Biological Functions Research Articles

Size distribution of extracellular vesicles in pretreatment ascites and plasma is correlated with primary treatment outcome in advanced high-grade serous carcinoma

Abstract To improve the treatment outcome and survival of patients with advanced high-grade serous carcinoma (HGSC), prognostic biomarkers for assessing the feasibility of complete (R0) or optimal (R1) primary cytoreductive surgery are needed. Additionally, biomarkers for predicting the response to neoadjuvant chemotherapy (NACT) in patients with primary inoperable disease could help stratify patients for tailored therapy and improve personalised approach. Such promising biomarkers are extracellular vesicles (EVs), which are present in ascites and plasma and are available for minimally invasive liquid biopsy. EV concentration and EV molecular profile have been at the forefront of research in the field of biomarkers for many years now, but recent studies have highlighted the importance of EV size distribution. Our study aimed to evaluate the potential of the EV concentration and size distribution in pretreatment ascites and plasma samples from patients with advanced HGSC as prognostic biomarkers. In our prospective cohort study, nanoparticle tracking analysis (NTA) was used to determine EV characteristics in paired pretreatment ascites and plasma samples from 37 patients with advanced HGSC. Patients were treated with primary cytoreductive surgery followed by adjuvant chemotherapy (ACT) (N = 15) or NACT followed by interval debulking surgery (IDS) when optimal cytoreduction was not feasible (N = 22). The correlations of the EV concentration and size distribution in ascites and plasma with treatment outcome, progression-free survival (PFS) and overall survival (OS) were analysed. We found a significant correlation between the EV size distribution in ascites and residual disease after primary cytoreductive surgery. Larger EVs in ascites correlated with worse resection success after primary cytoreductive surgery. A significant correlation between the D10 value of EVs in plasma and the chemotherapy response score (CRS) after NACT was observed. A smaller D10 value of plasma EVs was correlated with a better chemotherapy response. Receiver operating characteristic (ROC) curve analysis revealed excellent performance for D10 value in ascites for the prediction of suboptimal (R2) resection at primary debulking surgery and excellent performance for D10 value in plasma for the prediction of complete or near-complete chemotherapy response score (CRS 3) at interval debulking surgery. There was a significant correlation between the mean diameter, D90 value and proportion of medium/large (> 200 nm) EVs in ascites and those in plasma. On the other hand, there was no correlation of the EV concentration or D10 and D50 values between the ascites fluid and plasma samples. Our results indicate that the EV size distribution in ascites has the potential to predict resection success after primary cytoreductive surgery and that the EV size distribution of the smallest EVs in plasma might help predict the chemotherapy response of patients treated with NACT. In the future, molecular analyses of size-dependent EV cargo could provide more insight into their biological functions and potential as predictive biomarkers.

L-Theanine Metabolism in Tea Plants: Biological Functions and Stress Tolerance Mechanisms

L-theanine, a unique non-protein amino acid predominantly found in tea plants (Camellia sinensis), plays a pivotal role in plant responses to abiotic stress and significantly influences tea quality. In this review, the metabolism and transport mechanisms of L-theanine are comprehensively discussed, highlighting its spatial distribution in tea plants, where it is most abundant in young leaves and less so in roots, stems, and older leaves. The biosynthesis of L-theanine occurs through the enzymatic conversion of glutamate and ethylamine, catalyzed by theanine synthase, primarily in the roots, from where it is transported to aerial parts of the plant for further catabolism. Environmental factors such as temperature, light, drought, elevated CO2, nutrient unavailability, and heavy metals significantly affect theanine biosynthesis and hydrolysis, with plant hormones and transcription factors playing crucial regulatory roles. Furthermore, it has been demonstrated that applying L-theanine exogenously improves other crops’ resistance to a range of abiotic stresses, suggesting its potential utility in improving crop resilience amid climate change. This review aims to elucidate the physiological mechanisms and biological functions of L-theanine metabolism under stress conditions, providing a theoretical foundation for enhancing tea quality and stress resistance in tea cultivation.

Live imaging of the extracellular matrix with a glycan-binding fluorophore

Abstract All multicellular systems produce and dynamically regulate extracellular matrices (ECMs) that play essential roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to their biological functions, visualization of ECM structure is challenging, in part because the biomolecules that compose the ECM are difficult to fluorescently label individually and collectively. Here, we present a cell-impermeable small-molecule fluorophore, termed Rhobo6, that turns on and red shifts upon reversible binding to glycans. Given that most ECM components are densely glycosylated, the dye enables wash-free visualization of ECM, in systems ranging from in vitro substrates to in vivo mouse mammary tumors. Relative to existing techniques, Rhobo6 provides a broad substrate profile, superior tissue penetration, non-perturbative labeling, and negligible photobleaching. This work establishes a straightforward method for imaging the distribution of ECM in live tissues and organisms, lowering barriers for investigation of extracellular biology.

Absorbing Aerosol Effects on Hyperspectral Surface and Underwater UV Irradiances from OMI Measurements and Radiative Transfer Computations

Ultraviolet (UV) radiation effects on Earth’s ecosystems on a global scale can be assessed on a basis of satellite estimates of hyperspectral irradiance on the surface and in ocean waters and the spectral biological weighting functions. The satellite UV surface irradiance algorithms combine satellite retrievals of extraterrestrial solar irradiance, cloud/surface reflectivity, aerosol optical depth, and total column ozone with radiative transfer computations. The assessment of in-water irradiance requires additional information on inherent optical properties (IOPs) of ocean water. Our Ozone Monitoring Instrument (OMI) surface hyperspectral irradiance algorithm is updated by implementing a new absorbing aerosol correction based on OMI daily retrievals of UV aerosol absorption optical depth (AAOD). To provide insight into the temporal and spatial variability of absorbing aerosols, we consider a monthly global AAOD climatology derived from the OMI UV aerosol algorithm. Hyperspectral underwater irradiance is computed using Hydrolight radiative transfer calculations along with a Case I water model of IOPs extended into UV. Both planar and scalar irradiances are computed on the Earth’s surface and propagated underwater. The output surface products include the UV index. The output underwater products include the hyperspectral diffuse attenuation coefficients of the planar and scalar irradiances. Effects of the seasonal variability of AAOD on the UV index and the deoxyribonucleic acid (DNA) damage dose rates are considered. The reduction in the UV index and DNA damage dose rate due to the presence of absorbing aerosols can be as large as 30–40%.

Plectin, a novel regulator in migration, invasion and adhesion of ovarian cancer

Abstract Background Ovarian cancer (OC) is one of the most prevalent gynecologic malignancies and exhibites the highest fatality rate among all gynecologic malignancies. The absence of an early diagnostic biomarker and therapeutic target contributes to an overall 5-year survival rate ranging from 30 to 50%. Plectin (PLEC), a 500 kDa scaffolding protein, has gained prominence in recent years due to its pivotal role in various cellular biological functions such as cell morphology, migration and adhesion, while the accurate role of PLEC in OC remains elusive. Results In this study, our findings demonstrate that PLEC exerts a positive influence on the progression of OC, encompassing cellular proliferation, migration, invasion, and adhesion both in vitro and in vivo. Conclusions The results providing new insights for the diagnosis and treatment in OC.

Cyclization of Short Peptides Designed from Late Embryogenesis Abundant Protein to Improve Stability and Functionality.

LEA peptides, designed based on late embryogenic abundant (LEA) protein sequences, have demonstrated chaperone-like functions, such as improving drought stress tolerance of Escherichia coli (E. coli). Previous studies have focused on the biological functions of linear LEA peptides. However, the function of cyclic LEA peptide is still unknown. This study aimed to explore the cyclic LEA peptides' bio function like enhancing the drought stress tolerance of E. coli by cyclizing the LEA peptide using SICLOPPS (Split Intein Circular Ligation of Peptides and Proteins). The results indicated that cyclization significantly improved the function and extended the potential applications. At the same time, we found that peptides containing numerous lysine residues exhibited reduced performance, possibly due to the exteins' residues affecting the SICLOPPS efficiency.

Oncometabolite D-2HG drives tumor metastasis and protumoral macrophage polarization by targeting FTO/m6A/ANGPTL4/integrin axis in triple-negative breast cancer

BackgroundD-2-hydroxyglutarate (D-2HG), an oncometabolite derived from the tricarboxylic acid cycle. Previous studies have reported the diverse effects of D-2HG in pathophysiological processes, yet its role in breast cancer remains largely unexplored.MethodsWe applied an advanced biosensor approach to detect the D-2HG levels in breast cancer samples. We then investigated the biological functions of D-2HG through multiple in vitro and in vivo assays. A joint MeRIP-seq and RNA-seq strategy was used to identify the target genes regulated by D-2HG-mediated N6-methyladenosine (m6A) modification. RNA pull-down assays were further applied to identify the reader that could specifically recognize the m6A modification on angiopoietin like 4 (ANGPTL4) mRNA and RNA immunoprecipitation was used to confirm the findings.ResultsWe found that D-2HG accumulated in triple-negative breast cancer (TNBC), exerting oncogenic effects both in vitro and in vivo by promoting TNBC cell growth and metastasis. Mechanistically, D-2HG enhanced global m6A RNA modifications in TNBC cells, notably upregulating m6A modification on ANGPTL4 mRNA, which was mediated by the inhibition of Fat-mass and obesity-associated protein (FTO), resulting in increased recognition of m6A-modified ANGPTL4 by YTH N6-methyladenosine RNA binding protein F1 (YTHDF1), thereby promoting the enhanced translation of ANGPTL4. As a secretory protein, ANGPTL4 subsequently activated the integrin-mediated JAK2/STAT3 signaling cascade in TNBC cells through autocrine signaling. Notably, the knockdown of ANGPTL4 or treatment with GLPG1087 (an integrin antagonist) significantly reduced D-2HG-induced proliferation and metastasis in TNBC cells. Additionally, ANGPTL4 was found to promote macrophage M2 polarization within the tumor microenvironment via paracrine signaling, further driving TNBC progression. The association of ANGPTL4 with poor prognosis in TNBC patients underscores its clinical relevance.ConclusionsOur study unveils a previously unrecognized role for D-2HG-mediated RNA modification in TNBC progression and targeting the D-2HG/FTO/m6A/ANGPTL4/integrin axis can serve as a promising therapeutic target for TNBC patients.

TAp63γ is the primary isoform of TP63 for tumor suppression but not development

Abstract TP63 is expressed as TAp63 and ΔNp63 from the P1 and P2 promoters, respectively. While TAp63 and ΔNp63 are expressed as three TAp63α/β/γ and ΔNp63α/β/γ due to alternative splicing, only p63α (TA and ΔN) and p63γ (TA and ΔN) proteins are found to be detectable and likely to be responsible for p63-dependent activity. Previous studies implied and/or demonstrated that TAp63α, which contains an N-terminal activation domain conserved in p53, functions as a tumor suppressor by regulating an array of genes for growth suppression. By contrast, ΔNp63α, which also contains an N-terminal activation domain but is different from that in TAp63, regulates a unique set of genes and functions as a master regulator for development of epidermis and other stratified epithelial tissues. However, the biological function of p63γ is largely unexplored. To explore this, we generated a mouse model in that exon 10’, a coding exon specific for p63γ, was deleted by CRISPR-cas9. We showed that mice deficient in p63γ are viable and futile, which is different from mice deficient in total TP63 or p63α. Like TAp63-deficient mice, p63γ-deficient mice have a short lifespan and are prone to spontanenous tumors. Additionally, loss of p63γ shortens the lifespan of tumor-free mice potentially via increased cellular senescence. Moreover, mice deficient in p63γ are prone to chronic inflammation in multiple organs and liver steatosis potentially via altered lipid metabolism. Single-cell RNA-seq revealed that loss of p63γ increases the expression of SCD1, a rate-limiting enzyme for synthesis of monounsaturated fatty acids, leading to altered lipid homeostasis. Together, our data indicate that TP63γ is the primary isoform of TP63 for tumor suppression but not development by maintaining normal inflammatory response and lipid homeostasis.

DOCK1/ELMO1/Rac1 Signaling is Essential for Vitreous-Induced Migration and Contraction of ARPE19 Cells.

Purpose: To test the effects of dedicator of cytokinesis protein 1 (DOCK1) with its binding partner engulfment and cell motility protein 1 (ELMO1)-Rac1 axis on the vitreous-induced biological functions of retinal pigment epithelial (RPE) cells. Methods: Rac1 activity in RPE cells after vitreous stimulation was detected via a pull-down assay. The related protein expression levels were examined via western blot analysis. DOCK1 and ELMO1 knockdown cells were generated via CRISPR-Cas9 technology. Cytoskeletal reorganization was detected by immunofluorescent localization of F-actin. Cell proliferation, migration, invasion, and contraction ability were measured via the CCK8 assay, wound healing assay, transwell invasion assay, and collagen contraction assay. Results: Rac1 activity was significantly elevated in ARPE-19 cells stimulated with vitreous fluid for 30 min to 3 h. Depletion of either DOCK1 or ELMO1 with CRISPR/Cas9 attenuated vitreous-stimulated Rac1 activity, thus reversing the vitreous-induced cytoskeletal rearrangements. The functional cell biology results revealed that deficiencies of DOCK1 and ELMO1 significantly impeded the migration, invasion, and contraction abilities of vitreous-stimulated human RPE cells. Conclusion: This study demonstrated that the DOCK1/ELMO1-Rac1 axis plays an essential role in the pathogenesis of proliferative vitreoretinopathy (PVR), thus suggesting that interruption of this axis has potential for PVR therapy.

Unveiling the impact of CD133 on cell cycle regulation in radio- and chemo-resistance of cancer stem cells

The adaptation of malignancy to therapy presents a significant challenge in cancer treatment. The cell cycle plays a crucial role in regulating the evolution of radio- and chemo-resistance in tumor cells. Cancer stem cells (CSCs) are the primary source of therapy resistance, with CD133 being one of the most recognized and valuable cell surface markers of CSCs. Evidence increasingly suggests that CD133 is associated with cancer resistance. The current understanding of the molecular biological function of CD133 is limited, leading to ongoing debates about its role in cancer biology. In this review, we explore recent research and emerging trends related to CD133 through extensive literature and content analysis. It was summarized that new insights into the relationships of CD133 and cell cycle signaling pathways in resistant CSCs. The aim of this review is to provide a foundational understanding of how these signaling pathways and their interactions impact cancer prognosis and inform treatment strategies.

Quantitative Proteomic Analysis of Lysine Malonylation in Response to Salicylic Acid in the Roots of Platycodon grandiflorus

Salicylic acid, as a plant hormone, significantly affects the physiological and biochemical indexes of soluble sugar, malondialdehyde content, peroxidase, and superoxide dismutase enzyme activity in Platycodon grandiflorus. Lysine malonylation is a post-translational modification that involves various cellular functions in plants, though it is rarely studied, especially in medicinal plants. In this study, the aim was to perform a comparative quantitative proteomic study of malonylation modification on P. grandiflorus root proteins after salicylic acid treatment using Western blot with specific antibodies, affinity enrichment and LC-MS/MS analysis methods. The analysis identified 1907 malonyl sites for 809 proteins, with 414 proteins and 798 modification sites quantified with high confidence. Post-treatment, 361 proteins were upregulated, and 310 were downregulated. Bioinformatics analysis revealed that malonylation in P. grandiflorus is primarily involved in photosynthesis and carbon metabolism. Physiological and biochemical analysis showed that salicylic acid treatment increased the malondialdehyde levels, soluble protein, superoxide dismutase, and peroxidase activity but did not significantly affect the total saponins content in P. grandiflorus. These findings provide an important basis for exploring the molecular mechanisms of P. grandiflorus following salicylic acid treatment and enhance understanding of the biological function of protein lysine malonylation in plants.

Vitamin C: From Self-Sufficiency to Dietary Dependence in the Framework of Its Biological Functions and Medical Implications

Vitamin C is an organic compound biosynthesized in plants and most vertebrates. Since its discovery, the benefits of vitamin C use in the cure and prevention of various pathologies have been frequently reported, including its anti-oxidant, anti-inflammatory, anticoagulant, and immune modulatory properties. Vitamin C plays an important role in collagen synthesis and subsequent scurvy prevention. It is also required in vivo as a cofactor for enzymes involved in carnitine and catecholamine norepinephrine biosynthesis, peptide amidation, and tyrosine catabolism. Moreover, as an enzymatic cofactor, vitamin C is involved in processes of gene transcription and epigenetic regulation. The absence of the synthesis of L-gulono-1,4-lactone oxidase, a key enzyme in the pathway of vitamin C synthesis, is an inborn metabolism error in some fishes and several bird and mammalian species, including humans and non-human primates; it is caused by various changes in the structure of the original GULO gene, making these affected species dependent on external sources of vitamin C. The evolutionary cause of GULO gene pseudogenization remains controversial, as either dietary supplementation or neutral selection is evoked. An evolutionary improvement in the control of redox homeostasis was also considered, as potentially toxic H2O2 is generated as a byproduct in the vitamin C biosynthesis pathway. The inactivation of the GULO gene and the subsequent reliance on dietary vitamin C may have broader implications for aging and age-related diseases, as one of the most important actions of vitamin C is as an anti-oxidant. Therefore, an important aim for medical professionals regarding human and animal health should be establishing vitamin C homeostasis in species that are unable to synthesize it themselves, preventing pathologies such as cardiovascular diseases, cognitive decline, and even cancer.

The indispensability of relational, adapted, and derived proper functions

Since the early debates on teleosemantics, there have been people objecting that teleosemantics cannot account for evolutionarily novel contents such as “democracy” (e.g., Peacocke in A Study of Concepts, MIT Press, Cambridge, 1992). Most recently, this objection was brought up by Garson (What Biological Functions Are and Why They Matter, Cambridge University Press, Cambridge, 2019. https://doi.org/10.1017/9781108560764) and in a more moderate form by Garson and Papineau (Biol Philos 34(3):36, 2019. https://doi.org/10.1007/s10539-019-9689-8). The underlying criticism is that the traditional selected effects theory of functions on which teleosemantics is built is unable to ascribe new functions to the products of ontogenetic processes and thus unable to ascribe functions to new traits that appear during the lifetime of an individual organism. I will argue that this underlying thought rests on rather common misunderstandings of Millikan’s theory of proper functions, especially her notions of relational, adapted, and derived proper functions (Millikan in Language, Thought, and Other Biological Categories: New Foundations for Realism, MIT Press, Cambridge, 1984: Ch. 2). The notions of relational, adapted, and derived proper functions not only help us solve the problem of novel contents and can ascribe functions to the products of ontogenetic selection mechanisms but are indispensable parts of every selected effects theory.

Metabolomic-Based Assessment of Earthworm (Eisenia fetida) Exposure to Different Petroleum Fractions in Soils

Background/Objectives: Petroleum contamination in soil exerts toxic effects on earthworms (Eisenia fetida) through non-polar narcotic mechanisms. However, the specific toxicities of individual petroleum components remain insufficiently understood. Methods: This study investigates the effects of four petroleum components—saturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes—on earthworms in artificially contaminated soil, utilizing a combination of biochemical biomarker analysis and metabolomics to uncover the underlying molecular mechanisms. Results: The results revealed that aromatic hydrocarbons are the most toxic fraction, with EC50 concentrations significantly lower than those of other petroleum fractions. All tested fractions triggered notable metabolic disturbances and immune responses in earthworms after 7 days of exposure, as evidenced by significant changes in metabolite abundance within critical pathways such as arginine synthesis, a-linolenic acid metabolism, and the pentose phosphate pathway. According to the KEGG pathway analysis, saturated hydrocarbon fractions induced marked changes in glycerophospholipid metabolism, and arginine and proline metabolism pathways, contributing to the stabilization of the protein structure and membrane integrity. Aromatic hydrocarbon fractions disrupted the arachidonic acid metabolic pathway, leading to increased myotube production and enhanced immune defense mechanisms. The TCA cycle and riboflavin metabolic pathway were significantly altered during exposure to the colloidal fraction, affecting energy production and cellular respiration. The asphaltene fraction significantly impacted glycolysis, accelerating energy cycling to meet stress-induced increases in energy demands. Conclusions: Aromatic hydrocarbons accounted for the highest level of toxicity among the four components in petroleum-contaminated soils. However, the contributions of other fractions to overall toxicity should not be ignored, as each fraction uniquely affects key metabolic pathways and biological functions. These findings emphasize the importance of monitoring metabolic perturbations caused by petroleum components in non-target organisms such as earthworms. They also reveal the specificity of the toxic metabolic effects of different petroleum components on earthworms.

Long Non-Coding RNAs: Key Regulators of Tumor Epithelial/Mesenchymal Plasticity and Cancer Stemness

Long non-coding RNAs (lncRNAs) are a class of non-coding RNA molecules with transcripts longer than 200 bp, which were initially thought to be noise from genomic transcription without biological function. However, since the discovery of H19 in 1980 and Xist in 1990, increasing evidence has shown that lncRNAs regulate gene expression at epigenetic, transcriptional, and post-transcriptional levels through specific regulatory actions and are involved in the development of cancer and other diseases. Despite many lncRNAs being expressed at lower levels than those of protein-coding genes with less sequence conservation across species, lncRNAs have become an intense area of RNA research. They exert diverse biological functions such as inducing chromatin remodeling, recruiting transcriptional machinery, acting as competitive endogenous RNAs for microRNAs, and modulating protein–protein interactions. Epithelial–mesenchymal transition (EMT) is a developmental process, associated with embryonic development, wound healing, and cancer progression. In the context of oncogenesis, the EMT program is transiently activated and confers migratory/invasive and cancer stem cell (CSC) properties to tumor cells, which are crucial for malignant progression, metastasis, and therapeutic resistance. Accumulating evidence has revealed that lncRNAs play crucial roles in the regulation of tumor epithelial/mesenchymal plasticity (EMP) and cancer stemness. Here, we summarize the emerging roles and molecular mechanisms of lncRNAs in regulating tumor cell EMP and their effects on tumor initiation and progression through regulation of CSCs. We also discuss the potential of lncRNAs as diagnostic and prognostic biomarkers and therapeutic targets.

An Endogenous Aryl Hydrocarbon Receptor Ligand Dysregulates Endothelial Functions, Transcriptome, and Phosphoproteome.

We have reported that an endogenous aryl hydrocarbon receptor (AhR) ligand, 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE), inhibits functions of human umbilical vein endothelial cells (HUVECs) and induces preeclampsia (PE)-like symptoms in rats. Herein, we tested the hypothesis that ITE impairs endothelial functions via disturbing transcriptome and phosphoproteome in HUVECs. We measured AhR activity in human maternal and umbilical vein sera from PE and normotensive (NT) pregnancies. The serum-induced changes in CYP1A1/B1 mRNA (indexes of AhR activation) in HUVECs were quantified using RT-qPCR. ITE's effects on endothelial proliferation and monolayer integrity in female and male HUVECs were determined. We profiled ITE-induced changes in transcriptome and phosphoproteome in HUVECs using RNA-seq and bottom-up phosphoproteomics, respectively. After 12 hr of treatment, umbilical vein sera from PE increased CYP1A1 mRNA (1.7-fold of NT) HUVECs, which was blocked by CH223191, an AhR antagonist. ITE dose-dependently inhibited endothelial proliferation (76%-87% of control) and time-dependently reduced endothelial integrity with a maximum inhibition (~ 10%) at 40 hr. ITE induced 140 and 80 differentially expressed genes in female and male HUVECs, respectively. ITE altered phosphorylation of 92 and 105 proteins at 4 and 24 hr, respectively, in HUVECs. These ITE-dysregulated genes and phosphoproteins were enriched in biological functions and pathways are relevant to heart, liver, and kidney diseases, vascular functions, and inflammatory responses. Thus, endogenous AhR ligands may impair endothelial functions by disturbing transcriptome and phosphoproteome. These AhR ligand-dysregulated genes and phosphoproteins may be therapeutic and cell sex-specific targets for PE-induced endothelial dysfunction.

Heterologous expression of SpsTAC2 in Arabidopsis affected branch angle and secondary vascular system development

ABSTRACT To investigate the biological functions of Tiller Angle Control 2 (TAC2) in Salix psammophila. In this study, TAC2 was cloned from Salix psammophila, and an overexpression and subcellular localization expression vector for the SpsTAC2 gene was constructed. The SpsTAC2 gene was overexpressed in Arabidopsis and analyzed for phenotypic changes. The subcellular localization of SpsTAC2 was analyzed via Agrobacterium-mediated transient expression in onion (Allium cepa L.) epidermal cells. Phenotypic characterization of SpsTAC2 overexpressing Arabidopsis strains revealed that the branching angle of the transgenic strains was significantly greater than that of the wild type, and the anatomical structures of the stems and hypocotyls of the transgenic strains indicated that the vascular system of the transgenic strains developed more slowly than did that of the wild type. The subcellular localization of the SpsTAC2 gene revealed that the localization signals of the SpsTAC2 gene were mainly in the nucleus, and weak signals also appeared in the cell membrane, suggesting that the SpsTAC2 gene was mainly expressed mainly in the nucleus, with a small amount of expression in the cell membrane. This findings suggest that the SpsTAC2 gene influences the development of the branching angle of plants and xylem, and exerts its effects mainly in the nucleus and membrane. This study can help to characterize the regulatory effect of the TAC gene on the branching angle and explore its effect on the branching angle and vascular system development, and also help to explore the possible molecular regulatory mechanism, which can provide a theoretical basis for further elucidation of the mechanism of action of the IGT gene family.

Personalizing Dietary Polyphenols for Health Maintenance and Disease Management: A Nutrigenetic Approach.

This literature review provides examples of the influence of certain genetic variants on health outcomes after dietary polyphenol consumption or supplementation. Available evidence is organized according to the major classes of polyphenols (flavonoids, phenolic acids, stilbenes, lignans, and tannins) and their derived subgroups. Nutrigenetic studies have identified mainly single nucleotide polymorphisms located within genes involved in the biotransformation of phenolic acids, stilbenes, lignans and several flavonoid molecules. These genetic variants may affect polyphenol metabolism rates and related predisposition to chronic non-communicable diseases. Moreover, differential cardiometabolic outcomes upon polyphenol supplementation as dietary sources or nutraceuticals have been modulated by specific genotypes. Although current evidence is still limited, growing gene-polyphenol interactions are contributing to systematically elucidate the biological functions of polyphenols; determine individual risk phenotypes to specific diseases or particular responses upon polyphenol exposure; and facilitate the prescription of personalized genotype-based doses of dietary polyphenols to optimize related health benefits. Additionally, the integration of genetics with other omics insights (epigenomics, transcriptomics, metagenomics, and metabolomics) trough biological systems and high-dimensional data analyses and interpretation may provide a more comprehensive understanding of polyphenol metabolism for precision nutrition applications in health and disease.

Fragmentation and Isomerization Pathways of Natural and Synthetic Cannabinoids Studied via Higher Collisional Energy Dissociation Profiles

Cannabinoid molecules are the family of molecules that bind to the cannabinoid receptors (CB1 and CB2) of the human body and cause changes in numerous biological functions including motor coordination, emotion, and pain reception. Cannabinoids occur either naturally in the Cannabis Sativa plant or can be produced synthetically in the laboratory. The need for accurate analytical methods for analyzing cannabinoid molecules is of considerable current importance due to demands for detecting illegal cannabinoids and for monitoring the manufacture of popular, non-illegal cannabinoid products. Mass spectrometry has been shown to be an optimum technique for identifying cannabinoids. In this work, we perform Higher Collisional Dissociation (HCD) mass spectrometric measurements on an Orbitrap Fusion Tribrid Mass Spectrometer to measure the collision-energy-dependent molecular fragmentation pathways of a group of key cannabinoids and their metabolites (cannabidiol, Δ9-Tetrahydrocannabinol, 11-Hydroxy-Δ9-tetrahydrocannabinol, 11-nor-9-Carboxy-Δ9-tetrahydrocannabinol, cannabidiolic acid, tetrahydrocannabinolic acid), along with two synthetic cannabinoids (JWH-018 and MDMB-FUBINACA). This is the first time that cannabinoid molecules have been studied using energy-resolved HCD methods. We identified a number of common, primary fragmentation pathways, including loss of water, loss of other small neutral molecule units (e.g., butene), and rupture of the central C-C bond that links the aromatic and alkyl ring groups. Quantum chemical calculations are presented to provide insights into preferred protonation sites and to characterize isomerization of protonated open-ring cannabinoids (e.g., [CBDA + H]+) into closed-ring analogues (e.g., [THCA + H]+). A key result to emerge from our study is that energy-resolved HCD measurements are particularly valuable in identifying isomerization, since the isobaric pairs of molecular ions studied here (e.g., [CBDA + H]+ and [THCA + H]+) are associated with identical HCD profiles indicating that isomerization of one structure into the other has occurred during the electrospray–mass spectrometry process. This is an important result as it will have general applicability to other tautomeric ions and thus demonstrates the application of energy-resolved HCD as a tool for identifying tautomerization proclivity.

PIPENN-EMB ensemble net and protein embeddings generalise protein interface prediction beyond homology

Protein interactions are crucial for understanding biological functions and disease mechanisms, but predicting these remains a complex task in computational biology. Increasingly, Deep Learning models are having success in interface prediction. This study presents PIPENN-EMB which explores the added value of using embeddings from the ProtT5-XL protein language model. Our results show substantial improvement over the previously published PIPENN model for protein interaction interface prediction, reaching an MCC of 0.313 vs. 0.249, and AUROC 0.800 vs. 0.755 on the BIO_DL_TE test set. We furthermore show that these embeddings cover a broad range of ‘hand-crafted’ protein features in ablation studies. PIPENN-EMB reaches state-of-the-art performance on the ZK448 dataset for protein-protein interface prediction. We showcase predictions on 25 resistance-related proteins from Mycobacterium tuberculosis. Furthermore, whereas other state-of-the-art sequence-based methods perform worse for proteins that have little recognisable homology in their training data, PIPENN-EMB generalises to remote homologs, yielding stable AUROC across all three test sets with less than 30% sequence identity to the training dataset, and even to proteins with less than 15% sequence identity.