A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals

Changes provoked by altitudes and cooking methods in physicochemical properties, volatile profile, and sensory characteristics of yak meat

The present study aimed to shed light on the effects of altitudes and three cooking methods (boiling, steaming, and roasting) on the physicochemical quality, volatile profile, and sensorial characteristics of yak meat. Composite meat samples were prepared to represent each cooking method and altitude level from the longissimus thoracis et lumborum (LTL) muscle of nine yaks. The techniques employed were gas chromatography-mass spectrometry (GC-MS) and electronic nose (E-nose) along with chemometrics analysis to study the changes occurring in yak volatile profile, and TBARS measurement in lipid oxidation during cooking. Among the cooking methods, boiling and steaming exhibited higher protein and fat content while lower volatile compound contents. Additionally, roasted yak meat received the highest sensory scores, along with decreased L*-values, while elevated a*- and b*-values, and tenderness. A total of 138 volatile compounds were detected, and among them, 36 odorants were identified as odor-active compounds in cooked yak meat. It is evidenced that low-altitude yak presented more complex and richer flavor profiles than high-altitude ones. Moreover, yak meat from low- and high-altitude was classified into two groups by an electronic nose (E-nose) owing to distinct flavor characteristics. Overall, roasted yak meat originating from low altitudes tends to be more popular from a sensory perspective.

Identification of blood metabolic biomarkers associated with diabetic distal symmetric sensorimotor polyneuropathy in patients with type 2 diabetes mellitus

BACKGROUND

Distal symmetric sensorimotor polyneuropathy (DSPN) is a common neurologic complication of type 2 diabetes mellitus (T2DM), but the underlying mechanisms and changes in serum metabolites remain largely undefined. This study aimed to characterize the plasma metabolite profiles of participants with T2DM using targeted metabolomics analysis and identify potential biomarkers for DSPN.

METHODS

A combined liquid chromatography MS/MS and direct flow injection were used to quantify plasma metabolite obtained from 63 participants with T2DM, 81 with DSPN, and 33 nondiabetic control participants. A total of 130 metabolites, including amino acids, biogenic amines, sphingomyelins (SM), phosphatidylcholines, carnitines, and hexose, were analyzed.

RESULTS

A total of 16 plasma metabolites and 3 cholesterol-related laboratory parameters were found to have variable importance in the projection score >1.0 and false discovery rate <5.0% between control, T2DM, and DSPN. Among these variables, five serum metabolites, including phenylalanine (AUC = 0.653), alanine (AUC = 0.630), lysine (AUC = 0.622) tryptophan (AUC = 0.620), and SM C16:0 (AUC = 0.630), are potential biomarkers (all p < .05) in distinguishing T2DM with DSPN from those without (AUC = 0.720).

CONCLUSIONS

In this cross-sectional study, derangement of several metabolites in the plasma was observed in T2DM with and without DSPN, and these metabolites may be potential biomarkers for predicting DSPN. Longitudinal studies are warranted.

Metabolomics to Understand Alterations Induced by Physical Activity during Pregnancy

Physical activity (PA) and exercise have been associated with a reduced risk of cancer, obesity, and diabetes. In the context of pregnancy, maintaining an active lifestyle has been shown to decrease gestational weight gain (GWG) and lower the risk of gestational diabetes mellitus (GDM), hypertension, and macrosomia in offspring. The main pathways activated by PA include BCAAs, lipids, and bile acid metabolism, thereby improving insulin resistance in pregnant individuals. Despite these known benefits, the underlying metabolites and biological mechanisms affected by PA remain poorly understood, highlighting the need for further investigation. Metabolomics, a comprehensive study of metabolite classes, offers valuable insights into the widespread metabolic changes induced by PA. This narrative review focuses on PA metabolomics research using different analytical platforms to analyze pregnant individuals. Existing studies support the hypothesis that exercise behaviour can influence the metabolism of different populations, including pregnant individuals and their offspring. While PA has shown considerable promise in maintaining metabolic health in non-pregnant populations, our comprehension of metabolic changes in the context of a healthy pregnancy remains limited. As a result, further investigation is necessary to clarify the metabolic impact of PA within this unique group, often excluded from physiological research.

Microbiota-derived tryptophan metabolism: Impacts on health, aging, and disease

The intricate interplay between gut microbiota and the host is pivotal in maintaining homeostasis and health. Dietary tryptophan (TRP) metabolism initiates a cascade of essential endogenous metabolites, including kynurenine, kynurenic acid, serotonin, and melatonin, as well as microbiota-derived Trp metabolites like tryptamine, indole propionic acid (IPA), and other indole derivatives. Notably, tryptamine and IPA, among the indole metabolites, exert crucial roles in modulating immune, metabolic, and neuronal responses at both local and distant sites. Additionally, these metabolites demonstrate potent antioxidant and anti-inflammatory activities. The levels of microbiota-derived TRP metabolites are intricately linked to the gut microbiota's health, which, in turn, can be influenced by age-related changes. This review aims to comprehensively summarize the cellular and molecular impacts of tryptamine and IPA on health and aging-related complications. Furthermore, we explore the levels of tryptamine and IPA and their corresponding bacteria in select diseased conditions, shedding light on their potential significance as biomarkers and therapeutic targets.

4-Ethylphenol-fluxes, metabolism and excretion of a gut microbiome derived neuromodulator implicated in autism

Gut-microbiome-derived metabolites, such as 4-Ethylphenol [4EP], have been shown to modulate neurological health and function. Although the source of such metabolites is becoming better understood, knowledge gaps remain as to the mechanisms by which they enter host circulation, how they are transported in the body, how they are metabolised and excreted, and the way they exert their effects. High blood concentrations of host-modified 4EP, 4-ethylphenol sulfate [4EPS], are associated with an anxiety phenotype in autistic individuals. We have reviewed the existing literature and discuss mechanisms that are proposed to contribute influx from the gut microbiome, metabolism, and excretion of 4EP. We note that increased intestinal permeability is common in autistic individuals, potentially explaining increased flux of 4EP and/or 4EPS across the gut epithelium and the Blood Brain Barrier [BBB]. Similarly, kidney dysfunction, another complication observed in autistic individuals, impacts clearance of 4EP and its derivatives from circulation. Evidence indicates that accumulation of 4EPS in the brain of mice affects connectivity between subregions, particularly those linked to anxiety. However, we found no data on the presence or quantity of 4EP and/or 4EPS in human brains, irrespective of neurological status, likely due to challenges sampling this organ. We argue that the penetrative ability of 4EP is dependent on its form at the BBB and its physicochemical similarity to endogenous metabolites with dedicated active transport mechanisms across the BBB. We conclude that future research should focus on physical (e.g., ingestion of sorbents) or metabolic mechanisms (e.g., conversion to 4EP-glucuronide) that are capable of being used as interventions to reduce the flux of 4EP from the gut into the body, increase the efflux of 4EP and/or 4EPS from the brain, or increase excretion from the kidneys as a means of addressing the neurological impacts of 4EP.

Discovery of Novel Carboxamide Derivatives Containing Biphenyl Pharmacophore as Potential Fungicidal Agents Used for Resistance Management

Natural products are one of the main sources of drug and agrochemicals discovery. Biphenyls skeleton are ubiquitous structures in many classes of natural products, which indicate extensive biological activities. So, in order to investigate the potential applications for natural biphenyl derivatives, a series of novel carboxamide derivatives with diverse substituent patterns were designed and synthesized based on active pharmacophore from natural biphenyl lignans, and their in vitro antifungal activities against several typical plant pathogens belonging to oomycetes, ascomycete, deuteromycetes, and basidiomycetes were fully investigated. The highly potential compounds were further tested in vivo assay against Botrytis cinerea Pers. of cucumber to demonstrate a practical application for controlling common plant diseases, which indicated four compounds could effectively control the resistant strains of carbendazim, rutamycin, and pyrazolidide. The potential modes of action for compound B12 against B. cinerea were also explored using molecular docking, microscopic technology, and label-free quantitative proteomics analysis. The results show that compound B12 may be a potential novel fungicidal agent used for gray mold resistance control, which can influence the protein synthesis of B. cinerea. These findings can provide a certain theoretical basis for the development of novel biphenyl derivatives as potential green antifungal agents.

The biological functions and metabolic pathways of valine in swine

Valine is an essential amino acid and a type of branched-chain amino acid. Due to the involvement of branched-chain amino acids in various metabolic pathways, there has been a surge of interests in valine nutrition and its role in animal physiology. In pigs, the interactions between valine and other branched-chain amino acids or aromatic amino acids are complex. In this review, we delve into the interaction mechanism, metabolic pathways, and biological functions of valine. Appropriate valine supplementation not only enhances growth and reproductive performances, but also modulates gut microbiota and immune functions. Based on past observations and interpretations, we provide recommended feed levels of valine for weaned piglets, growing pigs, gilts, lactating sows, barrows and entire males. The summarized valine nutrient requirements for pigs at different stages offer valuable insights for future research and practical applications in animal husbandry.

Exogenous nanoselenium alleviates imidacloprid-induced oxidative stress toxicity by improving phenylpropanoid metabolism and antioxidant defense system in Perilla frutescens (L.) Britt

Few studies have been conducted to investigate the impact of pesticides on the secondary metabolism of traditional Chinese medicine and strategies to mitigate the toxicity of pesticide-induced oxidative stress. The current study focuses on evaluating the potential impacts of nano selenium (NSe) and imidacloprid (IMI) on the quality, physiological biochemistry, and secondary metabolites in Perilla frutescens (L.) Britt. (P. frutescens). The study utilized metabolome analysis to explore the toxicity mechanism of IMI. The study noted that IMI-induced stress could emerge with detrimental effects by targeting the destruction of the phenylpropanoid biosynthesis pathway. IMI-induced phenylpropanoid metabolism disorder resulted in an 8%, 17%, 25%, 10%, 65%, and 29% reduction in phenylalanine, coniferyl aldehyde, ferulic acid, cafestol, p-coumaraldehyde, and p-coumaric acid levels, respectively. Under the treatment of exogenous NSe, the levels of these metabolites were increased by 16%, 32%, 22%, 22%, 92%, and 29%, respectively. The application of exogenous NSe increased the levels of these metabolites and improved the biochemical disorder and quality of P. frutescens leaves by optimizing the phenylpropanoid metabolic pathway and enhancing the antioxidant system. Overall, the results suggest that foliar application of NSe could alleviate the oxidative stress toxicity induced by IMI and improve the quality of P. frutescens.

Raman spectroscopy and mass spectrometry identifies a unique group of epidermal lipids in active discoid lupus erythematosus

Discoid lupus erythematosus (DLE) is the most common form of cutaneous lupus1. It can cause permanent scarring. The pathophysiology of is not fully understood. Plasmacytoid dendritic cells are found in close association with apoptotic keratinocytes inferring close cellular signalling. Matrix Associated Laser Desorption Ionisation (MALDI) combined with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) is an exquisitely sensitive combination to examine disease processes at the cellular and molecular level. Active areas of discoid lupus erythematosus were compared with normal perilesional skin using MALDI combined with FT-ICR-MS. A unique set of biomarkers, including epidermal lipids is identified in active discoid lupus. These were assigned as sphingomyelins, phospholipids and ceramides. Additionally, increased levels of proteins from the keratin, and small proline rich family, and aromatic amino acids (tryptophan, phenylalanine, and tyrosine) in the epidermis are observed. These techniques, applied to punch biopsies of the skin, have shown a distinctive lipid profile of active discoid lupus. This profile may indicate specific lipid signalling pathways. Lipid rich microdomains (known as lipid rafts) are involved in cell signalling and lipid abnormalities have been described with systemic lupus erythematosus which correlate with disease activity.

Metabolomic Signatures of Alzheimer's Disease Indicate Brain Region-Specific Neurodegenerative Progression

Pathological mechanisms contributing to Alzheimer's disease (AD) are still elusive. Here, we identified the metabolic signatures of AD in human post-mortem brains. Using 1H NMR spectroscopy and an untargeted metabolomics approach, we identified (1) metabolomic profiles of AD and age-matched healthy subjects in post-mortem brain tissue, and (2) region-common and region-unique metabolome alterations and biochemical pathways across eight brain regions revealed that BA9 was the most affected. Phenylalanine and phosphorylcholine were mainly downregulated, suggesting altered neurotransmitter synthesis. N-acetylaspartate and GABA were upregulated in most regions, suggesting higher inhibitory activity in neural circuits. Other region-common metabolic pathways indicated impaired mitochondrial function and energy metabolism, while region-unique pathways indicated oxidative stress and altered immune responses. Importantly, AD caused metabolic changes in brain regions with less well-documented pathological alterations that suggest degenerative progression. The findings provide a new understanding of the biochemical mechanisms of AD and guide biomarker discovery for personalized risk prediction and diagnosis.

Melanin: a unifying theory of disease as exemplified by Parkinson's, Alzheimer's, and Lewy body dementia

Melanin, a ubiquitous dark pigment, plays important roles in the immune system, including scavenging reactive oxygen species formed in response to ultraviolet radiation absorption, absorbing metals, thermal regulation, drug uptake, innate immune system functions, redox, and energy transduction. Many tissue types, including brain, heart, arteries, ovaries, and others, contain melanin. Almost all cells contain precursors to melanin. A growing number of diseases in which there is a loss of melanin and/or neuromelanin are increasingly thought to have infectious etiologies, for example, Alzheimer's disease (AD), Parkinson's disease (PD), Lewy Body Dementia (LBD), and vitiligo. AD, PD, LBD, and vitiligo have been linked with herpesvirus, which enters melanosomes and causes apoptosis, and with gut dysbiosis and inflammation. Herpesvirus is also linked with gut dysbiosis and inflammation. We theorize that under normal healthy states, melanin retains some of the energy it absorbs from electromagnetic radiation, which is then used to fuel cells, and energy from ATP is used to compliment that energy supply. We further theorize that loss of melanin reduces the energy supply of cells, which in the case of AD, PD, and LBD results in an inability to sustain immune system defenses and remove the plaques associated with the disease, which appear to be part of the immune system's attempt to eradicate the pathogens seen in these neurodegenerative diseases. In addition, in an attempt to explain why removing these plaques does not result in improvements in cognition and mood and why cognitions and moods in these individuals have ebbs and flows, we postulate that it is not the plaques that cause the cognitive symptoms but, rather, inflammation in the brain resulting from the immune system's response to pathogens. Our theory that energy retained in melanin fuels cells in an inverse relationship with ATP is supported by studies showing alterations in ATP production in relationship to melanin levels in melanomas, vitiligo, and healthy cells. Therefore, alteration of melanin levels may be at the core of many diseases. We propose regulating melanin levels may offer new avenues for treatment development.

Heat hardening enhances metabolite-driven thermoprotection in the Mediterranean mussel Mytilus galloprovincialis

Introduction: Temperature affects organisms' metabolism and ecological performance. Owing to climate change, sea warming constituting a severe source of environmental stress for marine organisms, since it increases at alarming rates. Rapid warming can exceed resilience of marine organisms leading to fitness loss and mortality. However, organisms can improve their thermal tolerance when briefly exposed to sublethal thermal stress (heat hardening), thus generating heat tolerant phenotypes. Methods: We investigated the "stress memory" effect caused by heat hardening on M. galloprovincialis metabolite profile of in order to identify the underlying biochemical mechanisms, which enhance mussels' thermal tolerance. Results: The heat hardening led to accumulation of amino acids (e.g., leucine, isoleucine and valine), including osmolytes and cytoprotective agents with antioxidant and anti-inflammatory properties that can contribute to thermal protection of the mussels. Moreover, proteolysis was inhibited and protein turnover regulated by the heat hardening. Heat stress alters the metabolic profile of heat stressed mussels, benefiting the heat-hardened individuals in increasing their heat tolerance compared to the non-heat-hardened ones. Discussion: These findings provide new insights in the metabolic mechanisms that may reinforce mussels' tolerance against thermal stress providing both natural protection and potential manipulative tools (e.g., in aquaculture) against the devastating climate change effects on marine organisms.

Comprehensive metabolomics and transcriptomics analysis reveals protein and amino acid metabolic characteristics in liver tissue under chronic hypoxia

At high altitudes, oxygen deprivation can cause pathophysiological changes. Liver tissue function is known to impact whole-body energy metabolism; however, how these functions are affected by chronic hypoxia remains unclear. We aimed to elucidate changing characteristics underlying the effect of chronic hypoxia on protein and amino acid metabolism in mouse livers. Mice were maintained in a hypobaric chamber simulating high altitude for 4 weeks. Livers were collected for metabolomic analysis via ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry. For transcriptomics analysis, we conducted RNA sequencing of hepatic tissues followed by Gene Ontology and KEGG pathway enrichment analyses. Chronic hypoxic exposure caused metabolic disorders of amino acids and their derivatives in liver tissue. We identified a number of metabolites with significantly altered profiles (including amino acids, peptides, and analogues), of which serine, phenylalanine, leucine, proline, aspartic acid, L-glutamate, creatine, 5-aminovaleric acid, L-hydroxyarginin, and g-guanidinobutyrate showed great potential as biomarkers of chronic hypoxia. A total of 2124 genes with significantly different expression levels were identified in hypoxic liver tissue, of which 1244 were upregulated and 880 were downregulated. We found pathways for protein digestion and absorption, arginine and proline metabolism, and mineral absorption related to amino acid metabolism were affected by hypoxia. Our findings surrounding the regulation of key metabolites and differentially expressed genes provide new insights into changes in protein and amino acid metabolism in the liver that result from chronic hypoxia.

Identification and Expression Analysis of EPSPS and BAR Families in Cotton

Weeds seriously affect the yield and quality of crops. Because manual weeding is time-consuming and laborious, the use of herbicides becomes an effective way to solve the harm caused by weeds in fields. Both 5-enolpyruvyl shikimate-3-phosphate synthetase (EPSPS) and acetyltransferase genes (bialaphos resistance, BAR) are widely used to improve crop resistance to herbicides. However, cotton, as the most important natural fiber crop, is not tolerant to herbicides in China, and the EPSPS and BAR family genes have not yet been characterized in cotton. Therefore, we explore the genes of these two families to provide candidate genes for the study of herbicide resistance mechanisms. In this study, 8, 8, 4, and 5 EPSPS genes and 6, 6, 5, and 5 BAR genes were identified in allotetraploid Gossypium hirsutum and Gossypium barbadense, diploid Gossypium arboreum and Gossypium raimondii, respectively. Members of the EPSPS and BAR families were classified into three subgroups based on the distribution of phylogenetic trees, conserved motifs, and gene structures. In addition, the promoter sequences of EPSPS and BAR family members included growth and development, stress, and hormone-related cis-elements. Based on the expression analysis, the family members showed tissue-specific expression and differed significantly in response to abiotic stresses. Finally, qRT-PCR analysis revealed that the expression levels of GhEPSPS3, GhEPSPS4, and GhBAR1 were significantly upregulated after exogenous spraying of herbicides. Overall, we characterized the EPSPS and BAR gene families of cotton at the genome-wide level, which will provide a basis for further studying the functions of EPSPS and BAR genes during growth and development and herbicide stress.

Enzymatic synthesis of halogen derivatives of L-phenylalanine and phenylpyruvic acid stereoselectively labeled with hydrogen isotopes in the side chain

Halogenated, labeled with deuterium, tritium or doubly labeled with deuterium and tritium in the 3S position of the side chain isotopomers of L-phenylalanine and phenylpyruvic acid were synthesized. Isotopomers of halogenated L-phenylalanine were obtained by addition of ammonia from isotopically enriched buffer solution to the halogenated derivative of (E)-cinnamic acid catalyzed by phenylalanine ammonia lyase. Isotopomers of halogenated phenylpyruvic acid were obtained enzymatically by conversion of the appropriate isotopomer of halogenated L-phenylalanine in the presence of phenylalanine dehydrogenase. As a source of deuterium was used deuterated water, as a source of tritium was used a solution of highly diluted tritiated water. The labeling takes place in good yields and with high deuterium atom% abundance.

Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method

Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.

Primary Metabolite Screening Shows Significant Differences between Embryogenic and Non-Embryogenic Callus of Tamarillo (Solanum betaceum Cav.)

Tamarillo is a solanaceous tree that has been extensively studied in terms of in vitro clonal propagation, namely somatic embryogenesis. In this work, a protocol of indirect somatic embryogenesis was applied to obtain embryogenic and non-embryogenic callus from leaf segments. Nuclear magnetic resonance spectroscopy was used to analyze the primary metabolome of these distinct calli to elucidate possible differentiation mechanisms from the common genetic background callus. Standard multivariate analysis methods were then applied, and were complemented by univariate statistical methods to identify differentially expressed primary metabolites and related metabolic pathways. The results showed carbohydrate and lipid metabolism to be the most relevant in all the calli assayed, with most discriminant metabolites being fructose, glucose and to a lesser extent choline. The glycolytic rate was higher in embryogenic calli, which shows, overall, a higher rate of sugar catabolism and a different profile of phospholipids with a choline/ethanolamine analysis. In general, our results show that a distinct primary metabolome between embryogenic and non-embryogenic calli occurs and that intracellular levels of fructose and sucrose and the glucose to sucrose ratio seem to be good candidates as biochemical biomarkers of embryogenic competence.

Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato

Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring in tomato interacting with the beneficial fungus Beauveria bassiana. The tomato leaf proteome revealed perturbed molecular pathways during the establishment of the plant-fungus relationship. In the early stages of colonization (5-7 d), proteins related to defense responses to the fungus were down-regulated and proteins related to calcium transport were up-regulated. At later time points (12-19 d after colonization), up-regulation of molecular pathways linked to protein/amino acid turnover and to biosynthesis of energy compounds suggests beneficial interaction enhancing plant growth and development. At the later stage, the profile of leaf hormones and related compounds was also investigated, highlighting up-regulation of those related to plant growth and defense. Finally, B. bassiana colonization was found to improve plant resistance to Botrytis cinerea, impacting plant oxidative damage. Overall, our findings further expand current knowledge on the possible mechanisms underlying the beneficial role of B. bassiana in tomato plants.

Proteome of Agave angustifolia Haw.: Uncovering metabolic alterations, over-accumulation of amino acids, and compensatory pathways in chloroplast-deficient albino plantlets

Amino acids (AA) are essential molecules for plant physiology, acting as precursor molecules for proteins and other organic compounds. Chloroplasts play a vital role in AA metabolism, yet little is known about the impact on AA metabolism of albino plants' lack of chloroplasts. In this study, we conducted a quantitative proteome analysis on albino and variegated somaclonal variants of Agave angustifolia Haw. to investigate metabolic alterations in chloroplast-deficient plants, with a focus on AA metabolic pathways. We identified 82 enzymes involved in AA metabolism, with 32 showing differential accumulation between the somaclonal variants. AaCM, AaALS, AaBCAT, AaIPMS1, AaSHMT, AaAST, AaCGS, and AaMS enzymes were particularly relevant in chloroplast-deficient Agave plantlets. Both variegated and albino phenotypes exhibited excessive synthesis of AA typically associated with chloroplasts (aromatic AAs, BCAAs, Asp, Lys, Pro and Met). Consistent trends were observed for AaBCAT and AaCM at mRNA and protein levels in albino plantlets. These findings highlight the critical activation and reprogramming of AA metabolic pathways in plants lacking chloroplasts. This study contributes to unraveling the intricate relationship between AA metabolism and chloroplast absence, offering insights into survival mechanisms of albino plants.

Organic amendments alter microbiota assembly to stimulate soil metabolism for improving soil quality in wheat-maize rotation system

Straw retention (SR) and organic fertilizer (OF) application contribute to improve soil quality, but it is unclear how the soil microbial assemblage under organic amendments mediate soil biochemical metabolism pathways to perform it. This study collected soil samples from wheat field under different application of fertilizer (chemical fertilizer, as control; SR, and OF) in North China Plain, and systematically investigated the interlinkages among microbe assemblages, metabolites, and physicochemical properties. Results showed that the soil organic carbon (SOC) and permanganate oxidizable organic carbon (LOC) in soil samples followed the trend as OF > SR > control, and the activity of C-acquiring enzymes presented significantly positive correlation with SOC and LOC. In organic amendments, bacteria and fungi community were respectively dominated by deterministic and stochastic processes, while OF exerted more selective pressure on soil microbe. Compared with SR, OF had greater potential to boost the microbial community robustness through increasing the natural connectivity and stimulating fungal taxa activities in inter-kingdom microbial networks. Altogether 67 soil metabolites were significantly affected by organic amendments, most of them belonged to benzenoids (Ben), lipids and lipid-like molecules (LL), and organic acids and derivatives (OA). These metabolites were mainly derived from lipid and amino acid metabolism pathways. A list of keystone genera such as stachybotrys and phytohabitans were identified as important to soil metabolites, SOC, and C-acquiring enzyme activity. Structural equation modeling showed that soil quality properties were closely associated with LL, OA, and PP drove by microbial community assembly and keystone genera. Overall, these findings suggested that straw and organic fertilizer might drive keystone genera dominated by determinism to mediate soil lipid and amino acid metabolism for improving soil quality, which provided new insights into understanding the microbial-mediated biological process in amending soil quality.

Multi-stage nuclear transcriptomic insights of morphogenesis and biparental role changes in Lentinula edodes

Based on six offspring with different mitochondrial (M) and parental nuclear (N) genotypes, the multi-stage morphological characteristics and nuclear transcriptomes of Lentinula edodes were compared to investigate morphogenesis mechanisms during cultivation, the key reason for cultivar resistance to genotype changes, and regulation related to biparental role changes. Six offspring had specific transcriptomic data and morphological characteristics that were mainly regulated by the two parental nuclei, followed by the cytoplasm, at different growth stages. Importing a wild N genotype easily leads to failure or instability of fruiting; however, importing wild M genotypes may improve cultivars. Major facilitator superfamily (MFS) transporter genes encoding specific metabolites in spawns may play crucial roles in fruiting body formation. Pellets from submerged cultivation and spawns from sawdust substrate cultivation showed different carbon metabolic pathways, especially in secondary metabolism, degradation of lignin, cellulose and hemicellulose, and plasma membrane transport (mainly MFS). When the stage of small young pileus (SYP) was formed on the surface of the bag, the spawns inside were mainly involved in nutrient accumulation. Just broken pileus (JBP) showed a different expression of plasma membrane transporter genes related to intracellular material transport compared to SYP and showed different ribosomal proteins and cytochrome P450 functioning in protein biosynthesis and metabolism than near spreading pileus (NSP). Biparental roles mainly regulate offspring metabolism, growth, and morphogenesis by differentially expressing specific genes during different vegetative growth stages. Additionally, some genes encoding glycine-rich RNA-binding proteins, F-box, and folliculin-interacting protein repeat-containing proteins may be related to multi-stage morphogenesis. KEY POINTS: • Replacement of nuclear genotype is not suitable for cultivar breeding of L. edodes. • Some genes show a biparental role-divergent expression at mycelial growth stage. • Transcriptomic changes of some sawdust substrate cultivation stages have been elucidated.

Comparative Transcriptomics of Multi-Stress Responses in Pachycladon cheesemanii and Arabidopsis thaliana

The environment is seldom optimal for plant growth and changes in abiotic and biotic signals, including temperature, water availability, radiation and pests, induce plant responses to optimise survival. The New Zealand native plant species and close relative to Arabidopsis thaliana, Pachycladon cheesemanii, grows under environmental conditions that are unsustainable for many plant species. Here, we compare the responses of both species to different stressors (low temperature, salt and UV-B radiation) to help understand how P. cheesemanii can grow in such harsh environments. The stress transcriptomes were determined and comparative transcriptome and network analyses discovered similar and unique responses within species, and between the two plant species. A number of widely studied plant stress processes were highly conserved in A. thaliana and P. cheesemanii. However, in response to cold stress, Gene Ontology terms related to glycosinolate metabolism were only enriched in P. cheesemanii. Salt stress was associated with alteration of the cuticle and proline biosynthesis in A. thaliana and P. cheesemanii, respectively. Anthocyanin production may be a more important strategy to contribute to the UV-B radiation tolerance in P. cheesemanii. These results allowed us to define broad stress response pathways in A. thaliana and P. cheesemanii and suggested that regulation of glycosinolate, proline and anthocyanin metabolism are strategies that help mitigate environmental stress.

Whole-transcriptome RNA sequencing reveals changes in amino acid metabolism induced in harvested broccoli by red LED irradiation

Whole-transcriptomic profiling combined with amino acid analysis were conducted in order to gain a better understanding of global changes in amino acid metabolism induced in broccoli by red LED irradiation. The results showed that the contents of almost all 16 amino acids in postharvest broccoli were maintained under red LED illumination. The red LED irradiation enhanced the anabolism of amino acid, including the biosynthesis of aromatic amino acids by upregulating the genes' expression in the shikimate pathway, as well as by upregulating the genes' expression which encoding biosynthetic enzymes in the branched-chain amino acid biosynthesis pathway. Red LED irradiation induced the expression of genes encoding aspartate aminotransferase, which plays a role in Asp synthesis, aspartate kinase, which functions in aspartate metabolism, and a cytoplasmic aspartate aminotransferase that converts 2-Oxoglutarate into Glu. Genes encoding imidazole glycerol-phosphate synthase and histidinol-phosphatase, which function in the His biosynthesis pathway, were also upregulated. According to our results, red LED irradiation delays broccoli's yellowing and senescence by regulating amino acid metabolism. These results enhance our understanding of the role of amino acid metabolism in the senescence of broccoli and the mechanism of red LED irradiation to alter amino acid metabolism in harvested broccoli.

Response of Fragaria vesca to projected change in temperature, water availability and concentration of CO2 in the atmosphere

The high rate of climate change may soon expose plants to conditions beyond their adaptation limits. Clonal plants might be particularly affected due to limited genotypic diversity of their populations, potentially decreasing their adaptability. We therefore tested the ability of a widely distributed predominantly clonally reproducing herb (Fragaria vesca) to cope with periods of drought and flooding in climatic conditions predicted to occur at the end of the twenty-first century, i.e. on average 4 °C warmer and with twice the concentration of CO2 in the air (800 ppm) than the current state. We found that F. vesca can phenotypically adjust to future climatic conditions, although its drought resistance may be reduced. Increased temperature and CO2 levels in the air had a far greater effect on growth, phenology, reproduction, and gene expression than the temperature increase itself, and promoted resistance of F. vesca to repeated flooding periods. Higher temperature promoted clonal over sexual reproduction, and increased temperature and CO2 concentration in the air triggered change in expression of genes controlling the level of self-pollination. We conclude that F. vesca can acclimatise to predicted climate change, but the increased ratio of clonal to sexual reproduction and the alteration of genes involved in the self-(in)compatibility system may be associated with reduced genotypic diversity of its populations, which may negatively impact its ability to genetically adapt to novel climate in the long-term.

Comparative Analysis of Water Extracts from Roselle (Hibiscus sabdariffa L.) Plants and Callus Cells: Constituents, Effects on Human Skin Cells, and Transcriptome Profiles

Roselle (Hibiscus sabdariffa L.) is a plant that has traditionally been used in various food and beverage products. Here, we investigated the potential of water extracts derived from Roselle leaves and callus cells for cosmetic and pharmaceutical purposes. We generated calluses from Roselle leaves and produced two different water extracts through heat extraction, which we named Hibiscus sabdariffa plant extract (HSPE) and Hibiscus sabdariffa callus extract (HSCE). HPLC analysis showed that the two extracts have different components, with nucleic acids and metabolites such as phenylalanine and tryptophan being the most common components in both extracts. In vitro assays demonstrated that HSCE has strong anti-melanogenic effects and functions for skin barrier and antioxidant activity. Transcriptome profiling of human skin cells treated with HSPE and HSCE showed significant differences, with HSPE having more effects on human skin cells. Up-regulated genes by HSPE function in angiogenesis, the oxidation-reduction process, and glycolysis, while up-regulated genes by HSCE encode ribosome proteins and IFI6, functioning in the healing of radiation-injured skin cells. Therefore, we suggest that the two extracts from Roselle should be applied differently for cosmetics and pharmaceutical purposes. Our findings demonstrate the potential of Roselle extracts as a natural source for skincare products.

The Effects of Temperature and Humidity Index on Growth Performance, Colon Microbiota, and Serum Metabolome of Ira Rabbits

This study investigates the effects of different THI values on growth performance, intestinal microbes, and serum metabolism in meat rabbits. The results showed that there were significant differences in THI in different location regions of the rabbit house. The high-THI group (HG) could significantly reduce average daily gain and average daily feed intake in Ira rabbits (p < 0.05). The low-THI group (LG) significantly increased the relative abundance of Blautia (p < 0.05). The HG significantly increased the relative abundance of Lachnospiraceae NK4A136 group and reduced bacterial community interaction (p < 0.05). The cytokine-cytokine receptor interactions, nuclear factor kappa B signaling pathway, and toll-like receptor signaling pathway in each rabbit's gut were activated when the THI was 26.14 (p < 0.05). Metabolic pathways such as the phenylalanine, tyrosine, and tryptophan biosynthesis and phenylalanine metabolisms were activated when the THI was 27.25 (p < 0.05). Meanwhile, the TRPV3 and NGF genes that were associated with heat sensitivity were significantly upregulated (p < 0.05). In addition, five metabolites were found to be able to predict THI levels in the environment with an accuracy of 91.7%. In summary, a THI of 26.14 is more suitable for the growth of meat rabbits than a THI of 27.25, providing a reference for the efficient feeding of meat rabbits.

Metabolite profiling of susceptible and resistant wheat (Triticum aestivum) cultivars responding to Puccinia striiformis f. sp. tritici infection

BACKGROUND

Puccinia striiformis f. sp. tritici (Pst) is an economically devasting disease that is prominent in cereal crops such as wheat (Triticum aestivum). The fungal pathogen can cause approximately 30-70% losses in crop productivity and yields. Pst has become difficult to manage due to its ease of transmission through wind dispersal over long distances, and intercontinental dispersal has been previously reported. The ease of transmission has resulted in further destruction because of new and more virulent strains infecting crops previously resistant to a different strain.

RESULTS

In this study, a liquid chromatography-mass spectrometry-based untargeted metabolomics approach, in combination with multivariate data analytical tools, was used to elucidate the mechanistic nature of the defence systems of a Pst-resistant and a susceptible wheat cultivar infected with P. striiformis. We also investigated the time-dependant metabolic reconfiguration of infected plants over a four-week period. The untargeted metabolomic analysis revealed a time-course metabolic reprogramming involving phenylpropanoids (majority flavonoids), amino acids, lipids, benzoic acids, TCA cycle intermediates and benzoxazinoids responding to Pst infection. Interestingly, the results do not show a linear course for the decrease and increase (up-/down-regulation) of said classes of metabolites, but rather the up- or down-regulation of specific metabolites in response to the pathogen infection. The resistant Koonap cultivar had an abundance of phenolic compounds such as rutin, isoorintin-7-O-glucoside and luteolin-6-C-hexoside-O-hexoside. These compounds showed a decrease over time in control Koonap plants compared to an increase in Pst-infected plants. These metabolites were down-regulated in the susceptible Gariep cultivar, which could serve as biomarkers for plant responses to biotic stress and resistance against Pst.

CONCLUSIONS

Overall, an LC-MS-based metabolomics approach allowed for the metabolic profiling and analysis of the impact of plant-pathogen interactions on the overall plant metabolome and provided a real-time snapshot of the differential significant metabolic perturbations occurring in wheat plants responding to the Pst pathogen. The Pst-resistant Koonap cultivar showed a rapid accumulation of defence metabolites in response to pathogen infection compared to the susceptible Gariep cultivar. These findings provide insight into the mechanistic biochemical nature of plant-microbe interactions and the prospects of metabolic engineering for improved plant tolerance and resistance to biotic stresses.

Cadmium stimulated cooperation between bacterial endophytes and plant intrinsic detoxification mechanism in Lonicera japonica thunb

Due to the intimate association between plant physiology and metabolism, the internal colonizing microbe (endophytes) community must be adjusted to support plant productivity in response to cell damage in plants under stress. However, how endophytes coordinate their activities with plant intrinsic mechanisms such as antioxidative systems and detoxification pathways during Cd accumulation remains unknown. In this hydroponic pot study, we investigated how exposure of Lonicera japonica. thunb. to different levels of Cd (0.5, 2.5, 5, 10, and 20 mg kg^-1) affected plant growth, metabolic pathways, and endophyte community structure and function. Although Cd accumulation increased at 5 mg kg^-1 Cd, the biomass and height of L. japonica increased in association with elevated endophyte-involved plant detoxification activities. Endophytes, such as Sphingomonas, Klenkia, and Modestobacter, expressed major antioxidative regulators (superoxide dismutase and ascorbate acid) to detoxify Cd in L. japonica. Furthermore, L. japonica and its endophytes synergistically regulated the toxic effects of Cd accumulation via multiple plant metabolic defensive pathways to increase resistance to metal-induced stress.

Metabolomics and Network Analyses Reveal Phenylalanine and Tyrosine as Signatures of Anthracycline-Induced Hepatotoxicity

The chemotherapy drug doxorubicin (DOX) is an anthracycline with over 30% incidence of liver injury in breast cancer patients, yet the mechanism of its hepatotoxicity remains unclear. To identify potential biomarkers for anthracycline-induced hepatotoxicity (AIH), we generated clinically-relevant mouse and rat models administered low-dose, long-term DOX. These models exhibited significant liver damage but no decline in cardiac function. Through untargeted metabolic profiling of the liver, we identified 27 differential metabolites in a mouse model and 28 in a rat model. We then constructed a metabolite-metabolite network for each animal model and computationally identified several potential metabolic markers, with particular emphasis on aromatic amino acids, including phenylalanine, tyrosine, and tryptophan. We further performed targeted metabolomics analysis on DOX-treated 4T1 breast cancer mice for external validation. We found significant (p < 0.001) reductions in hepatic levels of phenylalanine and tyrosine (but not tryptophan) following DOX treatment, which were strongly correlated with serum aminotransferases (ALT and AST) levels. In summary, the results of our study present compelling evidence supporting the use of phenylalanine and tyrosine as metabolic signatures of AIH.

Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids

Essential aromatic amino acids (AAAs) are building blocks for synthesizing new biomasses in cells and sustaining normal biological functions. For example, an abundant supply of AAAs is important for cancer cells to maintain their rapid growth and division. With this, there is a rising demand for a highly specific, noninvasive imaging approach with minimal sample preparation to directly visualize how cells harness AAAs for their metabolism in situ. Here, we develop an optical imaging platform that combines deuterium oxide (D2O) probing with stimulated Raman scattering (DO-SRS) and integrates DO-SRS with two-photon excitation fluorescence (2PEF) into a single microscope to directly visualize the metabolic activities of HeLa cells under AAA regulation. Collectively, the DO-SRS platform provides high spatial resolution and specificity of newly synthesized proteins and lipids in single HeLa cell units. In addition, the 2PEF modality can detect autofluorescence signals of nicotinamide adenine dinucleotide (NADH) and Flavin in a label-free manner. The imaging system described here is compatible with both in vitro and in vivo models, which is flexible for various experiments. The general workflow of this protocol includes cell culture, culture media preparation, cell synchronization, cell fixation, and sample imaging with DO-SRS and 2PEF modalities.

Rapid and selective colorimetric determination of L-DOPA in human serum with silver nanoparticles

L-DOPA, or l-3,4-dihydroxyphenylalanine is an aromatic amino acid, which plays a significant role in human metabolism as a precursor of important neurotransmitters. We develop a fast and simple colorimetric method for the detection of L-DOPA in biological fluids. The method is based on the reduction of silver ions with L-DOPA and the subsequent formation of L-DOPA stabilized silver nanoparticles (Ag NPs). In this novel approach, L-DOPA works as both reducing and stabilizing agent, which provides selectivity and simplifies the procedure. HR-TEM images show very narrow Ag NPs distribution with an average size of 24 nm. Such sensor design is suggested for the first time. We also calculate vertical ionization potential, vertical electron affinity, and Gibbs free energy change of different ionic forms of L-DOPA and amino acids at the M06-2X/def2-TZVP level for the gas phase in comparison with that of silver. A model of silver ions reduction by aromatic amino acids is proposed: the ionic forms with charge -1 are suggested to reduce silver ions. High selectivity against aromatic amino acids, dopamine and serotonin is achieved by tuning pH and involving two L-DOPA forms with charged both hydroxyphenolate and carboxylate groups in the stabilization of uniform-sized Ag NPs. The method is applicable for the determination of L-DOPA in human serum with the 50 nM limit of detection and the linear range up to 5 μM. Ag NPs formation and coloring the solution proceeds in a few minutes. The suggested colorimetric method has potential application in clinical trials.

Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium

The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl⁺ and CdCl⁺, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl⁺(Phe), CdCl⁺(Phe), ZnCl⁺(Tyr), CdCl⁺(Tyr), and ZnCl⁺(Trp) species were examined because the CdCl⁺(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl⁺(Phe) and MCl⁺(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl⁺(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.

Innova 2020: A Follow-Up Study of the Fecal Microbiota of Infants Using a Novel Infant Formula between 6 Months and 12 Months of Age

The World Health Organization recommends exclusive breastfeeding on demand until at least the sixth month of life. Breast milk or infant formula is the infant's primary food source until the age of one year, followed by the gradual introduction of other foods. During weaning, the intestinal microbiota evolves to a profile close to that of the adult, and its disruption can result in an increased incidence of acute infectious diseases. We aimed to determine whether a novel starting formula (INN) provides gut microbiota compositions more similar to those of breastfed (BF) infants from 6 to 12 months of age compared to a standard formula (STD). This study included 210 infants (70 per group) who completed the intervention until they reached the age of 12 months. In the intervention period, infants were divided into three groups. Group 1 received an INN formula with a lower protein content, a casein to whey protein ratio of approximately 70/30, twice as much docosahexaenoic acid as the STD formula, a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis, BPL1TM HT), and twice as much arachidonic acid as the STD formula contained. The second group received the STD formula, while the third group was exclusively BF for exploratory purposes. In the course of the study, visits were conducted at 6 months and 12 months of age. Compared to the BF and STD groups, the Bacillota phylum levels in the INN group were significantly reduced after 6 months. At the end of 6 months, the alpha diversity indices of the BF and INN groups differed significantly from those of the STD group. At 12 months, the Verrucomicrobiota phylum levels in the STD group were significantly lower than those in the BF and INN groups. Based on the comparison between 6 and 12 months, the Bacteroidota phylum levels in the BF group were significantly higher than those in the INN and STD groups. When comparing the INN group with the BF and STD groups, Clostridium sensu stricto 1 was significantly higher in the INN group. The STD group had higher levels of calprotectin than the INN and BF groups at 6 months. The immunoglobulin A levels in the STD group were significantly lower than those in the INN and BF groups after 6 months. Both formulas had significantly higher levels of propionic acid than the BF group at 6 months. At 6 months, the STD group showed a higher quantification of all metabolic pathways than the BF group. The INN formula group exhibited similar behavior to the BF group, except for the superpathway of phospholipid biosynthesis (E. coli). We hypothesize that the novel INN formula may promote an intestinal microbiota that is more similar to the microbiota of an infant who consumes only human milk before the weaning period.

A comparative transcriptome analysis of the head of 1 and 9 days old worker honeybees (Apis mellifera)

The role of bees in the environment, economic, biodiversity and pharmaceutical industries is due to its social behavior, which is oriented from the brain and hypopharyngeal gland that is the center of royal jelly (RJ) production. Limited studies have been performed on the head gene expression profile at the RJ production stage. The aim of this study was to compare the gene expressions in 9 and 1-day-old (DO) honeybee workers in order to achieve better understanding about head gene expression pattern. After sequencing of RNAs, transcriptome and their networks were compared. The head expression profile undergoes various changes. 1662 gene transcripts had differential expressions which 1125 and 537 were up and down regulated, respectively, in 9_DO compared with 1_DO honey bees. The day 1th had more significant role in the expression of genes related to RJ production as major RJ protein 1, 2, 3, 5, 6 and 9 encoding genes, but their maximum secretion occurred at day 9th. All process related to hypopharyngeal glands activities as CYP450 gene, fatty acid synthase gene, vitamin B6 metabolism and some of genes involved in fatty acid elongation and degradation process had an upward trend from 1_DO and were age-dependent. By increasing the age, the activity of pathways related to immune system increased for keeping the health of bees against the chemical compound. The expression of aromatic amino acid genes involved in Phenylalanine, tyrosine and tryptophan biosynthesis pathway are essential for early stage of life. In 9_DO honeybees, the energy supplying, reducing stress, protein production and export pathways have a crucial role for support the body development and the social duties. It can be stated that the activity of honeybee head is focused on energy supply instead of storage, while actively trying to improve the level of cell dynamics for increasing the immunity and reducing stress. Results of current study identified key genes of certain behaviors of honeybee workers. Deeper considering of some pathways will be evaluated in future studies.

The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests

Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.

Metabolomic analysis of seminal plasma to identify goat semen freezability markers

Factors affecting sperm freezability in goat seminal plasma were investigated. Based on the total motility of thawed sperm, goats were divided into a high-freezability (HF) group with >60% total motility (n = 8) and a low-freezability (LF) group with <45% total motility (n = 8). Sperm and seminal plasma from the HF and LF groups were separated, HF seminal plasma was mixed with LF spermatozoa, LF seminal plasma was mixed with HF sperm, and the products were subjected to a freeze-thaw procedure. Semen from individual goats exhibited differences in freezability. HF semen had higher sperm motility parameters and plasma membrane and acrosome integrity after thawing; this difference could be related to the composition of seminal plasma. Seminal plasma from the HF and LF groups was evaluated using metabolomic analysis, and multivariate statistical analysis revealed a clear separation of metabolic patterns in the seminal plasma of goats with different freezability classifications. Forty-one differential metabolites were identified using the following screening conditions: variable importance in the projection > 1 and 0.05 < P-value < 0.1. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed significant enrichment of central carbon metabolism in cancer, protein digestion and absorption, aminoacyl-tRNA, and other pathways and significant differences in the abundance of seven differential metabolites, including L-glutamine, L-aspartate, L-arginine, phenylpyruvate, benzoic acid, ketoisocaproic acid, and choline between seminal plasma from the HF and LF groups (P-value < 0.05). These significantly differentially-expressed metabolites may be potential biomarkers for sperm freezability. L-glutamine, L-aspartate, and L-arginine may directly affect sperm freezability. Benzoic acid, ketoisocaproic acid, and choline may regulate sperm freezability by participating in anabolic processes involving phenylalanine, leucine, and phosphatidylcholine in sperm.

Antimicrobial Growth Promoters Altered the Function but Not the Structure of Enteric Bacterial Communities in Broiler Chicks ± Microbiota Transplantation

Non-antibiotic alternatives to antimicrobial growth promoters (AGPs) are required, and understanding the mode of action of AGPs may facilitate the development of effective alternatives. The temporal impact of the conventional antibiotic AGP, virginiamycin, and an AGP alternative, ceragenin (CSA-44), on the structure and function of the broiler chicken cecal microbiota was determined using next-generation sequencing and 1H-nuclear magnetic resonance spectroscopy (NMR)-based metabolomics. To elucidate the impact of enteric bacterial diversity, oral transplantation (±) of cecal digesta into 1-day-old chicks was conducted. Microbiota transplantation resulted in the establishment of a highly diverse cecal microbiota in recipient chicks that did not change between day 10 and day 15 post-hatch. Neither virginiamycin nor CSA-44 influenced feed consumption, weight gain, or feed conversion ratio, and did not affect the structure of the cecal microbiota in chicks possessing a low or high diversity enteric microbiota. However, metabolomic analysis of the cecal contents showed that the metabolome of cecal digesta was affected in birds administered virginiamycin and CSA-44 as a function of bacterial community diversity. As revealed by metabolomics, glycolysis-related metabolites and amino acid synthesis pathways were impacted by virginiamycin and CSA-44. Thus, the administration of AGPs did not influence bacterial community structure but did alter the function of enteric bacterial communities. Hence, alterations to the functioning of the enteric microbiota in chickens may be the mechanism by which AGPs impart beneficial health benefits, and this possibility should be examined in future research.

Identification of region-specific amino acid signatures for doxorubicin-induced chemo brain

Doxorubicin (DOX) is a cornerstone of chemotherapy for solid tumors and leukemias. DOX-induced cognitive impairment, termed chemo brain, has been reported in cancer survivors, whereas its mechanism remains poorly understood. Here we initially evaluated the cognitive impairments of mice treated with clinically relevant, long-term, low-dosage of DOX. Using HILIC-MS/MS-based targeted metabolomics, we presented the changes of 21 amino acids across six anatomical brain regions of mice with DOX-induced chemo brain. By mapping the altered amino acids to the human metabolic network, we constructed an amino acid-based network module for each brain region. We identified phenylalanine, tyrosine, methionine, and γ-aminobutyric acid as putative signatures of three regions (hippocampus, prefrontal cortex, and neocortex) highly associated with cognition. Relying on the reported mouse brain metabolome atlas, we found that DOX might perturb the amino acid homeostasis in multiple brain regions, similar to the changes in the aging brain. Correlation analysis suggested the possible indirect neurotoxicity of DOX that altered the brain levels of phenylalanine, tyrosine, and methionine by causing metabolic disorders in the liver and kidney. In summary, we revealed the region-specific amino acid signatures as actionable targets for DOX-induced chemo brain, which might provide safer treatment and improve the quality of life among cancer survivors.

Comparative untargeted metabolic analysis of natural- and laboratory-reared larvae of black soldier fly, Hermetia illucens (L.) (Diptera: Stratiomyidae)

In the present study, we examined the metabolic composition of black soldier fly (BSF) larvae from natural populations (Ruhama: R and She'ar Yashuv: S) and from a laboratory-reared colony (C) using untargeted metabolomics analysis. The results revealed significant over-accumulation of metabolites from phenylalanine and purine metabolism and biosynthesis of phenylalanine, tyrosine and tryptophan, and arginine in both natural populations, and enriched pathway analysis, compared to the laboratory-reared colony. In addition, we found accumulation of glutathione metabolism and aminoacyl tRNA biosynthesis related metabolites in R, and linoleic acid and tryptophan metabolism related metabolites in S. Moreover, we found down-accumulation of metabolites belonging to alanine, aspartate and glutamate metabolism in both natural populations: amino sugar and nucleotide sugar metabolism only in the R population and aminoacyl-tRNA biosynthesis, glyoxylate and dicarboxylate metabolism only in the S population. Overall, the results suggest that the naturally growing larvae require large quantities of metabolites from aromatic amino acids (phenylalanine, tyrosine and tryptophan) for defense against pathogens under natural conditions e.g., melanization. In addition, glutathione metabolites help the BSF to survive under oxidative stress. Further study of the functional metabolomics of naturally growing and laboratory-reared larvae could provide a platform for better understanding of BSF larval survival mechanisms in complex environments.

Preliminary insights on the metabolomics of Trichinella zimbabwensis infection in Sprague Dawley rats using GCxGC-TOF-MS (untargeted approach)

Trichinella infections have been documented globally and have been detected in wild and/or domestic animals except Antarctica. There is paucity of information in the metabolic responses of hosts during Trichinella infections and biomarkers for infection that can be used in the diagnosis of the disease. The current study aimed to apply a non-targeted metabolomic approach to identify Trichinella zimbabwensis biomarkers including metabolic response from sera of infected Sprague-Dawley rats. Fifty-four male Sprague-Dawley rats were randomly assigned into T. zimbabwensis infected group (n = 36) and the non-infected control (n = 18). Results from the study showed that the metabolic signature of T. zimbabwensis infection consists of enriched methyl histidine metabolism, disturbance of the liver urea cycle, impeded TCA cycle, and upregulation of gluconeogenesis metabolism. The observed disturbance in the metabolic pathways was attributed to the effects caused by the parasite during its migration to the muscles resulting in downregulation of amino acids intermediates in the Trichinella-infected animals, and therefore affecting energy production and degradation of biomolecules. It was concluded that T. zimbabwensis infection caused an upregulation of amino acids; pipecolic acid, histidine, and urea, and upregulation of glucose and meso-Erythritol. Moreover, T. zimbabwensis infection caused upregulation of the fatty acids, retinoic acid, and acetic acid. These findings highlight the potential of metabolomics as a novel approach for fundamental investigations of host-pathogen interactions as well as for disease progression and prognosis.

Glyphosate-based herbicide use affects individual microbial taxa in strawberry endosphere but not the microbial community composition

AIMS

In a field study, the effects of treatments of glyphosate-based herbicides (GBHs) in soil, alone and in combination with phosphate fertilizer, were examined on the performance and endophytic microbiota of garden strawberry.

METHODS AND RESULTS

The root and leaf endophytic microbiota of garden strawberries grown in GBH-treated and untreated soil, with and without phosphate fertilizer, were analyzed. Next, bioinformatics analysis on the type of 5-enolpyruvylshikimate-3-phosphate synthase enzyme was conducted to assess the potential sensitivity of strawberry-associated bacteria and fungi to glyphosate, and to compare the results with field observations. GBH treatments altered the abundance and/or frequency of several operational taxonomic units (OTUs), especially those of root-associated fungi and bacteria. These changes were partly related to their sensitivity to glyphosate. Still, GBH treatments did not shape the overall community structure of strawberry microbiota or affect plant performance. Phosphate fertilizer increased the abundance of both glyphosate-resistant and glyphosate-sensitive bacterial OTUs, regardless of the GBH treatments.

CONCLUSIONS

These findings demonstrate that although the overall community structure of strawberry endophytic microbes is not affected by GBH use, some individual taxa are.

Ocean acidificationf affects the bioenergetics of marine mussels as revealed by high-coverage quantitative metabolomics

Ocean acidification has become a major ecological and environmental problem in the world, whereas the impact mechanism of ocean acidification in marine bivalves is not fully understood. Cellular energy allocation (CEA) approach and high-coverage metabolomic techniques were used to investigate the acidification effects on the energy metabolism of mussels. The thick shell mussels Mytilus coruscus were exposed to seawater pH 8.1 (control) and pH 7.7 (acidification) for 14 days and allowed to recover at pH 8.1 for 7 days. The levels of carbohydrates, lipids and proteins significantly decreased in the digestive glands of the mussels exposed to acidification. The 14-day acidification exposure increased the energy demands of mussels, resulting in increased electron transport system (ETS) activity and decreased cellular energy allocation (CEA). Significant carry-over effects were observed on all cellular energy parameters except the concentration of carbohydrates and cellular energy demand (Ec) after 7 days of recovery. Metabolomic analysis showed that acidification affected the phenylalanine, tyrosine and tryptophan biosynthesis, taurine and hypotaurine metabolism, and glycine, serine and threonine metabolism. Correlation analysis showed that mussel cell energy parameters (carbohydrates, lipids, proteins, CEA) were negatively/positively correlated with certain differentially abundant metabolites. Overall, the integrated biochemical and metabolomics analyses demonstrated the negative effects of acidification on energy metabolism at the cellular level and implicated the alteration of biosynthesis and metabolism of amino acids as a mechanism of metabolic perturbation caused by acidification in mussels.

Gut microbiota-derived metabolites and their importance in neurological disorders

Microbial-derived metabolites are the intermediate or end products of bacterial digestion. They are one of the most important molecules for the gut to connect with the brain. Depending on the levels of specific metabolites produced in the host, it can exert beneficial or detrimental effects on the brain and have been linked to several neurodegenerative and neuropsychiatric disorders. However, the underlying mechanisms remain largely unexplored. Insight into these mechanisms could reveal new pathways or targets, resulting in novel treatment approaches targeting neurodegenerative diseases. We have reviewed selected metabolites, including short-chain fatty acids, aromatic amino acids, trimethylamine-N-oxide,  urolithin A, anthocyanins, equols, imidazole, and propionate to highlight their mechanism of action, underlying role in maintaining intestinal homeostasis and regulating neuro-immunoendocrine function. Further discussed on  how altered metabolite levels can influence the gut-brain axis could lead to new prevention strategies or novel treatment approaches to neural disorders.

Phytomediated Selenium Nanoparticles Improved Physio-morphological, Antioxidant, and Oil Bioactive Compounds of Sesame under Induced Biotic Stress

Vegetable oil consumption is expected to reach almost 200 billion kilograms by 2030 in the world and almost 2.97 million tons in Pakistan. A large quantity of edible oil is imported annually from other countries to fill the gap between local production and consumption. Compared to other edible oil crops such as soybean, rapeseed, peanut and olive, sesame has innately higher (55%) oil content, which makes it an excellent candidate to be considered to meet local edible oil production. Oil seed crops, especially sesame, are affected by various pathogens, which results in decreased oil production with low quality oil. Selenium nanoparticles (SeNPs) work synergistically, as it has antifungal activity along with improving plant growth. Different concentrations of SeNPs were used, on three different varieties of sesame (TS-5, TH-6, and Till-18). Plant growth and development were accelerated by SeNPs, which ultimately led to an increase in crop yield. Morphological parameters revealed that SeNPs resulted in a growth increase of 55.7% in root length, 48% increase in leaf number/plant, and 38% in stem diameter. Out of three sesame varieties, TS-5 seedlings treated with 40 mg/L SeNPs showed 96.7% germination and 53% SVI at 40 mg/L. Sesame varieties dramatically increased antioxidant capability using SeNPs, resulting in 147% increase in SOD and 140% increase in POD enzyme units in TH-6 and 76% elevation in CAT enzymes in TS-5 (mean ± S.E). GCMS analysis revealed that bioactive compound I, sesamin, sesamol, and tocopherol contents were increased along with enhanced production of different unsaturated fatty acids. Kegg pathway analysis and MSEA revealed that these compounds were mainly involved in biosynthesis of unsaturated fatty acids, suggesting that SeNPs have elicited the biosynthesis of unsaturated fatty acids such as oleic acid, linoleic acid, and α-linoleic acid. This study concluded that SeNPs (40 mg/L) have an excellent capability to be used for crop improvement along with better oil quality.

Dynamic Metabolic and Transcriptional Responses of Proteasome-Inhibited Neurons

Proteasome inhibition is associated with parkinsonian pathology in vivo and degeneration of dopaminergic neurons in vitro. We explored here the metabolome (386 metabolites) and transcriptome (3257 transcripts) regulations of human LUHMES neurons, following exposure to MG-132 [100 nM]. This proteasome inhibitor killed cells within 24 h but did not reduce viability for 12 h. Overall, 206 metabolites were changed in live neurons. The early (3 h) metabolome changes suggested a compromised energy metabolism. For instance, AMP, NADH and lactate were up-regulated, while glycolytic and citric acid cycle intermediates were down-regulated. At later time points, glutathione-related metabolites were up-regulated, most likely by an early oxidative stress response and activation of NRF2/ATF4 target genes. The transcriptome pattern confirmed proteostatic stress (fast up-regulation of proteasome subunits) and also suggested the progressive activation of additional stress response pathways. The early ones (e.g., HIF-1, NF-kB, HSF-1) can be considered a cytoprotective cellular counter-regulation, which maintained cell viability. For instance, a very strong up-regulation of AIFM2 (=FSP1) may have prevented fast ferroptotic death. For most of the initial period, a definite life-death decision was not taken, as neurons could be rescued for at least 10 h after the start of proteasome inhibition. Late responses involved p53 activation and catabolic processes such as a loss of pyrimidine synthesis intermediates. We interpret this as a phase of co-occurrence of protective and maladaptive cellular changes. Altogether, this combined metabolomics-transcriptomics analysis informs on responses triggered in neurons by proteasome dysfunction that may be targeted by novel therapeutic intervention in Parkinson's disease.

Identification of key genes involved in secondary metabolite biosynthesis in Digitalis purpurea

The medicinal plant Digitalis purpurea produces cardiac glycosides that are useful in the pharmaceutical industry. These bioactive compounds are in high demand due to ethnobotany's application to therapeutic procedures. Recent studies have investigated the role of integrative analysis of multi-omics data in understanding cellular metabolic status through systems metabolic engineering approach, as well as its application to genetically engineering metabolic pathways. In spite of numerous omics experiments, most molecular mechanisms involved in metabolic pathways biosynthesis in D. purpurea remain unclear. Using R Package Weighted Gene Co-expression Network Analysis, co-expression analysis was performed on the transcriptome and metabolome data. As a result of our study, we identified transcription factors, transcriptional regulators, protein kinases, transporters, non-coding RNAs, and hub genes that are involved in the production of secondary metabolites. Since jasmonates are involved in the biosynthesis of cardiac glycosides, the candidate genes for Scarecrow-Like Protein 14 (SCL14), Delta24-sterol reductase (DWF1), HYDRA1 (HYD1), and Jasmonate-ZIM domain3 (JAZ3) were validated under methyl jasmonate treatment (MeJA, 100 μM). Despite early induction of JAZ3, which affected downstream genes, it was dramatically suppressed after 48 hours. SCL14, which targets DWF1, and HYD1, which induces cholesterol and cardiac glycoside biosynthesis, were both promoted. The correlation between key genes and main metabolites and validation of expression patterns provide a unique insight into the biosynthesis mechanisms of cardiac glycosides in D. purpurea.

Metabolomic evaluation of PGPR defence priming in wheat (Triticum aestivum L.) cultivars infected with Puccinia striiformis f. sp. tritici (stripe rust)

Plant-microbe interactions are a phenomenal display of symbiotic/parasitic relationships between living organisms. Plant growth-promoting rhizobacteria (PGPR) are some of the most widely investigated plant-beneficial microbes due to their capabilities in stimulating plant growth and development and conferring protection to plants against biotic and abiotic stresses. As such, PGPR-mediated plant priming/induced systemic resistance (ISR) has become a hot topic among researchers, particularly with prospects of applications in sustainable agriculture. The current study applies untargeted ultra-high performance liquid chromatography-high-definition mass spectrometry (UHPLC-HDMS) to investigate PGPR-based metabolic reconfigurations in the metabolome of primed wheat plants against Puccinia striiformis f. sp. tricti (Pst). A seed bio-priming approach was adopted, where seeds were coated with two PGPR strains namely Bacillus subtilis and Paenibacillus alvei (T22) and grown under controlled conditions in a glasshouse. The plants were infected with Pst one-week post-germination, followed by weekly harvesting of leaf material. Subsequent metabolite extraction was carried out for analysis on a UHPLC-HDMS system for data acquisition. The data was chemometrically processed to reveal the underlying trends and data structures as well as potential signatory biomarkers for priming against Pst. Results showed notable metabolic reprogramming in primary and secondary metabolism, where the amino acid and organic acid content of primed-control, primed-challenged and non-primed-challenged plants were differentially reprogrammed. Similar trends were observed from the secondary metabolism, in which primed plants (particularly primed-challenged) showed an up-regulation of phenolic compounds (flavonoids, hydroxycinnamic acids-HCAs- and HCA amides) compared to the non-primed plants. The metabolomics-based semi-quantitative and qualitative assessment of the plant metabolomes revealed a time-dependent metabolic reprogramming in primed-challenged and primed-unchallenged plants, indicating the metabolic adaptations of the plants to stripe rust infection over time.

Influence of Lactobacillus (LAB) Fermentation on the Enhancement of Branched Chain Amino Acids and Antioxidant Properties in Bran among Wheat By-Products

The main objective of this study was to enhance the nutritional properties, including branched chain amino acids (BCAAs), through the solid-state fermentation (SSF) of wheat bran (WB) using lactic acid bacteria (LAB). The physicochemical properties, amino acid profiles, bioactive components, and antioxidant properties of raw and sterilized WB were compared with those of WB fermented with five different LAB strains. The highest level of BCAAs, isoleucine (Ile; 2.557 ± 0.05 mg/100 g), leucine (Leu; 7.703 ± 0.40 mg/100 g), and valine (Val; 7.207 ± 0.37 mg/100 g), was displayed in the WB fermented with Lactobacillus acidophilus (L.A WB). In addition, L.A WB showed the highest amount of total phenolic and flavonoid contents (2.80 mg GAE/g and 1.01 mg CE/g, respectively), and the highest Trolox equivalent antioxidant capacity (9.88 mM TE/g). Statistical analysis clearly revealed that L.A WB presented the highest abundance of branched chain amino acids as well as bioactive components. Overall, this study distinctly implemented the possibility of fermented WB with enhanced BCAAs for application in future functional food through experimental and statistical observations.

A new amino acid, hybrid peptides and BODIPY analogs: synthesis and evaluation of 2-aminotroponyl-L-alanine (ATA) derivatives

Natural aromatic α-amino acid residues play critical roles in the structural and functional organization of proteins owing to π-interactions. Their aromatic residues are derived from benzenoid scaffolds. Non-benzenoid aromatic scaffolds such as tropone and tropolone are also constituents of troponoid natural products. Tropolone has also the ability to exhibit π-interactions along with additional hydrogen bonding. Thus, amino acids comprising troponyl could be potential building blocks of novel peptidomimetics. This report describes the synthesis of the L-aminotroponylalanine amino acid (ATA) and its unusual activity with the peptide coupling agent EDC. Importantly, its di-peptides form β-sheet/-turn type secondary structures in organic solvents owing to the troponyl residue. This amino acid is an excellent scaffold for the synthesis of fluorescent amino acids such as BODIPY amino acid analogs. Nevertheless, this amino acid and its BODIPY derivatives can enter HeLa cells without exhibiting significant cytotoxicity at low concentrations (∼50 μM). Hence, ATA and its BODIPY derivatives are promising aromatic amino acids for the construction of potential peptidomimetics and fluorescent labelling of target peptides.

The Molecular Gut-Brain Axis in Early Brain Development

Millions of nerves, immune factors, and hormones in the circulatory system connect the gut and the brain. In bidirectional communication, the gut microbiota play a crucial role in the gut-brain axis (GBA), wherein microbial metabolites of the gut microbiota regulate intestinal homeostasis, thereby influencing brain activity. Dynamic changes are observed in gut microbiota as well as during brain development. Altering the gut microbiota could serve as a therapeutic target for treating abnormalities associated with brain development. Neurophysiological development and immune regulatory disorders are affected by changes that occur in gut microbiota composition and function. The molecular aspects relevant to the GBA could help develop targeted therapies for neurodevelopmental diseases. Herein, we review the findings of recent studies on the role of the GBA in its underlying molecular mechanisms in the early stages of brain development. Furthermore, we discuss the bidirectional regulation of gut microbiota from mother to infant and the potential signaling pathways and roles of posttranscriptional modifications in brain functions. Our review summarizes the role of molecular GBA in early brain development and related disorders, providing cues for novel therapeutic targets.