease activity in AOSD. Our findings suggest that circulating Gal-3 reflects the inflammatory component of AOSD, which corresponds to proinflammatory cytokine induction through inflammasome activation cascades.

Facile Synthesis of B/P Co-Doping Multicolor Emissive Carbon Dots Derived from Phenylenediamine Isomers and Their Application in Anticounterfeiting.

Carbon dots (CDs) possess a considerable number of beneficial features for latent applications in biotargeted drugs, electronic transistors, and encrypted information. The synthesis of fluorescent carbon dots has become a trend in contemporary research, especially in the field of controllable multicolor fluorescent carbon dots. In this study, an elementary one-step hydrothermal method was employed to synthesize the multicolor fluorescent carbon dots by co-doping unique phenylenediamine isomers (o-PD, m-PD, and p-PD) with B and P elements, which under 365 nm UV light exhibited signs of lavender-color, grass-color, and tangerine-color fluorescence, respectively. Further investigations reveal the distinctness in the polymerization, surface-specific functional groups, and graphite N content of the multicolor CDs, which may be the chief factor regarding the different optical behaviors of the multicolor CDs. This new work offers a route for the exploration of multicolor CDs using B/P co-doping and suggests great potential in the field of optical materials, important information encryption, and commercial anticounterfeiting labels.

Bioactivities and Synergistic Effect of Elsholtzia ciliata Essential Oil and Its Main Components against Lasioderma serricorne.

Investigations have shown that storage bugs seriously harm grains during storage. In the interim, essential oils (EOs) have been proven to be a good botanical pesticide. The anti-Lasioderma serricorne properties of Elsholtzia ciliata essential oil, which was obtained by steam distillation, were evaluated using DL-limonene, carvone, and their two optical isomer components using contact, repelling, and fumigation techniques. Simultaneously, the fumigation, contact, and repellent activities of carvone and its two optical isomers mixed with DL-limonene against L. serruricorne were evaluated. The results showed that E. ciliata, its main components (R-carvone, DL-limonene), and S-carvone exhibited both fumigations (LC50 = 14.47, 4.42, 20.9 and 3.78 mg/L) and contact (LD50 = 7.31, 4.03, 28.62 and 5.63 µg/adult) activity against L.serricorne. A binary mixture (1:1) of R-carvone and DL-limonene displayed an obvious synergistic effect. A binary mixture (1:1) of carvone and its two optical isomers exhibited an obvious synergistic effect, too. Furthermore, the repellent activity of the EO, carvone, and its two optical isomers, DL-limonene, and a combination of them varied. To stop insect damage during storage, E. ciliata and its components can be utilized as bio-insecticides.

Facile Energy Release from Substituted Dewar Isomers of 1,2-Dihydro-1,2-Azaborinines Catalyzed by Coinage Metal Lewis Acids.

Molecular solar thermal systems (MOST) represent an auspicious solution for the storage of solar energy. We report silver salts as a unique class of catalysts, capable of releasing the stored energy from the promising 1,2-dihydro-1,2-azaborinine based MOST system. Mechanistic investigations provided insights into the silver catalyzed thermal backreaction, concurrently unveiling the first crystal structure of a 2-aza-3-borabicyclo[2.2.0]hex-5-ene, the Dewar isomer of 1,2-dihydro-1,2-azaborinine. Quantification of activation energies by kinetic experiments has elucidated the advantageous energy change associated with Lewis acid catalysts, a phenomenon corroborated through computational analysis. By means of low temperature NMR spectroscopy, mechanistic insights into the coordination of Ag+ to the 1,2-dihydro-1,2-azaborinine were gained.

MilkOligoThesaurus, a dataset of mammalian milk oligosaccharide synonyms.

There is a growing interest in milk oligosaccharides (MOs) because of their numerous benefits for newborns' and long-term health. A large number of MO structures have been identified in mammalian milk. Mostly described in human milk, the oligosaccharide richness, although less broad, has also been reported for a wide range of mammalian species. The structure of MOs is particularly difficult to report as it results from the combination of 5 monosaccharides linked by various glycosidic bonds forming structurally diverse and complex matrices of linear and branched oligosaccharides. Exploring the literature and extracting relevant information on MO diversity within or across species appears promising to elucidate structure-function role of MOs. Currently, given the complexity of these molecules, the main issues in exploring literature to extract relevant information on MO diversity within or across species relate to the heterogeneity in the way authors refer to these molecules. Herein, we provide a thesaurus (MilkOligoThesaurus) including the names and synonyms of MOs collected from key selected articles on mammalian milk analyses. MilkOligoThesaurus gathers the names of the MOs with a complete description of their monosaccharide composition and structures. When available, each unique MO molecule is linked to its ID from the NCBI PubChem and ChEBI databases. MilkOligoThesaurus is provided in a tabular format. It gathers 245 unique oligosaccharide structures described by 22 features (columns) including the name of the molecule, its abbreviation, the chemical database IDs if available, the monosaccharide composition, chemical information (molecular formula, monoisotopic mass), synonyms, its formula in condensed form, and in abbreviated condensed form, the abbreviated systematic name, the systematic name, the isomer group, and scientific article sources. MilkOligoThesaurus is also provided in the SKOS (Simple Knowledge Organization System) format. This thesaurus is a valuable resource gathering MO naming variations that are not found elsewhere for (i) Text and Data Mining to enable automatic annotation and rapid extraction of milk oligosaccharide data from scientific papers; (ii) biology researchers aiming to search for or decipher the structure of milk oligosaccharides based on any of their names, abbreviations or monosaccharide compositions and linkages.

Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis.

The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.

Conjugated Linolenic Acid (CLnA) vs Conjugated Linoleic Acid (CLA): A Comprehensive Review of Potential Advantages in Molecular Characteristics, Health Benefits, and Production Techniques.

Conjugated linoleic acid (CLA) has been extensively characterized due to its many biological activities and health benefits, but conjugated linolenic acid (CLnA) is still not well understood. However, CLnA has shown to be more effective than CLA as a potential functional food ingredient. Current research has not thoroughly investigated the differences and advantages between CLnA and CLA. This article compares CLnA and CLA based on molecular characteristics, including structural, chemical, and metabolic characteristics. Then, the in vivo research evidence of CLnA on various health benefits is comprehensively reviewed and compared with CLA in terms of effectiveness and mechanism. Furthermore, the potential of CLnA in production technology and product protection is analyzed. In general, CLnA and CLA have similar physicochemical properties of conjugated molecules and share many similarities in regulation effects and pathways of various health benefits as well as in the production methods. However, their specific properties, regulatory capabilities, and unique mechanisms are different. The superior potential of CLnA must be specified according to the practical application patterns of isomers. Future research should focus more on the advantageous characteristics of different isomers, especially the effectiveness and safety in clinical applications in order to truly exert the potential value of CLnA.