Amino Acid Changes Research Articles

Testing the kinetic tradeoff between bicarbonate versus phosphoenolpyruvate affinity and glucose-6 phosphate response of phosphoenolpyruvate carboxylase from two C4grasses.

Phosphoenolpyruvate (PEP) carboxylase (PEPC) has an anaplerotic role in central plant metabolism but also initiates the carbon concentrating mechanism during C4 photosynthesis. The C4 PEPC has different binding affinities (Km) for PEP (K0.5PEP) and HCO3- (K0.5HCO3), and allosteric regulation by glucose-6-phosphate (G6-P) compared to non-photosynthetic isoforms. These differences are linked to specific changes in amino acids within PEPC. For example, region II (residues 302-433, Zea mays numbering) has been identified as important for G6-P regulation and within this region residue 353 may be conserved in C4 PEPC enzymes. Additionally, residue 780 influences the C4 PEPC kinetic properties and may interact with region II as well as residue 353 to influence G6-P regulation. We test the hypothesis that variation within region II, including residue 353, and their interactions with residue 780 influence the kinetic and allosteric regulation by G6-P of two C4 PEPC isozymes from two C4 grasses. The data does not support a kinetic tradeoff between K0.5HCO3 and K0.5PEP in these PEPC isozymes. Additionally, these enzymes had different response to G6-P that was only partially attributed to region II, residue 353 and residue 780. This data provides new insights into factors influencing the kinetic variation of C4 PEPC isozymes.

Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution

The family Daphniphyllaceae has a single genus, and no relevant comparative phylogenetic study has been reported on it. To explore the phylogenetic relationships and organelle evolution mechanisms of Daphniphyllaceae species, we sequenced and assembled the chloroplast and mitochondrial genomes of Daphniphyllum macropodum. We also conducted comparative analyses of organelles in Daphniphyllaceae species in terms of genome structure, phylogenetic relationships, divergence times, RNA editing events, and evolutionary rates, etc. Results indicated differences in the evolutionary patterns of the plastome and mitogenome in D. macropodum. The plastome had a more conserved structure but a faster nucleotide substitution rate, and the mitogenome showed a more complex structure while the mitotic genome shows a more complex structure but a slower nucleotide substitution rate. We identified several unidirectional protein-coding gene transfer events from the plastome to the mitogenome based on homology analysis, but no transfer events occurred from the mitogenome to the plastome. Multiple TE fragments existed in organelle genomes, and two organelles showed different preferences for nuclear TE insertion types. The estimation of divergence time indicated that the differentiation of Daphniphyllaceae and Altingiaceae at around 29.86 Mya might be due to the dramatic uplift of Tibetan Plateau during the Oligocene. About 75% of codon changes in organelles were found to be hydrophilic to hydrophobic amino acids. The RNA editing in protein-coding transcripts is the result of amino acid changes to increase their hydrophobicity and conservation in alleles, which may contribute to the formation of functional 3D structures in proteins. This study would enrich genomic resources and provide valuable insights into the structural dynamics and molecular biology of Daphniphyllaceae species.

SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients

BackgroundPrimary Immunodeficiency disorders (PID) can increase the risk of severe COVID-19 and prolonged infection. This study investigates the duration of SARS-CoV-2 excretion and the genetic evolution of the virus in pediatric PID patients as compared to immunocompetent (IC) patients.Materials and methodsA total of 40 nasopharyngeal and 24 stool samples were obtained from five PID and ten IC children. RNA detection was performed using RT-qPCR, and whole-genome sequencing was conducted with the NexSeq 1000 platform. Data analysis used the nextflow/viralrecon pipeline. Hotspot amino acid frequencies were investigated using GraphPad Prism v10. Phylodynamic analysis was conducted with BEAST software.ResultsIn IC children, the viral excretion period lasted up to 14 days in nasopharyngeal swabs, with an average duration of 7 days, and ranged from 7 to 14 days in stool samples. In PID patients, the viral RNA was detected in nasopharyngeal for periods between 7 and 28 days, with an average duration of 15 days, and up to 28 days in stool samples. Two SARS-CoV-2 variants were detected in PID patients: Delta (AY.122) and Omicron (BA.1.1). Patients with antibody and combined deficiencies, exhibited the most prolonged shedding periods in both nasopharyngeal and stool samples and one patient presented complications and fatal outcome. Specific Hotspot amino acid changes were detected in PID: A2821V and R550H (ORF1ab).ConclusionOur findings underscore the prolonged excretion of SARS-CoV-2 RNA in patients with antibody and combined deficiencies. Thus, specialized care is essential for effectively managing PID patients.

Characterization, Quantification, and Molecular Identification of Co-Infection of Canine Parvovirus (CPV-2) Variants in Dogs Affected by Gastroenteritis in Ecuador During 2022–2023

Canine parvovirus (CPV-2) is a highly contagious virus in canines, and it is mostly spread by touching infected feces. Dogs of all ages can catch it, but puppies are more likely to suffer from it. Severe signs include vomiting, diarrhea with blood, feeling tired, and not drinking enough water. There are three different types of the original CPV-2 that have been found so far, which are CPV-2a, 2b, and 2c. The genome of CPV-2 is about 5.2 kb long and has two open reading frames (ORFs), namely the VP region and the NS region. Based on changes in amino acids at position 426, the VP2 protein distinguishes the gene apart in the VP region. Using a molecular method, this study contemplated the presence of CPV-2 and its variants in dogs that had gastroenteritis, as well as other infections. There were 511 samples tested, and 401 (78.47%) of them were positive for CPV-2. Of these, 144 (25.91%) were positive for the original genotype, 258 (64.34%) for genotype 2a, 343 (85.54%) for genotype 2b, and 167 (41.65%) for genotype 2c. Using the multiplex qPCR for genotyping, CPV-2a and CPV-2b were determined as the most frequent co-infections (16.45%). The three genotypes (2a, 2b, and 2c) were found in the samples examined based on the amino acids at position 426 of the VP2 protein, as demonstrated by the VP2 gene sequencing. Furthermore, it was discovered that in certain samples, a genetic modification at position 297 was connected to the virus’s pathogenicity.

Exploring metabolic reprogramming in esophageal cancer: the role of key enzymes in glucose, amino acid, and nucleotide pathways and targeted therapies.

Esophageal cancer (EC) is one of the most common malignancies worldwide with the character of poor prognosis and high mortality. Despite significant advancements have been achieved in elucidating the molecular mechanisms of EC, for example, in the discovery of new biomarkers and metabolic pathways, effective treatment options for patients with advanced EC are still limited. Metabolic heterogeneity in EC is a critical factor contributing to poor clinical outcomes. This heterogeneity arises from the complex interplay between the tumor microenvironment and genetic factors of tumor cells, which drives significant metabolic alterations in EC, a process known as metabolic reprogramming. Understanding the mechanisms of metabolic reprogramming is essential for developing new antitumor therapies and improving treatment outcomes. Targeting the distinct metabolic alterations in EC could enable more precise and effective therapies. In this review, we explore the complex metabolic changes in glucose, amino acid, and nucleotide metabolism during the progression of EC, and how these changes drive unique nutritional demands in cancer cells. We also evaluate potential therapies targeting key metabolic enzymes and their clinical applicability. Our work will contribute to enhancing knowledge of metabolic reprogramming in EC and provide new insights and approaches for the clinical treatment of EC.

Characterizing phenotype variants of Cercosporidium personatum, causal agent of peanut late leaf spot disease, their morphology, genetics and metabolites

Cercosporidium personatum (CP) causes peanut late leaf spot (LLS) disease with 70% yield losses unless controlled by fungicides. CP grows slowly in culture, exhibiting variable phenotypes. To explain those variations, we analyzed the morphology, genomes, transcriptomes and chemical composition of three morphotypes, herein called RED, TAN, and BROWN. We characterized, for the first time in CP, anthraquinone (AQ) precursors of dothistromin (DOT), including averantin, averufin, norsolorinic acid, versicolorin B, versicolorin A, nidurufin and averufanin. BROWN had the highest AQ and melanin (15 mg/g DW) contents. RED had the highest ergosterol (855 µM FW) and chitin (beta-glucans, 4% DW) contents. RED and TAN had higher resistance to xenobiotics (p ≤ 1.0E-3), including chlorothalonil, tebuconazole and caffeine, compared to CP NRRL 64,463. In RED, TAN, and BROWN, rates of single nucleotide polymorphisms (SNP) (1.4–1.7 nt/kb) and amino acid changes (3k-4k) were higher than in NRRL 64,463. Differential gene expression (p ≤ 1.0E-5) was observed in 47 pathogenicity/virulence genes, 41 carbohydrate-active enzymes (CAZymes), and 23 pigment/mycotoxin biosynthesis genes. We describe the MAT1 locus, and a method to evaluate CP-xenobiotic resistance in 5 days. Chemical profiles indicate each CP morphotype could trigger different immune response in plants, probably hindering development of durable LLS resistance.

Integrated proteomic and metabolomic analysis reveals the potential therapeutic mechanism of Quanduzhong capsule in rats with spontaneous hypertension and knee osteoarthritis

Quanduzhong capsule (QDZ), derived from Eucommia ulmoides Oliv., has been traditionally used in Chinese medicine for its beneficial effects on musculoskeletal health. Its clinical application has extended to conditions such as spontaneous hypertension combined with knee osteoarthritis (SKOA). However, the specific mechanisms by which QDZ alleviates symptoms and improves outcomes in this complex condition remain to be fully elucidated. This study aims to evaluate the therapeutic potential of QDZ in treating SKOA. By performing serum proteomics and metabolomics, we seek to explore the related biological pathways and elucidate the mechanisms underlying QDZ's effects on SKOA. Serum samples from control, spontaneous hypertension (SHR), SKOA, and SKOA treated with QDZ groups were analyzed using data-independent acquisition-based proteomics to identify differentially expressed proteins. Serum levels of angiotensin II, norepinephrine, endothelin-1, classical pro-inflammatory factors such as macrophage colony-stimulating factor, tumor necrosis factor-alpha, and interleukin-1 beta were measured. Additionally, serum metabolomics was performed to examine the changes in metabolite profiles. Correlation analysis was conducted to link changed proteins and metabolites with key pathways affected by QDZ. Proteomics analysis revealed significant alterations in serum protein expression between control, SHR, and SKOA groups, with changes in pathways related to immune regulation and vascular function. KEGG enrichment analysis highlighted pathways such as endocytosis, synaptic vesicle cycling, and immune responses were enriched in SKOA group compared with control group. QDZ treatment significantly modulated above pathways and reduced inflammatory and cardiovascular markers which were upregulated in SKOA group. Metabolomics analysis showed that QDZ reversed SKOA-induced changes in amino acid and organic acid metabolism, affecting pathways including valine, leucine, and isoleucine metabolism, as well as the TCA cycle. Correlation analysis revealed significant relationships between key proteins and metabolites, underscoring the integrated role of immune and metabolic pathways in QDZ's effects. Our results indicate QDZ has a significant therapeutic potential for SKOA by modulating both protein and metabolite profiles associated with inflammation, vascular dysfunction, and metabolic imbalance. Our findings provide insights into the mechanisms through which QDZ exerts its effects and support its use as a promising treatment for SKOA. This study highlights the impact of QDZ on proteomic and metabolomic alterations, offering a basis for its broader application in treating SKOA.

Longitudinal analysis for predicting amino acid changes in HIV-1 using association rule mining

Longitudinal analysis for predicting amino acid changes in HIV-1 using association rule mining

Learning the fitness dynamics of pathogens from phylogenies

The dynamics of the genetic diversity of pathogens, including the emergence of lineages with increased fitness, is a foundational concept of disease ecology with key public-health implications. However, the identification of such lineages and estimation of associated fitness remain challenging, and is rarely done outside densely sampled systems1,2. Here we present phylowave, a scalable approach that summarizes changes in population composition in phylogenetic trees, enabling the automatic detection of lineages based on shared fitness and evolutionary relationships. We use our approach on a broad set of viruses and bacteria (SARS-CoV-2, influenza A subtype H3N2, Bordetella pertussis and Mycobacterium tuberculosis), which include both well-studied and understudied threats to human health. We show that phylowave recovers the main known circulating lineages for each pathogen and that it can detect specific amino acid changes linked to fitness changes. Furthermore, phylowave identifies previously undetected lineages with increased fitness, including three co-circulating B. pertussis lineages. Inference using phylowave is robust to uneven and limited observations. This widely applicable approach provides an avenue to monitor evolution in real time to support public-health action and explore fundamental drivers of pathogen fitness.

Serum NMR Metabolomics in Distinct Subtypes of Hematologic Malignancies.

Hematological malignancies encompass a diverse array of subtypes, contributing to substantial heterogeneity that poses challenges in predicting clinical outcomes. Leveraging the capabilities of nuclear magnetic resonance holds substantial promise in the detection of serum biomarkers and individual metabolic alterations in patients. The study involved the analysis of the sera from patients with acute myeloid leukemia, chronic lymphocytic leukemia, and non-Hodgkin lymphoma to investigate the impacted metabolites and their associated pathways. The quantitative 1D 1H nuclear magnetic resonance method was employed to identify alterations. Metabolite annotations were validated using 2D analyses. Discriminating chemometric models and receiver operating characteristic curves were created using the MetaboAnalyst platform. The findings revealed significant alterations in the serum levels of amino acid catabolism products, citrate cycle intermediates, and phospholipids. The acute myeloid leukemia group showed differences in glucogenic amino acids related to the glycolysis pathway, while the chronic lymphocytic leukemia and non-Hodgkin lymphoma groups displayed variances in fumarate and acetate levels linked to the citrate cycle pathway. In the leukemia groups, higher levels of products from the protein degradation pathway were observed. The biomarker panels for each malignancy group exhibited outstanding discrimination from controls. Healthy individuals differed distinctly from patients, indicating commonly observed metabolic adaptation patterns among frequent hematological malignancies. The small cohort study using nuclear magnetic resonance metabolomics in various hematological malignancy subtypes revealed significant changes in serum amino acid and protein degradation end-product levels, suggesting prolonged leukocyte lifespan and increased energy demand.

Complete Genome Characterization of Canine Adenovirus From Türkiye With Next-Generation Sequencing.

Determining the complete genome sequence data of adenoviruses has recently become greatly important due to their use by scientists as vectors in cancer studies and other fields, including vaccine development. However, the GenBank database currently has few complete genome sequences of adenoviruses, which are known for their large genomes. To address this gap, we analysed next-generation sequencing data obtained from our previous study to provide the complete genome sequence of the canine adenovirus-2 strain. For the obtained canine adenovirus-2 strain (OQ596341), comparative genomics, recombination and phylogenetic analysis were conducted. This sequence was compared and phylogenetically analysed with the 20 complete genome sequences of canine adenovirus previously reported in GenBank worldwide, as well as partial E3 ORFA sequences obtained from Türkiye. The nucleotide similarity rates of the sequence obtained from this study with other CAdV-2 whole genomes are over 99.04%. The gene alignment results reveal that the OQ596341 was found to be closely related to the AC000020 reference genome and LC557011. There are two recombination events related to the genome in this study. Comparisons with other complete genome sequences revealed several previously unseen mutations. These mutations include H34Y in the E1A gene; P55A in the E1B 55K gene; D13N and D202N in the IVa2 gene; K679R, V934I and K989N in the Pol gene; E205K in the pTP gene; T455A in the pIIIa gene; A310V in the V gene; G151R in the protease gene; E268K in the 100K gene; G66S and G141S in the 33K gene; T14A, E250K, D287N and I293T in the E3 ORFA gene; and L193F in the E434K gene. Moreover, a comparison with partial sequences obtained from Türkiye revealed the E250K mutation in the E3 ORFA gene, which we report for the first time in Türkiye. The complete CAdV-2 genome sequence obtained in the present study is the first sequence from Europe. Comparative analysis with other genomes revealed some unique mutations. This study is the first to report the E250K amino acid change in the E3 ORFA gene in Türkiye. We anticipate that this data can be used in future CAdV-2 vaccine development studies. Further studies are recommended to evaluate the impact of these mutations on viral tropism and other host interactions.

Recombination and amino acid point mutations in VP3 exhibit a synergistic effect on increased virulence of rMDPV

ABSTRACT Recombinant Muscovy duck parvovirus (rMDPV) is a product of genetic recombination between classical Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV). The recombination event took place within a 1.1-kb DNA segment located in the middle of the VP3 gene, and a 187-bp sequence extending from the P9 promoter to the 5′ initiation region of the Rep1 ORF. This resulted in the alteration of five amino acids within VP3. Despite these genetic changes, the precise influence of recombination and amino acid mutations on the pathogenicity of rMDPV remains ambiguous. In this study, based on the rMDPV strain ZW and the classical MDPV strain YY, three chimeric viruses (rZW-mP9, rZW-mPR187, and rYY-rVP3) and the five amino acid mutations-introduced mutants (rZW-g5aa and rYY-5aa(ZW)) were generated using reverse genetic technology. When compared to the parental virus rZW, rZW-g5aa exhibited a prolonged mean death time (MDT) and a decreased median lethal dose (ELD50) in embryonated duck eggs. In contrast, rYY-5aa(ZW) did not display significant differences in MDT and ELD50 compared to rYY. In 2-day-old Muscovy ducklings, infection with rZW-g5aa and rYY-5aa(ZW) resulted in mortality rates of only 20% and 10%, respectively, while infections with the three chimeric viruses (rZW-mP9, rZW-mPR187, rYY-rVP3) and rZW still led to 100% mortality. Notably, rYY-rVP3, containing the VP3 region from strain ZW, exhibited 50% mortality in 6-day-old Muscovy ducklings and demonstrated significant horizontal transmission. Collectively, our findings indicate that recombination and consequent amino acid changes in VP3 have a synergistic impact on the heightened virulence of rMDPV in Muscovy ducklings.

Multi-locus investigation of Anopheles-mediated selective pressure on Plasmodium falciparum in Africa

BackgroundThe high burden of malaria in Africa is largely due to the presence of competent and adapted Anopheles vector species. With invasive Anopheles stephensi implicated in malaria outbreaks in Africa, understanding the genomic basis of vector-parasite compatibility is essential for assessing the risk of future outbreaks due to this mosquito. Vector compatibility with P. falciparum arises from ancient coevolution and involves genes such as Pfs47 in P. falciparum and P47Rec in Anopheles. Questions remain about whether sub-continental vector variation is a selective pressure on current Plasmodium populations.MethodsWe analyzed the genetic diversity in parasite–vector interaction genes in P. falciparum and An. gambiae from 9 and 15 countries in Africa, respectively. Specifically, we looked for evidence of malaria vector-mediated selection within three P. falciparum genes (Pfs47, Pfs16, Pfs37) and conducted association analyses with occurrence probabilities of prominent malaria vectors.ResultsHigher protein haplotype diversities of Pfs47 and Pfs16 were associated with the probability of occurrence of An. arabiensis and An. funestus together. Only Pfs16 carried a signature of positive selection consistently (average Tajima’s D = −2.96), which was associated with the probability of occurrence of An. funestus. These findings support vector-mediated selection on the basis of vector species diversity that may be occurring within Africa. We also employed phylogenetic analyses of An. gambiae interaction genes (P47Rec, APN1, HPX15) to identify significant subspecies diversity as a prerequisite to vector-population-mediated selection. Anopheles gambiaeHPX15 revealed significant within-species differentiation (multiple branches bootstrap > 70) compared with absence of variation in P47Rec, suggesting that further investigation into subspecies-mediated selection on the basis of HPX15 is needed. Finally, we observed five amino acid changes at P47Rec in invasive An. stephensi compared with dominant African Anopheles species, calling for further investigation of the impact these distinct P47Rec variants might have on local African P. falciparumPfs47 diversity.ConclusionsOverall, these findings suggest that vector variation within Africa could influence P. falciparum diversity and lay a genomic framework for future investigation of invasive An. stephensi’s impact on African malaria.Graphical

NMR and LC-MS-Based Metabolomics to Study the Effect of Surfactin on the Metabolome of Flax

Flax (Linum usitatissimum) is a versatile plant used in a range of applications, from textiles to nutrition. Surfactin, a cyclic lipopeptide biosurfactant produced by bacteria such as Bacillus subtilis, has potential as a biocontrol agent or as a plant defense inducer in agriculture. This work aims to determine the effects of surfactin treatment at two kinetic points on the metabolism of flax hydroponic cultures, using advanced metabolomic techniques, including 1H NMR and LC-MS analyses. Surfactin, detected in the roots, has a significant local impact on the metabolic profiles of flax roots, leading mainly to a higher content of cyanogenic compounds and amino acids and a lower content of carbohydrates. Surfactin, which is not detected in the aerial parts, also induces contrasted changes in amino acids, sugars, and secondary metabolite accumulation between stems and leaves. Surfactin treatment of flax leads to both a local and systemic effect on flax metabolism. These changes suggest that plant response to surfactin treatment could induce an enhanced plant defense. This could suggest potential applications of surfactin in the agricultural field as a biostimulant or biocontrol agent, to limit the use of chemical compounds in culture, and to limit their negative impact on both health and the environment.

Optimized Directed Virus Evolution to Accelerate the Generation of Oncolytic Coxsackievirus B3 Adapted to Resistant Colorectal Cancer Cells.

Recently, we demonstrated that the oncolytic Coxsackievirus B3 (CVB3) strain PD-H can be efficiently adapted to resistant colorectal cancer cells through dose-dependent passaging in colorectal cancer cells. However, the method is time-consuming, which limits its clinical applicability. Here, we investigated whether the manufacturing time of the adapted virus can be reduced by replacing the dose-based passaging with volume-based passaging. For this purpose, the murine colorectal carcinoma cell line MC38, resistant to PD-H-induced lysis, was initially infected with PD-H at 0.1 multiplicity of infection (MOI). For subsequent passages, 15-30 µL of a 1:10 dilution of the cell culture supernatant was transferred to fresh MC38 cells early after virus-induced cell lysis became visible. By virus passage 10, complete cell lysis of MC38 cells was achieved. Sequencing of the passage 10 virus (P-10) revealed two nucleotide substitutions in the 5' UTR and six amino acid changes in the viral polyprotein compared to the PD-H founder. P-10, however, consisted of a heterogeneous virus population. Therefore, the detected mutations were introduced into the cDNA of PD-H, from which the recombinant virus PD-MC38 was generated. PD-MC38 exhibited significantly enhanced replication and lytic activity in MC38 cells compared to PD-H, whereas its oncolytic activity in other colorectal cancer cell lines was comparable to or even lower than that of PD-H. These findings demonstrate that volume-based passaging is suitable to generate tumor cell-specific adapted PD-H. Moreover, compared to the dose-dependent passaging, volume-based passaging significantly reduced the time required to generate the adapted virus.

Genetic diversity of dengue virus circulating in the Philippines (2014-2019) and comparison with dengue vaccine strains.

Dengue virus has four distinct serotypes and the genetic diversity within each of the four serotypes contribute to its complexity. An important aspect of dengue molecular evolutionary studies has been the dissection of the extent and structure of genetic variation among major genotypes within each serotype. It is important to understand the role of dengue genetic variability and its potential role and impact in the effectiveness of the dengue vaccine. Demographic data and blood were collected from patients seen at a tertiary hospital in the Philippines and clinically diagnosed with dengue from 2014-2019. Dengue virus (DENV) RT-PCR was used to confirm infection and positive samples underwent whole genome sequencing. Phylogenetic analysis was performed on 127 samples (25 DENV-1, 19 DENV-2, 70 DENV-3, and 13 DENV-4). We observed a serotype shift in 2014 and 2022. We detected the following genotypes per serotype for the wild-type (WT) DENV sequences: genotype IV (DENV-1), cosmopolitan (DENV-2), genotype I (DENV-3) and genotype IIa (DENV-4). WT DENV belonged to different genotypes versus the QDENGA strains and except for DENV-4, belonged to different genotypes versus the Dengvaxia strains. Comparing Dengvaxia vaccine sequences with WT DENV, we observed 23, 24, 34, and 9 positions with amino acid changes in the entire envelope protein, with 1, 5, 1, and 2 positions with amino acid changes identified among the important human monoclonal antibodies (mAbs) targeted epitope positions. We detected 24, 25, 36 and 12 positions with amino acid changes in the E protein with 0, 5, 1, and 2 positions with amino acid changes among the important mAbs targeted epitope positions for DENV-1, DENV-2, DENV-3, and DENV-4, respectively when comparing QDENGA vaccine sequences with the WT DENV. We showed low genotype complexity, genetically distinct clades and local evolution for DENV circulating in the Philippines.

Transcriptome-aligned metabolic profiling by SERSome reflects biological changes following mesenchymal stem cells expansion

BackgroundMesenchymal stem cells (MSCs) are widely applied in the treatment of various clinical diseases and in the field of medical aesthetics. However, MSCs exhibit greater heterogeneity limited stability, and more complex molecular and mechanistic characteristics compared to conventional drugs, making rapid and precise monitoring more challenging.MethodsSurface-enhanced Raman spectroscopy (SERS) is an ultrasensitive, tractable and low-cost fingerprinting technique capable of identifying a wide range of molecules related to biological processes. Here, we employed SERS for reproducible quantification of ultralow concentrations of molecules and utilized spectral sets, termed SERSomes, for robust and comprehensive intracellular multi-metabolite profiling.ResultsWe revealed that with increasing passage number, there is a gradual decline in cell expansion efficiency, accompanied by significant changes in intracellular amino acids, purines, and pyrimidines. By integrating these metabolic features detected by SERS with transcriptomic data, we established a correlation between SERS signals and biological changes, as well as differentially expressed genes.ConclusionIn this study, we explore the application of SERS technique to provide robust metabolic characteristics of MSCs across different passages and donors. These results demonstrate the effectiveness of SERSome in reflecting biological characteristics. Due to its sensitivity, adaptability, low cost, and feasibility for miniaturized instrumentation throughout pretreatment, measurement, and analysis, the label-free SERSome technique is suitable for monitoring MSC expansion and offers significant advantages for large-scale MSC manufacturing.

Evaluation of Serum Amino Acid and Carnitine Profile in Dogs with Transmissible Venereal Tumor

The presented study aimed to reveal the changes in serum amino acid and carnitine profiles in dogs with transmissible venereal tumor (TVT). The study material comprised 40 female dogs ranging in age from 3 to 5 years. The dogs were divided into two groups based on genital organ examinations. Group 1 (n=20) consisted of healthy dogs, while Group 2 (n=20) consisted of TVT-positive dogs. Blood samples were taken from dogs in both study groups, and serum was obtained. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for the determination of carnitine and amino acid profiles. The obtained data were compared using an independent samples t-test. The serum amino acid profiles of Lysine, Aspartic Acid, Tyrosine, Asparagine, Alanine, Arginine, Citrulline, Glutamic Acid, Glycine, Methylglutaryl, Phenylalanine, and Ornithine were found to be lower in the TVT group (P

A Comprehensive Metabolomic and Microbial Analysis Following Dietary Amino Acid Reduction in Mice.

Introduction: Nutritional metabolomics provides a comprehensive overview of the biochemical processes that are induced by dietary intake through the measurement of metabolite profiles in biological samples. However, there is a lack of deep phenotypic analysis that shows how dietary interventions influence the metabolic state across multiple physiologic sites. Dietary amino acids have emerged as important nutrients for physiology and pathophysiology given their ability to impact cell metabolism. Methods: The aim of the current study is to evaluate the effect of modulating amino acids in diet on the metabolome and microbiome of mice. Here, we report a comprehensive metabolite profiling across serum, liver, and feces, in addition to gut microbial analyses, following a reduction in either total dietary protein or diet-derived non-essential amino acids in mice. Results: We observed both distinct and overlapping patterns in the metabolic profile changes across the three sample types, with the strongest signals observed in liver and serum. Although amino acids and related molecules were the most commonly and strongly altered group of metabolites, additional small molecule changes included those related to glycolysis and the tricarboxylic acid cycle. Microbial profiling of feces showed significant differences in the abundance of select species across groups of mice. Conclusions: Our results demonstrate how changes in dietary amino acids influence the metabolic profiles across organ systems and the utility of metabolomic profiling for assessing diet-induced alterations in metabolism.

Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut (Cocos nucifera L.).

Coconut (Cocos nucifera L.) is a key tropical economic tree valued for its fruit flavor, particularly 2-acetyl-1-pyrroline (2AP), a vital aroma metabolite. To enhance high-aromatic coconut breeding efforts, it is essential to deeply understand the hereditary factors governing the production of 2AP. In this study, a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism (SNP) variations from 168 aromatic coconut germplasm resources. Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism. Proteins encoded by these genes involve in amino acid metabolism, glycolysis, and secondary metabolism. Among these, Asparagine synthetase coding gene ASN1, Gamma-glutamylcysteine synthetase coding gene GSH1, and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504. In particular, the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein, potentially resulting in differences in 2AP content among haplotype populations. Identifying variations in related candidate genes, particularly the gene CnASN1, provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.