Bioinformatics and systems biology of the lipidome

The Liebeskind-Srogl cross-coupling reaction towards the synthesis of biologically active compounds

In this review, we emphasize the significance of the Liebeskind-Srogl cross-coupling reaction, a palladium-catalyzed process involving the reaction between a thioester and a boronic acid. This reaction has emerged as a fundamental technique in synthetic methodologies aimed at the development of biologically active compounds. The Liebeskind-Srogl cross-coupling method has become an essential approach in chemistry, facilitating the diversification of complex structures that would be significantly more challenging to synthesize through alternative approaches. In this review, we aim to outline the numerous possibilities for preparing a wide range of derivatives, each with notable biological potential.

Spatial Metabolomics in Acute Kidney Injury

Acute kidney injury (AKI) is a common condition linked to increased morbidity, mortality, and substantial health care costs both in the United States and globally. Early diagnosis, prompt intervention, and effective therapeutic management of AKI are vital for improving patient outcomes. Recent advancements in renal imaging and omics technologies have provided new perspectives and deeper insights into kidney injury while also presenting challenges in developing a comprehensive cellular and molecular atlas of the condition. This review focuses on the application of mass spectrometry imaging-based spatial metabolomics in studying ischemia- and toxin-induced AKI in animal models and human patients. Spatial metabolomics offers a deeper understanding of the pathophysiological connections between various processes, such as dysregulated lipid metabolism and the shift from the tricarboxylic acid cycle to glycolytic flux, which contribute to functional impairment and structural damage in AKI. Continued research in renal multimodal imaging and omics is essential to further our understanding of kidney injury from diagnostic, mechanistic, and therapeutic perspectives. Semin Nephrol 36:x-xx © 20XX Elsevier Inc. All rights reserved.

Redox control of NRF2 signaling in oocytes harnessing Porphyra derivatives as a toggle

This study investigated the potential of Porphyra derivatives (PD), including Porphyra334, to activate the nuclear factor erythroid 2-related factor 2 (NRF2) pathway in porcine oocytes to enhance oocyte competency and intracellular networks. Conventional methods for manipulating mitochondrial functions and antioxidant pathways often rely upon genetic modifications that are impractical for direct application in humans. We hypothesized that PD serves as a natural regulator of the NRF2 pathway without requiring genetic intervention. To test this hypothesis, brusatol (Bru), a direct NRF2 inhibitor, was used to evaluate the specific role of PD in NRF2-mediated processes. The results demonstrated that PD significantly improved oocyte maturation, blastocyst formation, and mitochondrial function, including subsequent lipid metabolism. PD activates NRF2 and its downstream antioxidant response elements (AREs), whereas Bru inhibits these effects. Co-treatment with PD and Bru resulted in the partial recovery of NRF2 activity. These findings suggest that PD functions as a toggle for NRF2 activation, potentially offering a non-genetic strategy for enhancing oocyte quality and embryo development by modulating antioxidant mechanisms and mitochondrial functions. This study provides new avenues for investigating natural compounds in the context of reproductive biology and assisted reproductive technologies (ARTs).

Effect of Indigenous Non-Saccharomyces Yeasts on Lipid Compositions of Maraština Wine

This study is the first to investigate the impact of indigenous non-Saccharomyces yeasts, including Hypopichia pseudoburtonii, Metschnikowia sinensis/shanxiensis, Metschnikowia chrysoperlae, Metschnikowia pulcherrima, Lachancea thermotolerans, Hanseniaspora uvarum, Hanseniaspora guilliermondii, Hanseniaspora pseudoguilliermondii, Pichia kluyveri, and Starmerella apicola on the lipid composition of sterile Maraština grape juice and wines using the UHPLC-MS/MS method. Yeasts were tested in monoculture and sequential fermentations alongside commercial Saccharomyces cerevisiae. Indigenous non-Saccharomyces yeasts showed the potential to improve fermentation performance and enable the development of new wine styles through the biosynthesis of an unsaturated fatty acid pathway, which was identified as the most significant pathway. In monoculture fermentations, L. thermotolerans, H. uvarum, H. guilliermondii, H. pseudoguilliermondii, and P. kluyveri significantly reduced lignoceric acid, potentially influencing wine aroma through the formation of esters and higher alcohols. Hyp. pseudoburtonii, M. chrysoperlae, M. pulcherrima, P. kluyveri, and S. apicola increased the demand for lipids, such as stearic acid, which may help preserve membrane permeability by integrating into the membrane in response to ethanol shock. The most significant impact on free fatty esters was observed in fermentations with H. pseudoguilliermondii. Furthermore, L. thermotolerans in sequential fermentations significantly reduced arachidic, stearic, and palmitic acid. P. kluyveri reduced the content of erucic and linoleic acid.

Associations of lipids in adolescence and adulthood with self- and other-directed compassion in adulthood

Self- and other-directed compassion have been linked with better mental and physical health but research on factors contributing to their development is scarce. Previous studies indicate a possible causal relationship of lipids with personality and socioemotional functioning. As an extension to earlier research, in the present study we examine whether lipids assessed in adolescence and adulthood are associated with self-compassion and other-directed compassion in adulthood. The study utilizes data on lipids from two follow-ups in the Northern Finland Birth Cohort 1986 at ages 15-16 and 33-35. In the latter follow-up also self-compassion and other-directed compassion were assessed with the self-compassion scale - short form and the subscale for compassion in the dispositional positive emotions scale, respectively. The sample for the cross-sectional associations of lipids in adulthood with the compassion variables in adulthood includes 1,459 participants, whereas the sample for the longitudinal associations of lipids in adolescence and the compassion variables in adulthood consists of 1,509 participants. The associations were examined with hierarchical linear regression (lipids as continuous variables) and univariate general linear model (lipids as categorical variables). The results suggest that in women, high-density lipoprotein (HDL) cholesterol in adolescence is associated with high empathic concern (a component of other-directed compassion) in adulthood. The results show further that, in women, an HDL cholesterol level above 1.2 mmol/L in adulthood is associated with high other-directed compassion and empathic concern in adulthood. The present study provides tentative evidence that biological factors such as lipids might play a role in the development of empathic concern and other-directed compassion.

Combating antibiotic resistance in a one health context: a plethora of frontiers

One of the most significant medical advancements of the 20th century was the discovery of antibiotics, which continue to play a vital tool in the treatment and prevention of diseases in humans and animals. However, the imprudent use of antibiotics in all fields of One-Health and concerns about antibiotic resistance among bacterial pathogens have raised interest in antibiotic use restrictions on a global scale. Despite the failure of conventional antimicrobial agents, only about 15 new antibiotics have been introduced clinically since year 2000 to date. Moreover, there has been reports of resistance to some of these new antibiotics. This has necessitated a need to search for alternative strategies to combat antimicrobial resistant pathogens. Thus, this review compiles and evaluates the approaches-natural compounds, phage treatment, and nanomaterials-that are being used and/or suggested as the potential substitutes for conventional antibiotics.

Deceased donor kidney function and branched chain amino acid metabolism during ex vivo normothermic perfusion

Current kidney perfusion protocols are not optimized for addressing the ex vivo physiological and metabolic needs of the kidney. Ex vivo normothermic perfusion may be utilized to distinguish high-risk kidneys to determine suitability for transplantation. Here, we assessed the association of tissue metabolic changes with changes in a kidney injury biomarker and functional parameters in eight deceased donor kidneys deemed unsuitable for transplantation during a 12-hour ex vivo normothermic perfusion. The kidneys were grouped into good and poor performers based on blood flow and urine output. The mean age of the deceased kidney donors was 43 years with an average cold ischemia time of 37 hours. Urine output and creatinine clearance progressively increased and peaked at six hours post-perfusion among good performers. Poor performers had 71 ng/ml greater (95% confidence interval 1.5, 140) urinary neutrophil gelatinase-associated lipocalin at six hours compared to good performers corresponding to peak functional differences. Organ performance was distinguished by tissue metabolic differences in branched chain amino acid metabolism and that their tissue levels negatively correlated with urine output among all kidneys at six hours. Tissue lipid profiling showed poor performers were highlighted by the accumulation of membrane structure components including glycerolipids and sphingolipids at early perfusion time points. Thus, we showed that six hours is needed for kidney function recovery during ex vivo normothermic perfusion and that branched chain amino acid metabolism may be a major determinant of organ function and resilience.

In situ metabolomic analysis of osteonecrosis of the femoral head (ONFH) using MALDI MSI

Osteonecrosis of the femoral head (ONFH) is a common orthopedic disease characterized by disability and deformity. To better understand ONFH at molecular level and to explore the possibility of early diagnosis, instead of diagnosis based on macroscopic spatial characteristics, a matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) method was developed for ONFH disease for the first time. The most challenging step for ONFH MSI is to deal with human bone tissues which are much harder than the other biological samples studied by the reported MSI studies. In this work, the MSI sectioning method of hard bone tissues was established using tender acids and a series of test criteria. Small-molecule metabolites, such as lipids and amino acids, were detected in bone sections, realizing the in situ detection of spatial distribution of biometabolites. By comparing the distribution of metabolites from different regions of normal femoral head, ONFH bone tissue (ONBT), and adjacent ONFH bone tissue (ANBT), the whole process of femoral head from normal stage to necrosis was monitored and visualized at molecular level. Moreover, this developed MSI method was used for metabolomics study of ONFH. 72 differential metabolites were identified, suggesting that disturbances in energy metabolism and lipid metabolism affected the normal life activities of osteoblasts and osteoclasts. This study provides new perspectives for future pathological studies of ONFH.

Intercropping with maize and sorghum-induced saikosaponin accumulation in Bupleurum chinense DC. by liquid chromatography-mass spectrometry-based metabolomics

Bupleuri Radix is an important medicinal plant, which has been used in China and other Asian countries for thousands of years. Cultivated Bupleurum chinense DC. (B. chinense) is the main commodity of Bupleuri Radix. The benefits of intercropping with various crops for B. chinense have been recognized; however, the influence of intercropping on the chemical composition of B. chinense is still unclear yet. In this study, intercropping with sorghum and maize exhibited little effect on the root length, root diameter, and single root mass of B. chinense. Only the intercropping with sorghum increased the root length of B. chinense slightly compared to the monocropping. In addition, 200 compounds were identified by UHPLC-Q-TOF-MS, and metabolomic combined with the Venn diagram and heatmap analysis showed apparent separation between the intercropped and monocropped B. chinense samples. Intercropping with sorghum and maize could both increase the saikosaponins, fatty acyls, and organic acids in B. chinense while decreasing the phospholipids. The influence of intercropping on the saikosaponin biosynthesis was probably related with the light intensity and hormone levels in B. chinense. Moreover, we found intercropping increased the anti-inflammatory activity of B. chinense. This study provides a scientific reference for the beneficial effect of intercropping mode of B. chinense.

Improved lipid analysis using a 2D-LC-MS system with a novel injection procedure

The aim of this study was to improve analysis of nonpolar lipidomics sample extracts using reversed phase (RP) chromatography. A 4/3/3 (v/v/v) mixture of methanol/methyl tert-butyl ether/chloroform (MeOH/MTBE/CHCl3, MMC) was chosen for sample extraction solvent based on its proven extraction capability for several lipid classes. To avoid carry over, loss of analytes and peak distortion the loops and all capillaries of the presented LC system were flushed and filled up with methanol until the analytical column. The choice of methanol was due to its weak elution strength and being infinitely miscible with MMC and several other nonpolar solvents. This allowed injection of a 100 μl sample that was 20 μl nonpolar extraction solvent diluted fivefold with methanol. All lipids of 25 lipid classes were transferred quantitatively to the column head where the online dilution of methanol was carried out with aqueous eluent for focusing the lipid analytes. The weak elution strength of methanol prevented peak distortions. The consecutive reversed phase elution resulted in remarkably narrow peaks (full width at half maximum was 0.07-0.08 min typically) and enhanced sensitivity (limit of detection usually in sub nM region) because of increased sample injection volume and narrow peaks. Calibration and quality control samples made by diluting commercial lipid standards 200-50000 times confirmed the applicability of this approach both for targeted lipid quantification and for untargeted quantitative comparison of lipids from different sources.

What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota

Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.

Ceramides and ceramide synthases in cancer: Focus on apoptosis and autophagy

Different studies corroborate a role for ceramide synthases and their downstream products, ceramides, in modulation of apoptosis and autophagy in the context of cancer. These mechanisms of regulation, however, appear to be context dependent in terms of ceramides' fatty acid chain length, subcellular localization, and the presence or absence of their downstream targets. Our current understanding of the role of ceramide synthases and ceramides in regulation of apoptosis and autophagy could be harnessed to pioneer the development of new treatments to activate or inhibit a single type of ceramide synthase, thereby regulating the apoptosis induction or cross talk of apoptosis and autophagy in cancer cells. Moreover, the apoptotic function of ceramide suggests that ceramide analogues can pave the way for the development of novel cancer treatments. Therefore, in the current review paper we discuss the impact of ceramide synthases and ceramides in regulation of apoptosis and autophagy in context of different types of cancers. We also briefly introduce the latest information on ceramide synthase inhibitors, their application in diseases including cancer therapy, and discuss approaches for drug discovery in the field of ceramide synthase inhibitors. We finally discussed strategies for developing strategies to use lipids and ceramides analysis in biological fluids for developing early biomarkers for cancer.

The Potential of Salivary Lipid-Based Cannabis-Responsive Biomarkers to Evaluate Medical Cannabis Treatment in Children with Autism Spectrum Disorder

Introduction: Autism spectrum disorder (ASD) is a group of heterogeneous neurodevelopmental conditions affecting social communication and social interaction. Medical cannabis (MC) treatment shows promising results as an approach to reduce behavioral difficulties, as determined mainly by subjective observations. We have recently shown the potential of cannabis-responsive biomarkers detected in saliva of children with ASD to objectively quantify the impact of successful MC treatment using a metabolomics approach. Since the pathology of ASD is associated with abnormal lipid metabolism, we used lipidomics on the same samples to (1) expand the repertoire of cannabis-responsive biomarkers and (2) provide preliminary insight into the role of MC on lipid metabolism. Materials and Methods: Saliva samples collected from children with ASD (n=15) treated with MC (both before and at the time of maximal impact of treatment) and an age-matched group of typically developing (TD) children (n=9) were subjected to untargeted lipidomics. The study was observational. Each child from the ASD group was receiving a unique individualized MC treatment regimen using off-the-shelf products as permitted by California law under physician supervision for at least 1 year. Doses of tetrahydrocannabinol (THC) ranged from 0.05 to 50 mg and cannabidiol (CBD) from 7.5 to 200 mg per treatment. The ASD group was evaluated for signs of improvement using parental brief Likert scale surveys. Results: Twenty-two potential lipid-based cannabis-responsive biomarkers exhibiting a shift toward the TD physiological levels in children with ASD after MC treatment were identified. Members from all five lipid subclasses known to be present in saliva were characterized. Preliminary lipid association network analysis suggests involvement of two subnetworks previously linked to (1) inflammation and/or redox regulation and (2) oxidative stress. The significant changes in sphingomyelin in this study and in N-acetyl-aspartate (NAA) previously detected in the metabolomics analysis of the same saliva samples may indicate a role of MC in neuron function. Conclusions: Our findings suggest that lipid metabolites in saliva can potentially serve as cannabis-responsive biomarkers and objectively quantify the impact of MC treatment, and indicate a possible mechanism of action for MC. This preliminary study requires further investigation with a larger population and appropriate clinical trial monitoring.

Enhanced anti-inflammatory and ulcerogenicity of Ibuprofen microsphere formulations using Irvingia wombolu fat (IRW) and moringa oil (MO) as co-lipids

Ibuprofen is a member of the propionic acid class of nonsteroidal anti-inflammatory drugs (NSAIDs) with anti-inflammatory, analgesic, and antipyretic activities used to relieve a variety of pains. The objective of this study was to formulate, characterize and evaluate the in vitro and in vivo properties of ibuprofen formulated as solid lipid microspheres (SLMs) for enhanced delivery. The mixtures of Irvingia wombolu fat (IRW) and moringa oil (MO) each with Phospholipon® 90G (PL90G) at the ratio of 2:1 w/w were prepared by fusion, characterized and used to prepare SLMs. The SLMS were thereafter evaluated using the following parameters: particle size and morphology, stability, and encapsulation efficiency EE (%). In vitro release was carried out in phosphate buffer (pH 7.4). The ibuprofen based SLMs were also evaluated for anti-inflammatory and anti-ulcer effects using animal models. The pH showed significant increase after two months of formulation with a maximum value of 6.4 while the EE obtained were 95.6, 89.4 and 61.6% for SLMs formulated with lipid matrix of Phospholipon® 90G (1% and 2%), and MO (1%) respectively. The in vitro release showed maximum release of 87.8 and 98.97% of the two different lipid-based formulations while anti-inflammatory effect was up to 89.90% after 5 h of inducing inflammation. The SLMs did not show any lesion thus conferring gastroprotection on the formulations. The SLMs exhibited good anti-inflammatory property with gastroprotective action.

Eukaryotic Cell Membranes: Structure, Composition, Research Methods and Computational Modelling

This paper deals with the problems encountered in the study of eukaryotic cell membranes. A discussion on the structure and composition of membranes, lateral heterogeneity of membranes, lipid raft formation, and involvement of actin and cytoskeleton networks in the maintenance of membrane structure is included. Modern methods for the study of membranes and their constituent domains are discussed. Various simplified models of biomembranes and lipid rafts are presented. Computer modelling is considered as one of the most important methods. This is stated that from the study of the plasma membrane structure, it is desirable to proceed to the diverse membranes of all organelles of the cell. The qualitative composition and molar content of individual classes of polar lipids, free sterols and proteins in each of these membranes must be considered. A program to create an open access electronic database including results obtained from the membrane modelling of individual cell organelles and the key sites of the membranes, as well as models of individual molecules composing the membranes, has been proposed.

Oxidative stress: The nexus of obesity and cognitive dysfunction in diabetes

Obesity has been associated with oxidative stress. Obese patients are at increased risk for diabetic cognitive dysfunction, indicating a pathological link between obesity, oxidative stress, and diabetic cognitive dysfunction. Obesity can induce the biological process of oxidative stress by disrupting the adipose microenvironment (adipocytes, macrophages), mediating low-grade chronic inflammation, and mitochondrial dysfunction (mitochondrial division, fusion). Furthermore, oxidative stress can be implicated in insulin resistance, inflammation in neural tissues, and lipid metabolism disorders, affecting cognitive dysfunction in diabetics.

Characterization of structures and molecular interactions of RNA and lipid carriers using atomic force microscopy

Ribonucleic acid (RNA) and lipid are essential biomolecules in many biological processes, and hold a great prospect for biomedical applications, such as gene therapy, vaccines and therapeutic drug delivery. The characterization of morphology and intra-/inter-molecular interactions of RNA and lipid molecules is critical for understanding their functioning mechanisms. Atomic force microscopy (AFM) is a sophisticated technique for characterizing biomolecules featured by its piconewton force sensitivity, sub-nanometer spatial resolution, and flexible operation conditions in both air and liquid. The goal of this review is to highlight the representative and outstanding discoveries of the characterization of RNA and lipid molecules through morphology identification, physicochemical property determination and intermolecular force measurements by AFM. The first section introduces the AFM imaging of RNA molecules to obtain high-resolution morphologies and nanostructures in air and liquid, followed by the discussion of employing AFM force spectroscopy in understanding the nanomechanical properties and intra-/inter-molecular interactions of RNA molecules, including RNA-RNA and RNA-biomolecule interactions. The second section focuses on the studies of lipid and RNA encapsulated in lipid carrier (RNA-lipid) by AFM as well as the sample preparation and factors influencing the morphology and structure of lipid/RNA-lipid complexes. Particularly, the nanomechanical properties of lipid and RNA-lipid characterized by nanomechanical imaging and force measurements are discussed. The future perspectives and remaining challenges on the characterization of RNA and lipid offered by the versatile AFM techniques are also discussed. This review provides useful insights on the characterization of RNA and lipids nanostructures along with their molecular interactions, and also enlightens the application of AFM techniques in investigating a broad variety of biomolecules.

Lipid Adaptations against Oxidative Challenge in the Healthy Adult Human Brain

It is assumed that the human brain is especially susceptible to oxidative stress, based on specific traits such as a higher rate of mitochondrial free radical production, a high content in peroxidizable fatty acids, and a low antioxidant defense. However, it is also evident that human neurons, although they are post-mitotic cells, survive throughout an entire lifetime. Therefore, to reduce or avoid the impact of oxidative stress on neuron functionality and survival, they must have evolved several adaptive mechanisms to cope with the deleterious effects of oxidative stress. Several of these antioxidant features are derived from lipid adaptations. At least six lipid adaptations against oxidative challenge in the healthy human brain can be discerned. In this work, we explore the idea that neurons and, by extension, the human brain is endowed with an important arsenal of non-pro-oxidant and antioxidant measures to preserve neuronal function, refuting part of the initial premise.

Effects of polystyrene nanoplastics with different functional groups on rice (Oryza sativa L.) seedlings: Combined transcriptome, enzymology, and physiology

Plastic particles originate from the daily use of plastics and have become a new form of pollutant. However, the effects of nanoplastics (NPs) on higher plants remain largely unclear, thus requiring further research. In this study, rice plants were exposed to polystyrene (PS) NPs with different functional groups to determine their toxicity. The presence of NPs reduced the biomass and photosynthetic capacity of rice. Compared with control (CK), the heights of rice plants exposed to no-modified PS, carboxyl-modified PS (PS-COOH) and amino-modified PS (PS-NH₂) groups decreased by 13.59%, 26.61%, and 42.71%, while the dry shoot weight decreased by 47.46%, 50.09%, and 71.04%, respectively. All treatments activated the antioxidant levels of rice and reduced photosynthesis. Transcriptome analysis showed that NPs induced the expression of genes related to antioxidant enzyme activity in rice roots. Rice could partially reduce the xenobiotic toxicity caused by external sources by regulating phenylpropane biosynthesis and the processes involved in cell detoxification. PS mainly affected the process of RNA metabolism, while PS-COOH mainly affected ion transport, and PS-NH₂ mainly affected the synthesis of macromolecular protein, which had different effects on rice growth.

The Imprinted PARAFILM as a New Carrier Material for Dried Plasma Spots (DPSs) Utilizing Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) in Phospholipidomics

The application of desorption electrospray ionization mass spectrometry (DESI-MS) and dried blood spot (DBS) sampling has been successfully implemented several times. However, the difficulty of combining DBS sampling with DESI-MS is still the carrier material used for the blood samples. In this study, a new, easily obtained, and cost-effective carrier substrate for dried plasma spot (DPS) sampling and DESI-MS analysis and its application in phospholipidomics studies was described. First, the effects of several carrier materials, including cellulose-based materials (31 ET paper and filter paper) and non-cellulose-based materials (PARAFILM and its shape-modified material, PTFE-printed glass slide and polyvinylidene fluoride film), were tested. Second, a method combining DPS sampling with DESI-MS for phospholipidomics analysis was established, and parameters affecting compound signal intensities, such as sample volume and sprayer solvent system, were optimized. In conclusion, the total signal intensity obtained from shape-modified PARAFILM was the strongest. The suitable plasma sample volume deposited on PARAFILM carriers was 5 μl, and acetonitrile (ACN) was recommended as the optimal spray solvent for phospholipid (PL) profiling. Repeatability (87.5% of compounds with CV < 30%) and stability for data acquisition (48 h) were confirmed. Finally, the developed method was applied in phospholipidomics analysis of schistosomiasis, and a distinguished classification between control mice and infected mice was observed by using multivariate pattern recognition analysis, confirming the practical application of this new carrier material for DPS sampling and DESI-MS analysis. Compared with a previously reported method, the rapid metabolomics screening approach based on the implementation of DPS sampling coupled with the DESI-MS instrument developed in this study has increased analyte sensitivity, which may promote its further application in clinical studies.

A reversed phase ultra-high-performance liquid chromatography-data independent mass spectrometry method for the rapid identification of mycobacterial lipids

A rapid reversed-phase ultra-high-performance liquid chromatography-high resolution mass spectrometry based mycobacterial lipidomics approach is described. This method enables the separation of various lipid classes including lipids specific to mycobacterial, such as methoxy mycolic acid and α-mycolic acid. Lipid separation occurs during a relatively short runtime of 14 min on a charged surface hybrid C₁₈ column. A high-resolution quadrupole-time of flight mass spectrometer and a data independent acquisition mode allowed for the simultaneous acquisition of the full scan and collision induced dissociation fragmentation. The proposed method provides lipid detection results equivalent to or better than existing methods, but with a faster throughput and an overall higher sensitivity. The reversed-phase ultra-high-performance liquid chromatography-high resolution mass spectrometry method was shown to obtain structural information for lipids extracted from Mycobacterium smegmatis, but the method is applicable to the analysis of lipids from various bacterial and mammalian cell lines.

Modifying Chromatography Conditions for Improved Unknown Feature Identification in Untargeted Metabolomics

Untargeted metabolomics is an essential component of systems biology research, but it is plagued by a high proportion of detectable features not identified with a chemical structure. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments produce spectra that can be searched against databases to help identify or classify these unknowns, but many features do not generate spectra of sufficient quality to enable successful annotation. Here, we explore alterations to gradient length, mass loading, and rolling precursor ion exclusion parameters for reversed phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC) that improve compound identification performance for human plasma samples. A manual review of spectral matches from the HILIC data set was used to determine reasonable thresholds for search score and other metrics to enable semi-automated MS/MS data analysis. Compared to typical LC-MS/MS conditions, methods adapted for compound identification increased the total number of unique metabolites that could be matched to a spectral database from 214 to 2052. Following data alignment, 68.0% of newly identified features from the modified conditions could be detected and quantitated using a routine 20-min LC-MS run. Finally, a localized machine learning model was developed to classify the remaining unknowns and select a subset that shared spectral characteristics with successfully identified features. A total of 576 and 749 unidentified features in the HILIC and RPLC data sets were classified by the model as high-priority unknowns or higher-importance targets for follow-up analysis. Overall, our study presents a simple strategy to more deeply annotate untargeted metabolomics data for a modest additional investment of time and sample.

Lipid Droplet-Associated Proteins in Cardiomyopathy

BACKGROUND

The heart requires a high rate of fatty-acid oxidation (FAO) to meet its energy needs. Neutral lipids are the main source of energy for the heart and are stored in lipid droplets (LDs), which are cytosolic organelles that primarily serve to store neutral lipids and regulate cellular lipid metabolism. LD-associated proteins (LDAPs) are proteins either located on the surface of the LDs or reside in the cytosol and contribute to lipid metabolism. Therefore, abnormal cardiac lipid accumulation or FAO can alter the redox state of the heart, resulting in cardiomyopathy, a group of diseases that negatively affect the myocardial function, thereby leading to heart failure and even cardiac death.

SUMMARY

LDs, along with LDAPs, are pivotal for modulating heart lipid homeostasis. The proper cardiac development and the maintenance of its normal function depend largely on lipid homeostasis regulated by LDs and LDAPs. Overexpression or deletion of specific LDAPs can trigger myocardial dysfunction and may contribute to the development of cardiomyopathy. Extensive connections and interactions may also exist between LDAPs. Key Message: In this review, the various mechanisms involved in LDAP-mediated regulation of lipid metabolism, the association between cardiac development and lipid metabolism, as well as the role of LDAPs in cardiomyopathy progression are discussed.

Lipid Melting Transitions Involve Structural Redistribution of Interfacial Water

Morphological and gel-to-liquid phase transitions of lipid membranes are generally considered to primarily depend on the structural motifs in the hydrophobic core of the bilayer. Structural changes in the aqueous headgroup phase are typically not considered, primarily because they are difficult to quantify. Here, we investigate structural changes of the hydration shells around large unilamellar vesicles (LUVs) in aqueous solution, using differential scanning calorimetry (DSC), and temperature-dependent ζ-potential and high-throughput angle-resolved second harmonic scattering measurements (AR-SHS). Varying the lipid composition from 1,2-dimyristoyl-sn-glycero-3-phosphocholine(DMPC) to 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA), to 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine (DMPS), we observe surprisingly distinct behavior for the different systems that depend on the chemical composition of the hydrated headgroups. These differences involve changes in hydration following temperature-induced counterion redistribution, or changes in hydration following headgroup reorientation and Stern layer compression.

Metabolomic and proteomic characterization of sng and pain phenotypes in fibromyalgia

BACKGROUND

Fibromyalgia (FM) is characterized by chronic widespread pain. Its pathophysiological mechanisms remain poorly understood, and effective diagnosis and treatments are lacking. This study aimed to identify significantly changed biosignatures in FM and propose a novel classification for FM based on pain and soreness (sng) symptoms.

METHODS

Urine and serum samples from 30 FM patients and 25 controls underwent metabolomic and proteomic profiling.

RESULTS

Compared with controls, FM patients showed significant differential expression of three metabolites in urine and five metabolites and eight proteins in serum. Of them, DETP, 4-guanidinobutanoic acid, SM(d18:1/18:0), PC(20:1(11Z)/18:0), S100A7, SERPINB3, galectin-7 and LYVE1 were first reported as potential biomarkers for FM. Furthermore, lactate, 2-methylmaleate and cotinine in urine and lactate, SM(d18:1/25:1), SM(d18:1/26:1) and prostaglandin D2 (PGD2) and PCYOX1, ITIH4, PFN1, LRG1, C8G, C8A, CP, CDH5 and DBH in serum could differentiate pain- (PG) and sng-dominant groups (SG). Lactate, 2-methylmaleate, cotinine, PCYOX1, ITIH4, PFN1 and DBH have a higher level in SG. SM(d18:1/25:1), SM(d18:1/26:1), PGD2, LRG1, C8G, C8A, CP and CDH5 in SG are lower than PG. The omics results indicated disordered free radical scavenging, and lipid and amino acid metabolism networks and resulting NF-κB-dependent cytokine generation in FM. Lactate level was altered simultaneously in urine and serum and significantly higher in sng-dominant patients than others.

CONCLUSIONS

In this study, we identified potential biomarkers from FM patients. The selected biomarkers could discriminate sng and pain phenotypes in FM patients. These results could help elucidate the underlying pathological mechanisms for more effective diagnosis and therapy for FM.

Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations

Understanding the lateral organization in plasma membranes remains an open problem and is of great interest to many researchers. Model membranes consisting of coexisting domains are commonly used as simplified models of plasma membranes. The coarse-grained (CG) Martini force field has successfully captured spontaneous separation of ternary membranes into a liquid-disordered and a liquid-ordered domain. With all-atom (AA) models, however, phase separation is much harder to achieve due to the slow underlying dynamics. To remedy this problem, here, we apply the virtual site (VS) hybrid method on a ternary membrane composed of saturated lipids, unsaturated lipids, and cholesterol to investigate the phase separation. The VS scheme couples the two membrane leaflets at CG and AA resolution. We found that the rapid phase separation reached by the CG leaflet can accelerate and guide this process in the AA leaflet.

Lipid droplets and lipid mediators in viral infection and immunity

Lipid droplets (LDs) contribute to key pathways important for the physiology and pathophysiology of cells. In a homeostatic view, LDs regulate the storage of neutral lipids, protein sequestration, removal of toxic lipids and cellular communication; however, recent advancements in the field show these organelles as essential for various cellular stress response mechanisms, including inflammation and immunity, with LDs acting as hubs that integrate metabolic and inflammatory processes. The accumulation of LDs has become a hallmark of infection, and is often thought to be virally driven; however, recent evidence is pointing to a role for the upregulation of LDs in the production of a successful immune response to viral infection. The fatty acids housed in LDs are also gaining interest due to the role that these lipid species play during viral infection, and their link to the synthesis of bioactive lipid mediators that have been found to have a very complex role in viral infection. This review explores the role of LDs and their subsequent lipid mediators during viral infections and poses a paradigm shift in thinking in the field, whereby LDs may play pivotal roles in protecting the host against viral infection.

Effect of Polystyrene Microplastics on Rice Seed Germination and Antioxidant Enzyme Activity

The accumulation and distribution of microplastics (MPs) in agricultural soils, including rice fields, is well studied. However, only a few studies have investigated the uptake of MPs by rice plants and the consequential toxic effects of MPs under solid-phase culture conditions. Hence, in this study, we explored the effects of different concentrations of polystyrene MPs (PS-MPs, with a size of 200 nm) on rice seed germination, root growth, antioxidant enzyme activity, and transcriptome. PS-MPs exhibited no significant effect on the germination of rice seeds (p > 0.05). However, PS-MPs significantly promoted root length (10 mg L⁻¹; p < 0.05), and significantly reduced antioxidant enzyme activity (1000 mg L⁻¹; p < 0.05). Staining with 3,3-diaminobenzidine and nitrotetrazolium blue chloride further revealed significant accumulation of reactive oxygen species in the roots of rice treated with PS-MPs. In addition, transcriptome data analysis revealed that PS-MPs induce the expression of genes related to antioxidant enzyme activity in plant roots. Specifically, genes related to flavonoid and flavonol biosynthesis were upregulated, whereas those involved in linolenic acid and nitrogen metabolism were downregulated. These results enhance our understanding of the responses of agricultural crops to MP toxicity.

Fatty acids and beyond: Age and Alzheimer's disease related changes in lipids reveal the neuro-nutraceutical potential of lipids in cognition

Lipids are essential in maintaining brain function, and lipid profiles have been reported to be altered in aged and Alzheimer's disease (AD) brains as compared to healthy mature brains. Both age and AD share common metabolic hallmarks such as increased oxidative stress and perturbed metabolic function, and age remains the most strongly correlated risk factor for AD, a neurodegenerative disease. A major accompanying pathological symptom of these conditions is cognitive impairment, which is linked with changes in lipid metabolism. Thus, nutraceuticals that affect brain lipid metabolism or lipid levels as a whole have the potential to ameliorate cognitive decline. Lipid analyses and lipidomic studies reveal changes in specific lipid types with aging and AD, which can identify potential lipid-based nutraceuticals to restore the brain to a healthy lipid phenotype. The brain lipid profile can be influenced directly with dietary administration of lipids themselves, although because of synergistic effects of nutrients it may be more useful to consider a multi-component diet rather than single nutrient supplementation. Gut microbiota also serve as a source of beneficial lipids, and the value of treatments that manipulate the composition of gut microbiome should not be ignored. Lastly, instead of direct supplementation, compounds that affect pathways involved with lipid metabolism should also be considered as a way of manipulating lipid levels to improve cognition. In this review, we briefly discuss the role of lipids in the brain, the changing lipid profile in AD, current research on lipid-based nutraceuticals and their therapeutic potential to combat cognitive impairment.

Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications

Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.

New insights into human prefrontal cortex aging with a lipidomics approach

INTRODUCTION

Human prefrontal cortex (hPFC) is a recent evolutionarily developed brain region involved in cognitive functions. Human cognitive functions decline during aging. Yet the molecular mechanisms underlying the functional deterioration of the neural cells of this brain region still remain to be fully described.

AREAS COVERED

In this review, we explore the role of lipids in hPFC aging. Firstly, we briefly consider the approaches used to identify lipid species in brain tissue with special attention paid to a lipidomics analysis. Then, as the evolution process has conferred a specific lipid profile on the hPFC, we consider the lipidome of hPFC. In addition, the role of lipids in hPFC aging, and in particular, the cognitive decline associated with aging, is discussed. Finally, nutritional and pharmacological interventions designed to modulate this process are examined. It is suggested that the dysfunction of key cellular processes secondarily to the damage of lipid membrane underlies the cognitive decline of hPFC during aging.

EXPERT OPINION

Lipidomics methods are and will continue to be key tools in the effort to gain additional insights into the aging of the human brain.

Membrane lipids and transporter function

Transport proteins are essential for cells in allowing the exchange of substances between cells and their environment across the lipid bilayer forming a tight barrier. Membrane lipids modulate the function of transmembrane proteins such as transporters in two ways: Lipids are tightly and specifically bound to transport proteins and in addition they modulate from the bulk of the lipid bilayer the function of transport proteins. This overview summarizes currently available information at the ultrastructural level on lipids tightly bound to transport proteins and the impact of altered bulk membrane lipid composition. Human diseases leading to altered lipid homeostasis will lead to altered membrane lipid composition, which in turn affect the function of transporter proteins.

Lipidome is lipids regulator in gastrointestinal tract and it is a life collar in COVID-19: A review

The term lipidome is mentioned to the total amount of the lipids inside the biological cells. The lipid enters the human gastrointestinal tract through external source and internal source. The absorption pathway of lipids in the gastrointestinal tract has many ways; the 1st way, the lipid molecules are digested in the lumen before go through the enterocytes, digested products are re-esterified into complex lipid molecules. The 2nd way, the intracellular lipids are accumulated into lipoproteins (chylomicrons) which transport lipids throughout the whole body. The lipids are re-synthesis again inside the human body where the gastrointestinal lipids are: (1) Transferred into the endoplasmic reticulum; (2) Collected as lipoproteins such as chylomicrons; or (3) Stored as lipid droplets in the cytosol. The lipids play an important role in many stages of the viral replication cycle. The specific lipid change occurs during viral infection in advanced viral replication cycle. There are 47 lipids within 11 lipid classes were significantly disturbed after viral infection. The virus connects with blood-borne lipoproteins and apolipoprotein E to change viral infectivity. The viral interest is cholesterol- and lipid raft-dependent molecules. In conclusion, lipidome is important in gastrointestinal fat absorption and coronavirus disease 2019 (COVID-19) infection so lipidome is basic in gut metabolism and in COVID-19 infection success.

Tracing sources of carbon and hydrogen to stored lipids in migratory passerines using stable isotope (δ13C, δ2H) measurements

Using measurements of naturally occurring stable isotopes in feathers to determine avian origin and migratory patterns is well established. However, isotopically determining nutritional origins of lipids, a major migratory fuel, has not been attempted. This study explores isotopic links between diet and stored lipids in captive white-throated sparrows (Zonotrichia albicollis) by providing isotopically distinct mixtures of carbohydrates/oils and drinking water and assessing the δ¹³C and δ²H values of stored lipid, breath CO₂ (δ¹³C) and breath water vapour (δ²H). Stored lipid δ¹³C and δ²H values correlated with the isotopic values found in dietary carbohydrates/oils and drinking water treatments, respectively, indicating a clear traceable transfer of environmental dietary isotopic signals into body lipids. Dietary oils and carbohydrates contributed 80-82% of carbon and 44-46% of hydrogen, respectively, to stored lipids. Drinking water contributed 18-28% of hydrogen to stored lipids. Isotopic relationships were quantifiable using linear calibration algorithms which provide the basis for the construction of tissue isoscapes for migratory passerines. Breath CO₂ δ¹³C values and breath water vapour δ²H values for fed and fasted birds reflected dietary sources. Breath CO₂ δ¹³C values were higher for fasted birds than for fed birds by an average of 4.5‰ while breath water vapour δ²H values were lower for fasted birds by an average of 48.9‰. These results indicate that lipids and metabolites from their subsequent breakdown for fuel isotopically reflect dietary sources but complicate interpretation of such data, especially for wild migrating birds. Applications and limitations of these findings to the creation of "liposcapes" are examined.

Transcriptomics reveals the action mechanisms and cellular targets of citrate-coated silver nanoparticles in a ubiquitous aquatic fungus

Silver nanoparticles (AgNPs) are among the major groups of contaminants of emerging concern for aquatic ecosystems. The massive application of AgNPs relies on the antimicrobial properties of Ag, raising concerns about their potential risk to ecologically important freshwater microbes and the processes they drive. Moreover, it is still uncertain whether the effects of AgNPs are driven by the same mechanisms underlying those of Ag ions (Ag⁺). We employed transcriptomics to better understand AgNP toxicity and disentangle the role of Ag⁺ in the overall toxicity towards aquatic fungi. To that end, the worldwide-distributed aquatic fungus Articulospora tetracladia, that plays a central role in organic matter turnover in freshwaters, was selected and exposed for 3 days to citrate-coated AgNPs (∼20 nm) and Ag⁺ at concentrations inhibiting 20% of growth (EC₂₀). Responses revealed 258 up- and 162 down-regulated genes upon exposure to AgNPs and 448 up- and 84 down-regulated genes under exposure to Ag⁺. Different gene expression patterns were found after exposure to each silver form, suggesting distinct mechanisms of action. Gene ontology (GO) analyses showed that the major cellular targets likely affected by both silver forms were the biological membranes. GO-based biological processes indicated that AgNPs up-regulated the genes involved in transport, nucleobase metabolism and energy production, but down-regulated those associated with redox and carbohydrate metabolism. Ag⁺ up-regulated the genes involved in carbohydrate and steroid metabolism, whereas genes involved in localization and transport were down-regulated. Our results showed, for the first time, distinct profiles of gene expression in aquatic fungi exposed to AgNPs and Ag⁺, supporting different modes of toxicity of each silver form. Also, our results suggest that Ag⁺ had a negligible role in the toxicity induced by AgNPs. Finally, our study highlights the power of transcriptomics in portraying the stress induced by different silver forms in organisms.

Comprehensive Survey on Nanobiomaterials for Bone Tissue Engineering Applications

One of the most important ideas ever produced by the application of materials science to the medical field is the notion of biomaterials. The nanostructured biomaterials play a crucial role in the development of new treatment strategies including not only the replacement of tissues and organs, but also repair and regeneration. They are designed to interact with damaged or injured tissues to induce regeneration, or as a forest for the production of laboratory tissues, so they must be micro-environmentally sensitive. The existing materials have many limitations, including impaired cell attachment, proliferation, and toxicity. Nanotechnology may open new avenues to bone tissue engineering by forming new assemblies similar in size and shape to the existing hierarchical bone structure. Organic and inorganic nanobiomaterials are increasingly used for bone tissue engineering applications because they may allow to overcome some of the current restrictions entailed by bone regeneration methods. This review covers the applications of different organic and inorganic nanobiomaterials in the field of hard tissue engineering.

Cationic amphiphilic drugs induce elevation in lysoglycerophospholipid levels and cell death in leukemia cells

INTRODUCTION

Repurposing of cationic amphiphilic drugs (CADs) emerges as an attractive therapeutic solution against various cancers, including leukemia. CADs target lysosomal lipid metabolism and preferentially kill cancer cells via induction of lysosomal membrane permeabilization, but the exact effects of CADs on the lysosomal lipid metabolism remain poorly illuminated.

OBJECTIVES

We aimed to systematically monitor CAD-induced alterations in the quantitative lipid profiles of leukemia cell lines in order to chart effects of CADs on the metabolism of various lipid classes present in these cells.

METHODS

We conducted this study on eight cultured cell lines representing two leukemia types, acute lymphoblastic leukemia and acute myeloid leukemia. Mass spectrometry-based quantitative shotgun lipidomics was employed to quantify the levels of around 400 lipid species of 26 lipid classes in the leukemia cell lines treated or untreated with a CAD, siramesine.

RESULTS

The two leukemia types displayed high, but variable sensitivities to CADs and distinct profiles of cellular lipids. Treatment with siramesine rapidly altered the levels of diverse lipid classes in both leukemia types. These included sphingolipid classes previously reported to play key roles in CAD-induced cell death, but also lipids of other categories. We demonstrated that the treatment with siramesine additionally elevated the levels of numerous cytolytic lysoglycerophospholipids in positive correlation with the sensitivity of individual leukemia cell lines to siramesine.

CONCLUSIONS

Our study shows that CAD treatment alters balance in the metabolism of glycerophospholipids, and proposes elevation in the levels of lysoglycerophospholipids as part of the mechanism leading to CAD-induced cell death of leukemia cells.

Ultrahigh-Performance capillary liquid chromatography-mass spectrometry at 35 kpsi for separation of lipids

Improvements in sample preparation, separation, and mass spectrometry continue to expand the coverage in LC-MS based lipidomics. While longer columns packed with smaller particles in theory give higher separation performance compared to shorter columns, the implementation of this technology above commercial limits has been sparse due to difficulties in packing long columns and successfully operating instruments at ultrahigh pressures. In this work, a liquid chromatograph that operates up to 35 kpsi was investigated for the separation and identification of lipid species from human plasma. Capillary columns between 15-50 cm long were packed with 1.7 µm BEH C18 particles and evaluated for their ability to separate lipid isomers and complex lipid extracts from human plasma. Putative lipid class identifications were assigned using accurate mass and relative retention time data of the eluting peaks. Our findings indicate that longer columns packed and operated at 35 kpsi outperform shorter columns packed and run at lower pressures in terms of peak capacity and numbers of features identified. Packing columns with relatively high concentration slurries (200 mg/mL) while sonicating the column resulted in 6-34% increase in peak capacity for 50 cm columns compared to lower slurry concentrations and no sonication. For a given analysis time, 50 cm long columns operated at 35 kpsi provided a 20-95% increase in chromatographic peak capacity compared with 15 cm columns operated at 15 kpsi. Analysis times up to 4 h were evaluated, generating peak capacities up to 410 ± 5 (n = 3, measured at 4σ) and identifying 480 ± 85 lipids (n = 2). Importantly, the results also show a correlation between the peak capacity and the number of lipids identified from a human plasma extract. This correlation indicates that ionization suppression is a limiting factor in obtaining sufficient signal for identification by mass spectrometry. The result also shows that the higher resolution obtained by shallow gradients overcomes possible signal reduction due to broader, more dilute peaks in long gradients for improving detection of lipids in LC-MS. Lastly, longer columns operated at shallow gradients allowed for the best separation of both regional and geometrical isomers. These results demonstrate a system that enables the advantages of using longer columns packed and run at ultrahigh pressure for improving lipid separations and lipidome coverage.

Enhanced Catalytic Activity of Gold@Polydopamine Nanoreactors with Multi-compartment Structure Under NIR Irradiation

Photothermal conversion (PTC) nanostructures have great potential for applications in many fields, and therefore, they have attracted tremendous attention. However, the construction of a PTC nanoreactor with multi-compartment structure to achieve the combination of unique chemical properties and structural feature is still challenging due to the synthetic difficulties. Herein, we designed and synthesized a catalytically active, PTC gold (Au)@polydopamine (PDA) nanoreactor driven by infrared irradiation using assembled PS-b-P2VP nanosphere as soft template. The particles exhibit multi-compartment structure which is revealed by 3D electron tomography characterization technique. They feature permeable shells with tunable shell thickness. Full kinetics for the reduction reaction of 4-nitrophenol has been investigated using these particles as nanoreactors and compared with other reported systems. Notably, a remarkable acceleration of the catalytic reaction upon near-infrared irradiation is demonstrated, which reveals for the first time the importance of the synergistic effect of photothermal conversion and complex inner structure to the kinetics of the catalytic reduction. The ease of synthesis and fresh insights into catalysis will promote a new platform for novel nanoreactor studies.

Transcriptome sequencing of a toxic dinoflagellate, Karenia mikimotoi subjected to stress from solar ultraviolet radiation

Solar ultraviolet radiation (UVR) is a stress factor in aquatic environments and may act directly or indirectly on orgnisms in the upper layers of the water column. However, UVR effects are usually species-specific and difficult to extrapolate. Here we use the HAB-forming, toxic dinoflagellate Karenia mikimotoi (which was found to be relatively resistant in previous studies) to investigate its transcriptional responses to a one-week UVR exposure. For this, batch cultures of K. mikimotoi were grown with and without UVR, and their transcriptomes (generated via RNAseq technology) were compared. RNA-seq generated 45.31 million reads, which were further assembled to 202600 unigenes (>300bp). Among these, ca. 61% were annotated with NCBI, NR, GO, KOG, PFAM, Swiss-Prot, and KEGG database. Transcriptomic analysis revealed 722 differentially expressed unigenes (DEGs, defined as being within a |log2 fold change| ≥ 2 and padj < 0.05) responding to solar UVR, which were only 0.36% of all unigenes. 716 unigenes were down-regulated, and only 6 unigenes were up-regulated in the UVR compared to non-UVR treatment. KEGG pathway further analysis revealed DEGs were involved in the different pathway; genes involved in the ribosome, endocytosis and steroid biosynthesis pathways were highly down-regulated, but this was not the case for those involved in the energy metabolisms (including photosynthesis, oxidative phosphorylation) which may contribute to the sustainable growth observed in UVR treatment. The up-regulated expression of both zinc-finger proteins (ZFPs) and ribosomal protein L11 (RPL11) may be one of the acclimated mechanisms against UVR. In addition, this work identified down-regulated genes involved in fatty acid degradation and the hydrophobic branched chain amino acids (e.g., Valine, leucine, and isoleucine), which act as structural components of cell membranes modulating lipid homeostasis or turnover. In conclusion, the present study suggests that the toxic dinoflagellate K. mikimotoi has limited transcriptomic regulation but confirms that it appears as a tolerant species in response to solar UVR. These findings expand current knowledge of gene expression in HAB-forming species in response to natural environment factors such as solar radiation.

LC-MS/MS analysis of free fatty acid composition and other lipids in skins and seeds of Vitis vinifera grape cultivars

Lipids are important constituents of plant and animal cells, being essential due to their biological functions. Despite the significant role of these compounds in grape berries, knowledge of grape lipid composition is still limited. This study addresses the free fatty acid composition and other lipids in skins and seeds of several Vitis vinifera grape cultivars using LC-MS/MS. A different profile of free fatty acids was determined in the grape tissues, showing a higher proportion of unsaturated fatty acids in seeds (ca. 60%). Lignoceric acid was one of the main free saturated fatty acids found in grape skins, together with palmitic and stearic acids. Berry skins showed similar ranges of C18-unsaturated fatty acids, whereas linoleic acid was predominant in the seed fatty acid composition. Higher content of glycerophospholipids was determined in grape seeds. Uvaol and oleanolic acid were only quantified in skins (1.5-3.9 and 38.6-57.6 mg/kg fresh weight, respectively). These preliminary results suggest a certain diversity in grape lipids according to their location in the berry tissues and cultivar, providing useful information for the fermentation process due to their role in wine sensory profile and yeast growth.

Tutorial on lipidomics

The mainstream of lipidomics involves mass spectrometry-based, systematic, and large-scale studies of the structure, composition, and quantity of lipids in biological systems such as organs, cells, and body fluids. As increasingly more researchers in broad fields are beginning to pay attention to and actively learn about the lipidomic technology, some introduction on the topic is needed to help the newcomers to better understand the field. This tutorial seeks to introduce the basic knowledge about lipidomics and to provide readers with some core ideas and the most important approaches for studying the field.

Fat, fight, and beyond: The multiple roles of lipid droplets in infections and inflammation

Increased accumulation of cytoplasmic lipid droplets (LDs) in host nonadipose cells is commonly observed in response to numerous infectious diseases, including bacterial, parasite, and fungal infections. LDs are lipid-enriched, dynamic organelles composed of a core of neutral lipids surrounded by a monolayer of phospholipids associated with a diverse array of proteins that are cell and stimulus regulated. Far beyond being simply a deposit of neutral lipids, LDs have come to be seen as an essential platform for various cellular processes, including metabolic regulation, cell signaling, and the immune response. LD participation in the immune response occurs as sites for compartmentalization of several immunometabolic signaling pathways, production of inflammatory lipid mediators, and regulation of antigen presentation. Infection-driven LD biogenesis is a complexly regulated process that involves innate immune receptors, transcriptional and posttranscriptional regulation, increased lipid uptake, and new lipid synthesis. Accumulating evidence demonstrates that intracellular pathogens are able to exploit LDs as an energy source, a replication site, and/or a mechanism of immune response evasion. Nevertheless, LDs can also act in favor of the host as part of the immune and inflammatory response to pathogens. Here, we review recent findings that explored the new roles of LDs in the context of host-pathogen interactions.

A Cybernetic Approach to Modeling Lipid Metabolism in Mammalian Cells

The goal-oriented control policies of cybernetic models have been used to predict metabolic phenomena such as the behavior of gene knockout strains, complex substrate uptake patterns, and dynamic metabolic flux distributions. Cybernetic theory builds on the principle that metabolic regulation is driven towards attaining goals that correspond to an organism’s survival or displaying a specific phenotype in response to a stimulus. Here, we have modeled the prostaglandin (PG) metabolism in mouse bone marrow derived macrophage (BMDM) cells stimulated by Kdo2-Lipid A (KLA) and adenosine triphosphate (ATP), using cybernetic control variables. Prostaglandins are a well characterized set of inflammatory lipids derived from arachidonic acid. The transcriptomic and lipidomic data for prostaglandin biosynthesis and conversion were obtained from the LIPID MAPS database. The model parameters were estimated using a two-step hybrid optimization approach. A genetic algorithm was used to determine the population of near optimal parameter values, and a generalized constrained non-linear optimization employing a gradient search method was used to further refine the parameters. We validated our model by predicting an independent data set, the prostaglandin response of KLA primed ATP stimulated BMDM cells. We show that the cybernetic model captures the complex regulation of PG metabolism and provides a reliable description of PG formation.