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Scientific Reports Mar 2024In this study, we investigated the composition of free amino acids and lactate (Lac) in polychaetes in river estuaries and inner bays using chromatographic techniques....
In this study, we investigated the composition of free amino acids and lactate (Lac) in polychaetes in river estuaries and inner bays using chromatographic techniques. Both L-amino acids and D-amino acids (D-asparagine, D-alanine (D-Ala), D-serine, D-aspartic acid, and D-proline (D-Pro)) were detected, indicating that polychaetes contain some D-amino acids. Some polychaete species exhibited notable amino acid levels, such as glycine in Capitellidae sp. and Thelepus sp., D-Pro in Glycera sp., and β-Ala in Scoletoma nipponica and Scoletoma sp.. High D-Lac levels were detected in Tylorrhynchus osawai and Hediste diadroma, (691 and 797 μmol/100 g-wet, respectively), with the D-form exceeding 98%. T. osawai was dominant in the upper tidal-sensitive zone, wherein other organisms were less abundant because of low salinity (3-8 PSU). Seasonal differences in the concentrations of components in T. osawai were observed, particularly a significant increase in D-Lac in the reproductive period. Notably, the D-Lac concentrations of T. osawai were higher upstream than downstream. Thus, D-Lac might be involved in strategies underlying adaptations to low salinity and reproductive activity. These results suggest that both the D-form of Lac and amino acids may play certain physiological roles in the life of polychaetes.
Topics: Animals; Lactic Acid; Amino Acids; Bays; Estuaries; Proline; Antifibrinolytic Agents; Polychaeta
PubMed: 38448449
DOI: 10.1038/s41598-024-55861-5 -
Cancer Cell International Mar 2024The present study aimed to investigate the expression level, biological function, and underlying mechanism of transmembrane protein 176B (TMEM176B) in gastric cancer...
BACKGROUND
The present study aimed to investigate the expression level, biological function, and underlying mechanism of transmembrane protein 176B (TMEM176B) in gastric cancer (GC).
METHODS
TMEM176B expression was detected by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting (WB). The function of TMEM176B was determined by various in vitro assays including colony formation, 5-ethynyl-2'-deoxyuridine (EdU), Transwell, and flow cytometry. Bioinformatics techniques were then used to elucidate the signaling pathways associated with TMEM176B activity. Tumor formation experiments were conducted on nude mice for in vivo validation of the preceding findings. TMEM176B expression was cross-referenced to clinicopathological parameters and survival outcomes.
RESULTS
It was observed that TMEM176B was overexpressed in GC cells and tissues. Targeted TMEM176B abrogation inhibited colony formation, proliferation, migration, and invasion but promoted apoptosis in GC cell lines while TMEM176B overexpression had the opposite effects. Subsequent experimental validation disclosed an association between TMEM176B and the phosphatidylinositol 3-carboxykinase (PI3K)-protein kinase B (Akt)-mammalian target of rapamycin (mTOR) signaling axis. Moreover, TMEM176B affects GC cancer progression by regulating asparagine synthetase (ASNS). The in vivo assays confirmed that TMEM176B is oncogenic and the clinical data revealed a connection between TMEM176B expression and the clinicopathological determinants of GC.
CONCLUSION
The foregoing results suggest that TMEM176B significantly promotes the development of gastric cancer and is an independent prognostic factor of it.
PubMed: 38438907
DOI: 10.1186/s12935-024-03279-4 -
Mass Spectrometry (Tokyo, Japan) 2024Among the most typical posttranslational modifications is glycosylation, which often involves the covalent binding of an oligosaccharide (glycan) to either an asparagine... (Review)
Review
Among the most typical posttranslational modifications is glycosylation, which often involves the covalent binding of an oligosaccharide (glycan) to either an asparagine (N-linked) or a serine/threonine (O-linked) residue. Studies imply that the N-glycan portion of a glycoprotein could serve as a particular disease biomarker rather than the protein itself because N-linked glycans have been widely recognized to evolve with the advancement of tumors and other diseases. N-glycans found on protein asparagine sites have been especially significant. Since N-glycans play clearly defined functions in the folding of proteins, cellular transport, and transmission of signals, modifications to them have been linked to several illnesses. However, because these N-glycans' production is not template driven, they have a substantial morphological range, rendering it difficult to distinguish the species that are most relevant to biology and medicine using standard techniques. Mass spectrometry (MS) techniques have emerged as effective analytical tools for investigating the role of glycosylation in health and illness. This is due to developments in MS equipment, data collection, and sample handling techniques. By recording the spatial dimension of a glycan's distribution , mass spectrometry imaging (MSI) builds atop existing methods while offering added knowledge concerning the structure and functionality of biomolecules. In this review article, we address the current development of glycan MSI, starting with the most used tissue imaging techniques and ionization sources before proceeding on to a discussion on applications and concluding with implications for clinical research.
PubMed: 38435075
DOI: 10.5702/massspectrometry.A0142 -
Applied Spectroscopy Feb 2024Clinical antibodies are an important class of drugs for the treatment of both chronic and acute diseases. Their manufacturability is subject to evaluation to ensure...
Clinical antibodies are an important class of drugs for the treatment of both chronic and acute diseases. Their manufacturability is subject to evaluation to ensure product quality and efficacy. One critical quality attribute is deamidation, a non-enzymatic process that is observed to occur during thermal stress, at low or high pH, or a combination thereof. Deamidation may induce antibody instability and lead to aggregation, which may pose immunogenicity concerns. The introduction of a negative charge via deamidation may impact the desired therapeutic function (i) within the complementarity-determining region, potentially causing loss of efficacy; or (ii) within the fragment crystallizable region, limiting the effector function involving antibody-dependent cellular cytotoxicity. Here we describe a transformative solution that allows for a comparative assessment of deamidation and its impact on stability and aggregation. The innovative streamlined method evaluates the intact protein in its formulation conditions. This breakthrough platform technology is comprised of a quantum cascade laser microscope, a slide cell array that allows for flexibility in the design of experiments, and dedicated software. The enhanced spectral resolution is achieved using two-dimensional correlation, co-distribution, and two-trace two-dimensional correlation spectroscopies that reveal the molecular impact of deamidation. Eight re-engineered immunoglobulin G4 scaffold clinical antibodies under control and forced degradation conditions were evaluated for deamidation and aggregation. We determined the site of deamidation, the overall extent of deamidation, and where applicable, whether the deamidation event led to self-association or aggregation of the clinical antibody and the molecular events that led to the instability. The results were confirmed using orthogonal techniques for four of the samples.
PubMed: 38419510
DOI: 10.1177/00037028241231824 -
The Journal of Biological Chemistry Apr 2024Cytosolic peptide:N-glycanase (PNGase/NGLY1 in mammals) catalyzes deglycosylation of N-glycans on glycoproteins. A genetic disorder caused by mutations in the NGLY1 gene...
Cytosolic peptide:N-glycanase (PNGase/NGLY1 in mammals) catalyzes deglycosylation of N-glycans on glycoproteins. A genetic disorder caused by mutations in the NGLY1 gene leads to NGLY1 deficiency with symptoms including motor deficits and neurological problems. Effective therapies have not been established, though, a recent study used the administration of an adeno-associated viral vector expressing human NGLY1 to dramatically rescue motor functions in young Ngly1 rats. Thus, early therapeutic intervention may improve symptoms arising from central nervous system dysfunction, and assay methods for measuring NGLY1 activity in biological samples are critical for early diagnostics. In this study, we established an assay system for plate-based detection of endogenous NGLY1 activity using a FRET-based probe. Using this method, we revealed significant changes in NGLY1 activity in rat brains during aging. This novel assay offers reliable disease diagnostics and provides valuable insights into the regulation of PNGase/NGLY1 activity in diverse organisms under different stress conditions.
Topics: Animals; Humans; Male; Rats; Aging; Brain; Congenital Disorders of Glycosylation; Fluorescence Resonance Energy Transfer; HEK293 Cells; Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase
PubMed: 38417795
DOI: 10.1016/j.jbc.2024.107121 -
Nutrients Feb 2024the aim of this study was to identify plasma metabolomic markers of Dietary Approaches to Stop Hypertension (DASH) dietary patterns in pregnant women. This study...
the aim of this study was to identify plasma metabolomic markers of Dietary Approaches to Stop Hypertension (DASH) dietary patterns in pregnant women. This study included 186 women who had both dietary intake and metabolome measured from a nested case-control study within the NICHD Fetal Growth Studies-Singletons cohort (FGS). Dietary intakes were ascertained at 8-13 gestational weeks (GW) using the Food Frequency Questionnaire (FFQ) and DASH scores were calculated based on eight food and nutrient components. Fasting plasma samples were collected at 15-26 GW and untargeted metabolomic profiling was performed. Multivariable linear regression models were used to examine the association of individual metabolites with the DASH score. Least absolute shrinkage and selection operator (LASSO) regression was used to select a panel of metabolites jointly associated with the DASH score. Of the total 460 known metabolites, 92 were individually associated with DASH score in linear regressions, 25 were selected as a panel by LASSO regressions, and 18 were identified by both methods. Among the top 18 metabolites, there were 11 lipids and lipid-like molecules (i.e., TG (49:1), TG (52:2), PC (31:0), PC (35:3), PC (36:4) C, PC (36:5) B, PC (38:4) B, PC (42:6), SM (d32:0), gamma-tocopherol, and dodecanoic acid), 5 organic acids and derivatives (i.e., asparagine, beta-alanine, glycine, taurine, and hydroxycarbamate), 1 organic oxygen compound (i.e., xylitol), and 1 organoheterocyclic compound (i.e., maleimide). our study identified plasma metabolomic markers for DASH dietary patterns in pregnant women, with most of being lipids and lipid-like molecules.
Topics: Humans; Female; Pregnancy; Dietary Approaches To Stop Hypertension; Pregnant Women; Dietary Patterns; Case-Control Studies; Hypertension; Lipids; Biomarkers
PubMed: 38398816
DOI: 10.3390/nu16040492 -
ELife Feb 2024Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many...
Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 26 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including RNA-mediated transposition and pseudohyphal growth, filamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement, xylan catabolism and meiosis, development and sexual cycles, infection, and the nervous systems of and . We also show that Q-rich-motif proteins are expanded massively in 10 ciliates with reassigned TAA and TAG codons. Notably, the usage frequency of CAG is much lower in ciliates with reassigned TAA and TAG codons than in organisms with expanded and unstable Q runs (e.g. and ), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.
Topics: Animals; Mice; Codon, Terminator; Drosophila melanogaster; Dictyostelium; Fungal Proteins; Glutamine
PubMed: 38393970
DOI: 10.7554/eLife.91405 -
Food Chemistry: X Mar 2024This study investigated the impact of 60 kV Cold Atmospheric Plasma (CAP) pretreatment for varying durations (5, 10, and 15 min) on potato strip characteristics before...
This study investigated the impact of 60 kV Cold Atmospheric Plasma (CAP) pretreatment for varying durations (5, 10, and 15 min) on potato strip characteristics before and after frying, emphasizing oil uptake, acrylamide formation. Potato samples treated with cap showed significantly better physicochemical characteristics. Scanning electron microscopy revealed deformation of cell wall due to CAP treatment. Fourier-transform infrared spectroscopy indicated structural changes, while X-ray diffraction analysis suggested that starch remained amorphous state in CAP-pretreated samples. Post-frying, CAP-treated potato strips exhibited altered oil distribution with reduced absorption, possibly due to microstructural changes. CAP substantially reduced acrylamide formation during frying by degrading asparagine and inactivating amylase. CAP affected strip color, with increased brightness and decreased redness and yellowness after 14 days. Sensory evaluation showed no significant difference, with prolonged CAP-treated strips receiving higher overall acceptability scores. These findings highlight CAP as a non-thermal technology to enhance fried potato product quality and safety.
PubMed: 38379802
DOI: 10.1016/j.fochx.2024.101194 -
EFSA Journal. European Food Safety... Feb 2024The food enzyme asparaginase (l-asparagine amidohydrolase; EC 3.5.1.1) is produced with the genetically modified strain AGN by DSM Food Specialties B.V. The genetic...
The food enzyme asparaginase (l-asparagine amidohydrolase; EC 3.5.1.1) is produced with the genetically modified strain AGN by DSM Food Specialties B.V. The genetic modifications do not give rise to safety concerns. The food enzyme is free from viable cells of the production organism and its DNA. It is intended to be used to prevent acrylamide formation in food processing. The dietary exposure to the food enzyme-total organic solids (TOS) was estimated to be up to 1.434 mg TOS/kg body weight (bw) per day in European populations. The toxicity studies were carried out with an asparaginase from (strain ASP). The Panel considered this food enzyme as a suitable substitute for the asparaginase to be used in the toxicological studies, because the genetic differences between the production strains are not expected to result in a different toxigenic potential, and the raw materials and manufacturing processes of both food enzymes are comparable. Genotoxicity tests did not indicate a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 1038 mg TOS/kg bw per day, which, when compared with the estimated dietary exposure, resulted in a margin of exposure of at least 724. A search for the similarity of the amino acid sequence of the food enzyme to known allergens was made and no match was found. The Panel considered that the risk of allergic reactions by dietary exposure cannot be excluded, but the likelihood is low. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns under the intended conditions of use.
PubMed: 38379730
DOI: 10.2903/j.efsa.2024.8617 -
Journal of Advanced Veterinary and... Dec 2023This study aimed to examine the concentration of nonessential amino acids (NEAAs) in ruminant feed in tropical areas, with a focus on forage grasses and legumes in...
OBJECTIVE
This study aimed to examine the concentration of nonessential amino acids (NEAAs) in ruminant feed in tropical areas, with a focus on forage grasses and legumes in Indonesia.
MATERIALS AND METHODS
A total of 11 grasses ( and ) and six legumes ( and ) were analyzed for NEAA content using high-performance liquid chromatography (HPLC).
RESULTS
Based on the results of this research, it was found that almost all NEAA content in forage was less than 3% (Serine (Ser), Alanine (Ala), Glycine (Gly), Tyrosine (Tyr), Proline (Pro), Cysteine (Cys), and Asparagine (Asn), except for glutamic (Glu) acid and arginine (Arg) in some legumes. The Glu content in grass ranges from 0.76% to 2.61%, and the Arg content ranges from 0.92% to 2.09%. These two NEAAs were most abundant in grasses and legumes, with concentrations of 5.10% to 6.27% and 3.10% to 5.53%, respectively.
CONCLUSION
Our study concluded that Glu and Arg were the most abundant NEAAs in tropical forages in Indonesia, with legumes having a higher concentration of NEAAs compared to grasses. Among the legumes, had the highest NEAA content (23.40%), while among the forages, had the highest NEAA content (12.37%). However, it was observed that neither legumes nor grasses could fulfill the metabolizable TNEAAs requirements for gaining cattle (250 kg of empty body weight gain), unlike commercial concentrates, which were found to meet the requirements, especially for Arg, Glu, and thyronine. The provision of concentrate is necessary to supplement forage to meet the NEAA needs for cattle.
PubMed: 38370889
DOI: 10.5455/javar.2023.j739