Distribution Of Amino Acids Research Articles

Suppressive cancer nonstop extension mutations increase C-terminal hydrophobicity and disrupt evolutionarily conserved amino acid patterns

Nonstop extension mutations, a.k.a. stop-lost or stop-loss mutations, convert a stop codon into a sense codon resulting in translation into the 3’ untranslated region until the next in-frame stop codon, thereby extending the C-terminus of a protein. In cancer, only nonstop mutations in SMAD4 have been functionally characterized, while the impact of other nonstop mutations remain unknown. Here, we exploit our pan-cancer NonStopDB dataset and test all 2335 C-terminal extensions arising from somatic nonstop mutations in cancer for their impact on protein expression. In a high-throughput screen, 56.1% of the extensions effectively reduce protein abundance. Extensions of multiple tumor suppressor genes like PTEN, APC, B2M, CASP8, CDKN1B and MLH1 are effective and validated for their suppressive impact. Importantly, the effective extensions possess a higher hydrophobicity than the neutral extensions linking C-terminal hydrophobicity with protein destabilization. Analyzing the proteomes of eleven different species reveals conserved patterns of amino acid distribution in the C-terminal regions of all proteins compared to the proteomes like an enrichment of lysine and arginine and a depletion of glycine, leucine, valine and isoleucine across species and kingdoms. These evolutionary selection patterns are disrupted in the cancer-derived effective nonstop extensions.

LLM4THP: a computing tool to identify tumor homing peptides by molecular and sequence representation of large language model based on two-layer ensemble model strategy

Tumor homing peptides (THPs) have a distinctive capacity to specifically attach to tumor cells, providing a promising approach for targeted cancer treatment and detection. Although THPs have the potential for significant impact, their detection by conventional methods is both time-consuming and expensive. To tackle this issue, we provide LLM4THP, an innovative computational approach that utilizes large language models (LLMs) to quickly and effectively detect THPs. LLM4THP utilizes two protein LLMs, ESM2 and Prot_T5_XL_UniRef50, to encode peptide sequences. This allows for the capture of complex patterns and relationships within the peptide data. In addition, we utilize inherent sequence characteristics such as Amino Acid Composition (AAC), Pseudo Amino Acid Composition (PAAC), Amphiphilic Pseudo Amino Acid Composition (APAAC), and Composition, Transition, and Distribution (CTD) to improve the representation of peptides. The RDKitDescriptors feature representation approach transforms peptide sequences into molecular objects and computes chemical characteristics, resulting in enhanced THP identification. The LLM4THP ensemble strategy incorporates various features into a two-layer learning architecture. The first layer consists of LightGBM, XGBoost, Random Forest, and Extremely Randomized Trees, which generate a set of meta results. The second layer utilizes Logistic Regression to further refine the identification of sequences as either THP or non-THP. LLM4THP exhibits exceptional performance compared to the most advanced methods, showcasing enhancements in accuracy, Matthew’s correlation coefficient, F1 score, area under the curve, and average precision. The source code and dataset can be accessed at the following URL: https://github.com/abcair/LLM4THP.

Segment-Based Peptide Design Reveals the Importance of N-Terminal High Cationicity for Antimicrobial Activity Against Gram-Negative Pathogens.

Host defense antimicrobial peptides (AMPs) are recognized candidates to develop a new generation of peptide antibiotics. While high hydrophobicity can be deployed in peptides for eliminating Gram-positive bacteria, high cationicity is usually observed in AMPs against Gram-negative pathogen. This study investigates how the sequence distribution of basic amino acids affects peptide activity. For this purpose, we utilized human cathelicidin LL-37 as a template and designed four highly selective ultrashort peptides with similar length, net charge, and hydrophobic content. LL-10 + , RK-9 + , KR-8 + , and RIK-10 + showed similar activity against methicillin-resistant Staphylococcus aureus in vitro and comparable antibiofilm efficacy in a murine wound model. However, these peptides showed clear activity differences against Gram-negative pathogens with RIK-10 + (i.e., LL-37mini2) being the strongest and LL-10 + the weakest. To understand this activity difference, we characterized peptide toxicity; the effects of salts, pH, and serum on peptide activity; and the mechanism of action and determined the membrane-bound helical structure for RIK-10 + by two-dimensional NMR spectroscopy. By writing an R program, we generated charge density plots for these peptides and uncovered the importance of the N-terminal high-density basic charges for antimicrobial potency. To validate this finding, we reversed the sequences of two peptides. Interestingly, sequence reversal weakened the activity of RIK-10 + but increased the activity of LL-10 + especially against Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii. Those more active peptides with high cationicity at the N-terminus are also more hydrophobic based on HPLC retention times. A database search found numerous natural sequences that arrange basic amino acids primarily at the N-terminus. Combined, this study not only obtained novel peptide leads but also discovered one useful strategy for designing novel antimicrobials to control drug-resistant Gram-negative pathogens.

Nanoscale Chemical Imaging of Amyloid Fibrils in Water Using Total-Internal-Reflection Tip-Enhanced Raman Spectroscopy.

Total-internal-reflection tip-enhanced Raman spectroscopy (TIR-TERS) imaging of amyloid-β (Aβ1-42-L34T) fibrils is performed with nanoscale spatial resolution in water, using TERS tips fabricated by bipolar electrodeposition. Ideal experimental parameters are corroborated by both theoretical simulations and TIR-TERS measurements. TIR-TERS imaging reveals the predominant parallel β-sheet secondary structure of Aβ1-42-L34T fibrils as well as the nanoscale spatial distribution of tyrosine, histidine, and phenylalanine aromatic amino acids. Their proportion in TERS spectra can be qualitatively explained by the combined effect of their localization in the Aβ1-42-L34T fibril structure and their molecular orientation with respect to the excitation laser light polarization. Conclusions drawn from the TERS experiments in water corroborate and significantly enrich our previous study in ambient air, thus confirming that hydration has only a marginal impact on the structure of such amyloid fibrils. This first TIR-TERS study in liquid opens fascinating perspectives for future applications in biology.

Amino Acid Transporters on Amino Acid Absorption, Transport and Distribution in Crops

Amino Acid Transporters on Amino Acid Absorption, Transport and Distribution in Crops

Metabolic imaging in living plants: A promising field for chemical exchange saturation transfer (CEST) MRI.

Magnetic resonance imaging (MRI) is a versatile technique in the biomedical field, but its application to the study of plant metabolism in vivo remains challenging because of magnetic susceptibility problems. In this study, we report the establishment of chemical exchange saturation transfer (CEST) for plant MRI. This method enables noninvasive access to the metabolism of sugars and amino acids in complex sink organs (seeds, fruits, taproots, and tubers) of major crops (maize, barley, pea, potato, sugar beet, and sugarcane). Because of its high signal detection sensitivity and low susceptibility to magnetic field inhomogeneities, CEST analyzes heterogeneous botanical samples inaccessible to conventional magnetic resonance spectroscopy. The approach provides unprecedented insight into the dynamics and distribution of sugars and amino acids in intact, living plant tissue. The method is validated by chemical shift imaging, infrared microscopy, chromatography, and mass spectrometry. CEST is a versatile and promising tool for studying plant metabolism in vivo, with many applications in plant science and crop improvement.

Enhancement of catechin loaded in BSA-pullulan nanoparticles on the oxidation stability of pickering emulsion: Effect of concentration

Preventing and delaying the lipid rancidity especial O/W emulsion system is an important task in the food industry. Low solubility in aqueous/lipid phases and poor stability of catechins limited the antioxidant effect in O/W emulsion. To enhance the oxidative stability of O/W emulsions, bovine serum albumin (BSA)-pullulan (PUL) nanoparticles (BPNs) and catechins-loaded BPNs (BPCNs) were successfully fabricated via self-assembly in this paper. Fourier transform infrared (FTIR) spectra of BPNs and BPCNs indicated that self-assembly of BSA and PUL to form nanoparticles and loading of catechins in BPNs are all maintained through non-covalent interactions. Particle size distribution, zeta-potential, structural characterization and interfacial properties of BPNs and BPCNs showed that catechins act as cross-linking “bridge” among BSA molecules, leading to an increase in the mean particle size, surface charges, interfacial properties, radical scavenging activity of BSA-PUL nanoparticles. Compared with BPNs, BPCNs can significantly enhance the storage stability and oxidative stability of Pickering emulsions. In conclusion, enhancement of BPCNs on oxidative stability of the Pickering emulsions not only because of the radical scavenging activity of the loaded catechins, but also attributed to the effect of catechin loading on the increased interfacial charge and balanced the amino acids distribution of BSA in the BPCNs. This study highlights the excellent properties of BSA-pullulan-catechin nanoparticles as novel emulsifiers with high antioxidant activity and potential applications in the food industry.

Upcycling Shellfish Waste: Distribution of Amino Acids, Minerals, and Carotenoids in Body Parts of North Atlantic Crab and Shrimp.

The snow/pink crab (Chionoecetes opilio) and Northern shrimp (Pandalus borealis) are widely distributed in the North Atlantic Ocean. During processing/consumption, about 80% of the harvest is discarded as processing waste, which is a rich source of protein, chitin, minerals, and carotenoids. This study, for the first time, investigated the proximate composition and individual amino acids, minerals, and carotenoids from different body parts (carapace, shoulder, claw, tip, and leg) of snow crabs and shrimp shells. Shrimp proteins were found to be abundant and well-balanced in their amino acid composition. Compared to shrimp shells, a lower content of amino acids was found in the snow crab, depending on the part of the shell used. Moreover, crab shells, mainly crab claws, contained a higher (p < 0.05) level of chitin compared to shrimp shells. Seven micro-elements (Mn, Fe, Cu, Zn, As, Ba, and Ce) and six macro-elements (Ca, Na, K, Mg, P, and Sr) were identified using inductively coupled plasma-mass spectrometry (ICP-MS). Among them, calcium and iron were higher in crab carapaces (p < 0.05), followed by shrimp shells and other crab shell segments. Additionally, shrimp and crab carapaces contained a significant level of carotenoids, and these were mainly composed of astaxanthin and its mono- and diesters, along with zeaxanthin, astacene, canthaxanthin, and lutein. Thus, this investigation provides detailed information to allow upcycling of shellfish waste and addresses the knowledge gap concerning the availability of various nutrients in different crab sections and shrimp shells.

Methane hydrate formation in amino acids / sodium montmorillonite systems

To understand the occurrence of natural gas hydrates in seabed sediments, it is crucial to examine the mechanisms of methane (CH4) hydrate formation in sodium montmorillonite (Na-Mt) systems in the presence of amino acid. Accordingly, this study employed kinetics experiments and molecular dynamics simulations to investigate CH4 hydrate nucleation and growth in an Na-Mt system containing alanine (Ala), leucine (Leu), and phenylalanine (Phe), respectively. Kinetics and Raman experiments showed that, compared with Ala, Leu and Phe enhanced hydrogen bonding between water molecules surrounding Na-Mt. This enhancement was due to the long carbon chain of Leu and the phenyl ring of Phe and facilitated CH4 hydrate formation. Moreover, in the Na-Mt system, Ala reduced CH4 consumption, whereas Leu and Phe increased CH4 consumption. Molecular dynamics simulations revealed that the strength of electrostatic interactions between the negatively charged Na-Mt surface and the functional groups of amino acids affected the distribution of amino acids, thereby altering CH4 aggregation and CH4 hydrate nucleation processes. The strong interaction between Na-Mt and Ala significantly disrupted interfacial interactions between Na-Mt and water molecules. In contrast, the weaker interactions between Na-Mt and Leu and Phe, respectively, meant that these amino acids affected CH4 hydrate nucleation in the bulk-like solution by influencing the arrangement of water molecules. These findings indicate that interfacial interactions between Na-Mt and amino acids play a crucial role in CH4 hydrate formation. Overall, this study generated insights into the formation kinetics and nucleation properties of CH4 hydrates in clay mineral–amino acid complexes that may increase understanding about the occurrence of natural gas hydrates in marine sediments.

Unveiling the genetic landscape: Exploring the SSR-based genetic architecture and amino acid dissection of Gossypium barbadense and G. darwinii genomes

Genetic maps highlight the genome organization and structure but also provide the chance of tagging superior traits for crop improvement through marker-assisted selection. Amino acids are building blocks of proteins and perform crucial function in regulating the signaling of molecules involved in the development and growth of plants. Plant architecture also have an impact on crop productivity. In order to select elite cultivars for breeding and identification of favorable alleles and their functional properties, a deep understanding of genetic architecture and development of genetic map is essential. In present investigation, an interspecific cross of Gossypium barbadense XH-18 × G. darwinii 5-7 was made to develop a genetic map utilizing single sequence repeat markers for the dissection of amino acids involved in genetic architecture of G. barbadense and G. darwinii. We measured chromosomal distribution of 20 amino acids across the whole genome of both species. The map consists of 613 markers spread across all 26 chromosomes, covering 2371.4 cM of cotton genome with an average inter-marker distance of 9.35 cM. The marker number anchored on the chromosomes varied from 5 to 76 with an average of 23.57 on each chromosome. The Dt sub-genome had more markers (83.03%) than the At sub-genome (15.66%). Moreover, the longest chromosome was 143.387 cM, the shortest was 58.430 cM, and the average length was 91.207 cM. The Dt subgenome spans a greater genomic distance than the At subgenome. A sum of 21,035 genes were discovered, covering the complete genome of G. barbadense; G. darwinii and have been found to be involved in tRNA 3'-trailer cleavage, macromolecule modification, peptide deformylase activity, response to biotic stimulus and defense response. The minimum Glutamic acid (Glu), Histidine (His), and Lysine (Lys) were found on Chr.13 (0.00-17.74), Chr.02 (0.00-8.01), and Chr.06 (0.00-17.97), respectively found through chromosomal amino acid dissection. The genome-wide SSR interspecific genetic map of G. barbadense and G. darwinii is first of its kind, and studying chromosomal distribution of amino acids will set a landmark step to dissect the genome structure of G. darwinii.

Haemonchus contortus alters distribution and utilization of protein and amino acids in different tissues of host sheep

The objective was to determine host animal protein/amino acid redistribution and use among the abomasum, duodenum and muscle of sheep infected with Haemonchus contortus. Sixteen male Ujumqin sheep (32.4 ± 3.9 kg) were dewormed and randomly assigned to two groups, infected or not infected with H. contortus (GIN and CON). The GIN group had lower (P < 0.05) dry matter intake, average daily gain, and live body weight than CON, with extensive focal infiltration of lymphocytes in the lamina propria and bottom of the abomasal epithelium. In the abomasum and duodenum, there were 100 and 220 genes, respectively, that were up-regulated, whereas 56 and 149 were down-regulated. In the abomasum, the most enriched KEGG pathways were related to immunity and inflammation reaction, including: viral protein interaction with cytokine and cytokine receptor (P = 0.017), influenza A (P = 0.030), IL-17 signaling pathway (P = 0.030). In the duodenum, KEGG pathways were more enriched in nutrient metabolism, including pancreatic secretion (P < 0.001), protein digestion and absorption (P < 0.001), graft-versus-host disease (P = 0.004). Furthermore, most genes related with the above KEGG pathways were increased in the abomasum but decreased in the duodenum. Amino acid profiles in abomasum and duodenum of CON and GIN groups were clustered in a partial least-squares discriminant analysis model, with significant changes in 36 and 19 metabolites in abomasal and duodenal chyme, respectively. Further confirmed by transcriptome-targeted metabolome association analysis, GIN mainly enhanced metabolism of arginine and sulphur amino acids in abomasum and those metabolic pathways were associated. Meanwhile, GIN mainly decreased pyruvate related amino acid metabolism in duodenum. Moreover, concentrations of Arg (P = 0.036), His (P = 0.027), and Cys (P = 0.046) in longissimus thoracis et lumborum were decreased in GIN, whereas concentrations of Gly (P = 0.012) and Ala (P = 0.046) were increased. In conclusion, H. contortus enhanced metabolism of arginine and sulphur amino acids in the abomasum; decreased pyruvate metabolism in the duodenum; and drove more protein/amino acids for abomasal tissues to resist physical and immune damage, reducing protein and amino acids in duodenum and muscle for support host growth. Specific nutrients (such like arginine, histidine, and cysteine) may play important role in control gastrointestinal nematode infection for ruminant.

Alterations in the gut microbiome and metabolism profiles reveal the possible molecular mechanism of renal injury induced by hyperuricemia in a mouse model of renal insufficiency

Objectives: To investigate the role of the intestinal flora and metabolites in the development of hyperuricemic renal injury in chronic kidney disease (CKD).Methods: Unilaterally nephrectomized mice were fed with adenine and potassium oxonate for 9 weeks. HE staining combined with plasma biochemical indicators was used to evaluate renal pathological and functional changes. We conducted 16S rRNA sequencing and untargeted metabolomics on feces and plasma samples to reveale changes in intestinal microbiota and metabolites.Result: Our analysis revealed significant differences in 15 bacterial genera, with 7 being upregulated and 8 being downregulated. Furthermore, metabolomic analysis revealed changes in the distribution of amino acid and biotin metabolites in basic metabolic pathways in both feces and serum. Specifically, differentially abundant metabolites in feces were associated primarily with histidine metabolism; the biosynthesis of phenylalanine, tyrosine, and tryptophan; and tyrosine metabolism. In plasma, the differentially abundant metabolites were involved in multiple metabolic pathways, including aminoacyl-tRNA biosynthesis; glycine, serine, and threonine amino acid metabolism; valine, leucine, and isoleucine biosynthesis; tyrosine biosynthesis and metabolism; biotin metabolism; and taurine and hypotaurine metabolism. Furthermore, correlation analysis revealed that Akkermansia, UCG-005, Lachnospiraceae_NK4A136_group, Lactococcus, and Butymonas were associated with various differentially abundant metabolites as well as renal function, oxidative stress, and mitophagy. The changes in the intestinal flora observed in hyperuricemia may lead to imbalances in amino acid and biotin metabolism in both the intestine and host, ultimately affecting oxidative stress and mitophagy in mice and accelerating the progression of CKD.Conclusion: Our findings provide insights into a potential pathogenic mechanism by which hyperuricemia exacerbates renal injury in mice with renal insufficiency. Understanding these pathways may offer new therapeutic strategies for managing hyperuricemic renal injury in CKD patients.

Cellular Contributions to Glymphatic and Lymphatic Waste Clearance in the Brain.

Cerebrospinal fluid (CSF) bathes and cushions the brain; however, it also serves a major role in the clearance of metabolic wastes and in the distribution of glucose, lipids, and amino acids. Unlike every other organ in the body, the brain parenchyma lacks a traditional lymphatic system to drain fluids and central nervous system (CNS) antigens. It was historically assumed that all brain wastes were removed by endogenous processing, such as phagocytosis and autophagy, while excess fluids drained directly into the blood. However, the twin discoveries of the glial-lymphatic (glymphatic) system and meningeal lymphatics have transformed our understanding of brain waste clearance. The glymphatic system describes the movement of fluids through the subarachnoid space (SAS), the influx along periarterial spaces into the brain parenchyma, and the ultimate efflux back into the SAS along perivenous spaces where it comes into direct contact with the meningeal lymphatics. The dura mater of the meninges contains a bona fide lymphatic network that can drain CSF that has entered the dura. Together, these pathways provide insights into the clearance of molecules and fluids from the brain, and show that the CNS is physically connected to the adaptive immune system. Here, we outline the glymphatic and lymphatic systems, and describe the cellular components that are important to their function.

Structure-informed protein language models are robust predictors for variant effects.

Emerging variant effect predictors, protein language models (pLMs) learn evolutionary distribution of functional sequences to capture fitness landscape. Considering that variant effects are manifested through biological contexts beyond sequence (such as structure), we first assess how much structure context is learned in sequence-only pLMs and affecting variant effect prediction. And we establish a need to inject into pLMs protein structural context purposely and controllably. We thus introduce a framework of structure-informed pLMs (SI-pLMs), by extending masked sequence denoising to cross-modality denoising for both sequence and structure. Numerical results over deep mutagenesis scanning benchmarks show that our SI-pLMs, even when using smaller models and less data, are robustly top performers against competing methods including other pLMs, which shows that introducing biological context can be more effective at capturing fitness landscape than simply using larger models or bigger data. Case studies reveal that, compared to sequence-only pLMs, SI-pLMs can be better at capturing fitness landscape because (a) learned embeddings of low/high-fitness sequences can be more separable and (b) learned amino-acid distributions of functionally and evolutionarily conserved residues can be of much lower entropy, thus much more conserved, than other residues. Our SI-pLMs are applicable to revising any sequence-only pLMs through model architecture and training objectives. They do not require structure data as model inputs for variant effect prediction and only use structures as context provider and model regularizer during training.

Lotus seed protein ameliorates hepatic lipid metabolic disorders in high-fat diet-fed mice via activating the PPARα signaling pathway

Obesity, one of the prevalent chronic diseases globally, is a serious threat to human health. Dietary natural compounds intervention is an effective means to alleviate obesity. The objective of this study was to investigate the potential protective role of lotus seed protein (LSP) against obesity. The results of amino acid composition analysis indicated that LSP possessed a well-balanced distribution of amino acids and was rich in branched-chain amino acids (BCAAs). Meanwhile, LSP exhibited better ABTS radical scavenging, DPPH radical scavenging, hydroxyl radical scavenging, and Fe2+ chelating ability in vitro. In vivo, LSP intervention remarkably alleviated body weight gain, organ index gain, dyslipidemia, and hepatic lipid deposition in high-fat diet (HFD)-fed mice. Meanwhile, LSP enhanced hepatic antioxidant enzyme activities (superoxide dismutase (SOD) and catalase (CAT)) and decreased malondialdehyde (MDA) levels, subsequently alleviated liver injury. In addition, LSP intervention significantly improved insulin sensitivity and glucose tolerance in obese mice, thereby alleviating hyperglycemia and insulin resistance. At the molecular level, LSP intervention up-regulated the mRNA and protein expression of fatty acid oxidation-related genes (FATP1, CPT-1a, ACOX1) and down-regulated the mRNA and protein expression of lipid synthesis-related genes (SREBP-1c, ACC, SCD-1, FASN) by activating the PPARα signaling pathway, thereby promoting hepatic fatty acid oxidation and reducing lipogenesis. These results demonstrate that LSP has the potential as a dietary supplementation to prevent and ameliorate obesity.

Sperm-Specific CatSper is Not Conserved in All Vertebrates and May Not be the Only Progesterone-Responsive Ion Channel Present in Sperm.

Progesterone (P4) acts as a key conserved signalling molecule in vertebrate reproduction. P4 is especially important for mature sperm physiology and subsequent reproductive success. "CatSpermasome", a multi-unit molecular complex, has been suggested to be the main if not the only P4-responsive atypical Ca2+-ion channel present in mature sperm. Altogether, here we analyse the protein sequences of CatSper1-4 from more than 500 vertebrates ranging from early fishes to humans. CatSper1 becomes longer in mammals due to sequence gain mainly at the N-terminus. Overall the conservation of full-length CatSper1-4 as well as the individual TM regions remain low. The lipid-water-interface residues (i.e. a 5 amino acid stretch sequence present on both sides of each TM region) also remain highly diverged. No specific patterns of amino acid distributions were observed. The total frequency of positively charged, negatively charged or their ratios do not follow in any specific pattern. Similarly, the frequency of total hydrophobic, total hydrophilic residues or even their ratios remain random and do not follow any specific pattern. We noted that the CatSper1-4 genes are missing in amphibians and the CatSper1 gene is missing in birds. The high variability of CatSper1-4 and gene-loss in certain clades indicate that the "CatSpermasome" is not the only P4-responsive ion channel. Data indicate that the molecular evolution of CatSper is mostly guided by diverse hydrophobic ligands rather than only P4. The comparative data also suggest possibilities of other Ca2+-channel/s in vertebrate sperm that can also respond to P4.

Structural arrangement, electroconductivical and electrochemical behaviours of solid amino acid-based electrodes

This paper presents the study on the structural dependence of the electroconductivity and electrochemical activity of model amino acids, aspartate and glycine, which are used as solid electrodes in hybrid capacitor systems. It has been established that the presence of carbonyl, aliphatic, and amide functional groups on the surface enhances the electrochemical activity and electrical conductivity. The frequency dependence of conductivity is typical for polymer compounds with a proton conduction mechanism, which is provided by the surface migration of the charge. It was found that deposition on the surface of carbon templates of the amino acids in the formation of biocomposites increases the number of active reaction centers and provides effective electronic charge transport. As a result, it leads to a significant increase in the contribution of pseudocapacitance and capacitance processes. The electrochemical activity was caused by the pseudocapacitive accumulation of charge due to the course of redox reactions with amino acids and capacitive accumulation of charge, which occurs with the participation of amino acids and carbon templates. It has been proven that the porous structure of the carbon nanotubes provides a more dispersed and uniform distribution of amino acids on the surface, which is ensured in the growth of pseudocapacitive charge accumulation.

Effects of dietary β‐carotene on color and flavor quality of ovaries in adult female Chinese mitten crab (Eriocheir sinensis)

AbstractThis study aimed to investigate the effects of adding different levels (0, 50, 100, 200 and 300 mg/kg) of dietary β‐carotene on the color and flavor quality of adult female E. sinensis ovaries. Adding moderate amount of β‐carotene to the feed could regulate the distribution of carotenoids, fatty acids, and free amino acids in the ovaries of E. sinensis, as well as increase the content of total carotenoids, total fatty acids, sweet and umami amino acids in the ovaries. The dietary β‐carotene have limited coloring effects and a significant impact on the flavor of the ovaries. During thermal process, the addition of 100 mg/kg β‐carotene could effectively promote formation of aroma precursors and generate more characteristic aroma components (2‐methylbutanal, 3‐methylbutanal, hexanal, benzaldehyde, methylpyrazine). However, excessive β‐carotene supplementation (300 mg/kg) led to adverse effects on physiological metabolism and flavor of E. sinensis ovaries. Considering both feed cost and quality improvement, β‐carotene supplementation at 100 mg/kg can be considered the optimal feed supplementation for adult female E. sinensis within a 70‐day rearing period to improve edible quality of ovaries.

Insights into the quality changes of edible sea urchin (Echinus esculentus) gonads during ice storage

The study aimed to assess the quality changes of E. esculentus gonads during 14-days of ice storage. Microbial quality and community composition succession were examined using both culture-dependent and independent methods. Additionally, the chemical profile, including spoilage metabolite production, proximate composition, fatty acids and amino acids distribution, was investigated. Colorimetric and texture parameters were also assessed. Microbial counts were relatively stable until day 4, followed by rapid growth, reaching 7.3 ± 0.1 log CFU/g on day 8 for psychrotrophic counts. Pseudomonas emerged as the primary specific spoilage organism, followed by Photobacterium and Psychrobacter. Concurrently, inosine, hypoxanthine and biogenic amines formation correlated with the rapid microbial proliferation. The fresh gonads' lipid consisted of 29.4 ± 1.0% SFA, 18.7 ± 1.0% MUFA and 46.5 ± 2.7% PUFA, with no significant changes up to day 8 of ice storage. The initial ratio of essential to non-essential amino acids was 62.3 ± 1.8% and declined during storage, while the concentration of free amino acids significantly increased after 4 days of ice storage. Notable shifts in the lightness and texture parameters coincided with the water content reduction. Overall, the results indicated satisfactory gonad quality for up to 4 days of ice storage, beyond which significant degradation and spoilage processes were initiated. This study could offer insights to enhance comprehension and prolong the quality stability of gonads.

Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast

Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, "universal" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.