m6Aexpress-enet: Predicting the regulatory expression m6A sites by an enet-regularization negative binomial regression model.

As the most abundant mRNA modification, m6A controls and influences many aspects of mRNA metabolism including the mRNA stability and degradation. However, the role of specific m6A sites in regulating gene expression still remains unclear. In additional, the multicollinearity problem caused by the correlation of methylation level of multiple m6A sites in each gene could influence the prediction performance. To address the above challenges, we propose an elastic-net regularized negative binomial regression model (called m6Aexpress-enet) to predict which m6A site could potentially regulate its gene expression. Comprehensive evaluations on simulated datasets demonstrate that m6Aexpress-enet could achieve the top prediction performance. Applying m6Aexpress-enet on real MeRIP-seq data from human lymphoblastoid cell lines, we have uncovered the complex regulatory pattern of predicted m6A sites and their unique enrichment pathway of the constructed co-methylation modules. m6Aexpress-enet proves itself as a powerful tool to enable biologists to discover the mechanism of m6A regulatory gene expression. Furthermore, the source code and the step-by-step implementation of m6Aexpress-enet is freely accessed at https://github.com/tengzhangs/m6Aexpress-enet.

Comparative Proteomics Elucidates the Potential Mechanism of Sperm Capacitation of Chinese Mitten Crabs (Eriocheir sinensis).

Sperm capacitation is broadly defined as a suite of biochemical and biophysical changes resulting from the acquisition of fertilization ability. To gain insights into the regulation mechanism of crustacean sperm capacitation, 4D label-free quantitative proteomics was first applied to analyze the changes of sperm in Eriocheir sinensis under three sequential physiological conditions: seminal vesicles (X2), hatched with the seminal receptacle content (X3), and incubated with egg water (X5). In total, 1536 proteins were identified, among which 880 proteins were quantified, with 82 and 224 proteins significantly altered after incubation with the seminal receptacle contents and egg water. Most differentially expressed proteins were attributed to biological processes by Gene Ontology annotation analysis. As the fundamental bioenergetic metabolism of sperm, the oxidative phosphorylation, glycolysis, and the pentose phosphate pathway presented significant changes under the treatment of seminal receptacle contents, indicating intensive regulation for sperm in the seminal receptacle. Additionally, the seminal receptacle contents also significantly increased the oxidation level of sperm, whereas the enhancement of abundance in superoxide dismutase, peroxiredoxin 1, and glutathione S-transferase after incubation with egg water significantly improved the resistance against oxidation. These results provided a new perspective for reproduction studies in crustaceans.

Progress in extracellular vesicle homeostasis as it relates to cardiovascular diseases.

Extracellular vesicles (EVs) are involved in both physiological and pathological processes in many organ systems and are essential in mediating intercellular communication and maintaining organismal homeostasis. It is helpful to propose new strategies for disease treatment by elucidating the mechanisms of EV release and sorting. An increasing number of studies have shown that there is specific homeostasis in EVs, which is helpful for the human body to carry out physiological activities. In contrast, an EV homeostasis im-balance promotes or accelerates disease onset and development. Alternatively, regulating the quality of EVs can maintain homeostasis and even achieve the purpose of treating conditions. An analysis of the role of EV homeostasis in the onset and development of cardiovascular disease is presented in this review. This article also summarizes the methods that regulate EV homeostasis and their application in cardiovascular diseases. In particular, this study focuses on the connection between EV steady states and the cardiovascular system and the potential value of EVs in treating cardiovascular diseases.

Near-field coupling of interlayer excitons in MoSe2/WSe2 heterobilayers to surface plasmon polaritons.

Two-dimensional (2D) transition metal dichalcogenides have emerged as promising quantum functional blocks benefitting from their unique combination of spin, valley, and layer degrees of freedom, particularly for the tremendous flexibility of moiré superlattices formed by van der Waals stacking. These degrees of freedom coupled with the enhanced Coulomb interaction in 2D structures allow excitons to serve as on-chip information carriers. However, excitons are spatially circumscribed due to their low mobility and limited lifetime. One way to overcome these limitations is through the coupling of excitons with surface plasmon polaritons (SPPs), which facilitates an interaction between remote quantum states. Here, we showcase the successful coupling of SPPs with interlayer excitons in molybdenum diselenide/tungsten diselenide heterobilayers. Our results indicate that the valley polarization can be efficiently transferred to SPPs, enabling preservation of polarization information even after propagating tens of micrometers.

A pattern recognition receptor interleukin-1 receptor is involved in reproductive immunity in Macrobrachium nipponense ovary.

The family of TIR domain-containing receptors includes numerous proteins involved in innate immunity. In this study, a member of this family was characterized from the ovary of the oriental river prawn Macrobrachium nipponense and identified as interleukin-1 receptor (MnIL-1R). Meanwhile, to elucidate the conservation of IL-1R, its orthologous were identified in several crustacean species as well. In addition, the expression pattern of MnIL-1R in various adult tissues and post different pathogen-associated molecular patterns (PAMPs) challenge in ovary was analyzed with qRT-PCR technology. Finally, the roles of MnIL-1R in the ovary were analyzed by RNAi technology. The main results are as follows: (1) MnIL-1R comprises a 1785 bp ORF encoding 594 amino acids and is structurally composed of five domains: a signal peptide, two immunoglobulin (IG) domains, a transmembrane region, and a TIR-2 domain; (2) the TIR domain showed a high conservation among analyzed crustacean species; (3) MnIL-1R is widely detected in all tested tissues including ovary; (4) MnIL-1R showed a positive response to challenges with LPS, PGN, and polyI:C in the ovary; (5) its IG domain showed strong binding ability to LPS and PGN, confirming its role as a pattern recognition receptor; (6) the expression patterns of several members of the Toll signaling pathway (Myd88, TRAF-6, Dorsal, and Relish) was similar to that of MnIL-1R after challenges with LPS, PGN, and polyI:C in the ovary; (7) the silencing of MnIL-1R resulted in down-regulation of theses gene' (Myd88, TRAF-6, Dorsal, and Relish) expression level in the ovary. These results suggest that MnIL-1R can activate the Toll signaling pathway in the ovary by directly recognizing LPS and PGN through its IG domain, thereby contributing to the immune response in the ovary of M. nipponense.

Micropeptides: origins, identification, and potential role in metabolism-related diseases. / å¾®è‚½ï¼šèµ·æºã€é‰´å®šåŠå ¶åœ¨ä»£è°¢ç›¸å ³ç–¾ç— ä¸­çš„ä½œç”¨.

With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides (miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function. MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.

Antioxidant Peptides Derived from Millet Bran Promote Longevity and Stress Resistance in Caenorhabditis elegans.

Millet bran as a by-product of millet grain processing remains a reservoir of active substances. In this study, functional millet bran peptides (MBPE) were obtained from bran proteins after alcalase hydrolysis and ultrafiltration. The activity of MBPE was assessed in vitro and in the model organism Caenorhabditis elegans (C. elegans). In vitro, compared to unhydrolyzed proteins, MBPE significantly enhanced the 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-Azinobis-(3-ethylbenzthiazoline-6-sulphonate (ABTS) and hydroxyl radicals scavenging activity, and the scavenging rate of MBPE with 15,000 U/g alcalase reached 42.79 ± 0.31%, 61.38 ± 0.41 and 45.69 ± 0.84%, respectively. In C. elegans, MBPE at 12.5 µg/mL significantly prolonged the lifespan by reducing lipid oxidation, oxidative stress, and lipofuscin levels. Furthermore, MBPE increased the activities of the antioxidant enzymes. Genetic analyses showed that MBPE-mediated longevity was due to a significant increase in the expression of daf-16 and skn-1, which are also involved in xenobiotic and oxidative stress responses. In conclusion, this study found that MBPE had antioxidant and life-prolonging effects, which are important for the development and utilization of millet bran proteins as resources of active ingredients.

In-Plane Electric-Field-Induced Orbital Hybridization of Excitonic States in Monolayer WSe_{2}.

The giant exciton binding energy and the richness of degrees of freedom make monolayer transition metal dichalcogenide an unprecedented playground for exploring exciton physics in 2D systems. Thanks to the well-energetically separated excitonic states, the response of the discrete excitonic states to the electric field could be precisely examined. Here we utilize the photocurrent spectroscopy to probe excitonic states under a static in-plane electric field. We demonstrate that the in-plane electric field leads to a significant orbital hybridization of Rydberg excitonic states with different angular momentum (especially orbital hybridization of 2s and 2p) and, consequently, optically actives 2p-state exciton. Besides, the electric-field controlled mixing of the high lying exciton state and continuum band enhances the oscillator strength of the discrete excited exciton states. This electric field modulation of the excitonic states in monolayer TMDs provides a paradigm of the manipulation of 2D excitons for potential applications of the electro-optical modulation in 2D semiconductors.

Research on the Relationship between Exosome Production and Atherosclerosis.

Atherosclerosis (AS) is the leading cause of cardiovascular disease, causing a major burden on patients as well as families and society. Exosomes generally refer to various lipid bilayer microvesicles originating from different cells that deliver various bioactive molecules to the recipient cells, exerting biological effects in cellular communication and thereby changing the internal environment of the body. The mechanisms of correlation between exosomes and the disease process of atherosclerosis have been recently clarified. Exosomes are rich in nucleic acid molecules and proteins. For example, the exosome miRNAs reportedly play important roles in the progression of atherosclerotic diseases. In this review, we focus on the composition of exosomes, the mechanism of their biogenesis and release, and the commonly used methods for exosome extraction. By summarizing the latest research progress on exosomes and atherosclerosis, we can explore the advances in the roles of exosomes in atherosclerosis to provide new ideas and targets for atherosclerosis prevention, diagnosis, and treatment.

Assessment of genetic diversity and population structure of Neocaridina denticulata sinensis in the Baiyangdian drainage area, China, using microsatellite markers and mitochondrial cox1 gene sequences.

Neocaridina denticulata sinensis is a crustacean of major economic significance in the Baiyangdian drainage area. In this study, the first assessment of N. denticulata sinensis genetic diversity and population structure was performed based on sequence analysis of nine polymorphic microsatellite loci and the mitochondrial cytochrome oxidase subunit I (cox1) gene. Samples (n = 192) were collected from four different regions in the Baiyangdian drainage area i.e., Baiyangdian Lake, Jumahe River, Xidayang Reservoir, and Fuhe River. Microsatellite loci analysis identified high levels of genetic diversity represented by observed heterozygosity (Ho) of 0.6865 âˆ¼ 0.9583, expected heterozygosity (He) of 0.7151 âˆ¼ 0.8723, and polymorphism information content (PIC) of 0.6676 âˆ¼ 0.8585. Based on the analysis of cox1 sequences, haplotype diversity (Hd) ranged from 0.568 to 0.853 while nucleotide diversity (π) ranged from 0.0029 to 0.2236. Furthermore, there was no evidence of expansion events in the N. denticulata sinensis populations. Pairwise FST revealed pronounced genetic differentiation, and clustering analyses showed defined genetic structures within the N. denticulata sinensis population. Three groups were identified from four sampled stocks, with Xidayang Reservoir, and Fuhe River populations clustered in the same group. This work identified novel molecular markers and provided an important reference to guide management strategies to assist conservation of N. denticulata sinensis resources.

Proso millet peroxidase-mediated degradation and detoxification of Rhodamine B in water.

Enzymatic catalysis is a promising approach for the degradation of organic pollutants and peroxidases (PODs) are one of the most common enzyme classes used to degrade organic pollutants. Proso millet peroxidase (PmPOD) is a peroxidase extracted and purified from proso millet bran which is the by-product of proso millet processing. In this study, we investigated the effects of PmPOD on the degradation of typical organic pollutants (Rhodamine B (RhB), bisphenol A, sulfadiazine) for the first time. Moreover, we screened RhB as the substrate with the best degradation effect. The degradation rate of RhB catalyzed by PmPOD (10 nM) reached 99.46% in 30 min under the optimal conditions (pH 5, 30°C, and molar ratio of RhB, H2O2 and HOBT of 1:9.58:1.94 × 10-3). The reaction kinetics parameters of PmPOD-mediated RhB degradation Km, Vmax and kcat were 62.2, 935.7 and 9.357 × 104, respectively. High-performance liquid chromatography analyses confirmed that PmPOD transformed RhB into two new products. Furthermore, toxicological evaluation in Caenorhabditis elegans demonstrated that 10 µg/mL RhB significantly reduced the lifespan by 8.3%, reduced the motility and pharynx-pumping rate compared with the control group, while the 10 µg/mL RhB product had no significant effect on these indexes. These data indicated that the toxicity of RhB disappeared after catalytic degradation by PmPOD. Taken together, these data suggest that catalysis of PmPOD is an effective method for degradation and detoxification of RhB. This study provides a potential candidate method for the biological treatment of RhB, and improves the added value of proso millet bran.

Oxidized quercetin has stronger anti-amyloid activity and anti-aging effect than native form.

Quercetin (QUE) is one of the most widely distributed and used flavonoid. It has many biological activities and pharmacological effect. As a polyhydroxy phenol, QUE is easily oxidized. However, it is unclear how its biology efficacy changes after oxidation. In this study, we prepared QUE oxidation product (QUE-ox) through enzymatic oxidation of QUE. We found the oxidation reduced the antioxidant activity of QUE but increased its anti-amyloid activity in vitro. In C. elegans, oxidation increased the anti-aging effects of QUE. Further experiments showed that both QUE and QUE-ox delayed aging by improving stress resistance, but they have different molecular mechanisms. QUE mainly increased the transcriptional activities of DAF-16 and SKN-1, resulting in the enhancement of expression of oxidative stress resistance genes, and further increased the oxidative resistance in C. elegans. QUE-ox increased the transcriptional activities of DAF-16 and HSF-1 transcription factors to enhance the heat stress resistance. In summary, our study indicated oxidized QUE has stronger anti-amyloid activity and anti-aging effect than native form. This study provides a theoretical basis for the safe and rational application of QUE, especially for its antioxidant, anti-amyloid and anti-aging effects.

Characterization of the LysP2110-HolP2110 Lysis System in Ralstonia solanacearum Phage P2110.

Ralstonia solanacearum, a pathogen causing widespread bacterial wilt disease in numerous crops, currently lacks an optimal control agent. Given the limitations of traditional chemical control methods, including the risk of engendering drug-resistant strains and environmental harm, there is a dire need for sustainable alternatives. One alternative is lysin proteins that selectively lyse bacteria without contributing to resistance development. This work explored the biocontrol potential of the LysP2110-HolP2110 system of Ralstonia solanacearum phage P2110. Bioinformatics analyses pinpointed this system as the primary phage-mediated host cell lysis mechanism. Our data suggest that LysP2110, a member of the Muraidase superfamily, requires HolP2110 for efficient bacterial lysis, presumably via translocation across the bacterial membrane. LysP2110 also exhibits broad-spectrum antibacterial activity in the presence of the outer membrane permeabilizer EDTA. Additionally, we identified HolP2110 as a distinct holin structure unique to the Ralstonia phages, underscoring its crucial role in controlling bacterial lysis through its effect on bacterial ATP levels. These findings provide valuable insights into the function of the LysP2110-HolP2110 lysis system and establish LysP2110 as a promising antimicrobial agent for biocontrol applications. This study underpins the potential of these findings in developing effective and environment-friendly biocontrol strategies against bacterial wilt and other crop diseases.

Sequence Analysis and Biochemical Characteristics of Two Non-specific Lipid Transfer Proteins from Tartary Buckwheat Seeds.

INTRODUCTION: Plant non-specific lipid transfer proteins (nsLTPs) play an important role in plant resistance to various stresses, and show potential applications in agriculture, industrial manufacturing, and medicine. In addition, as more and more nsLTPs are identified as allergens, nsLTPs have attracted interest due to their allergenicity. Two nsLTPs from Tartary buckwheat have been isolated and identified. There is a need to study their biochemical characteristics and allergenicity. OBJECTIVE: The study aims to investigate the biochemical characteristics of two nsLTPs from Tartary buckwheat seeds and evaluate their potential allergenicity. METHODS: Two nsLTPs derived from Tartary buckwheat, namely FtLTP1a and FtLTP1b, were produced by gene cloning, expression, and purification. Sequence analysis and biochemical characteristics of the proteins, including lipid binding ability, α-amylase inhibition activity, antifungal activity, and allergenic activity, were investigated. RESULTS: High-purity recombinant FtLTP1a and FtLTP1b were obtained. FtLTP1a and FtLTP1b exhibited similar lipid binding and antifungal properties. Only FtLTP1b showed weak inhibitory activity against α-amylase. CONCLUSION: FtLTP1b could specifically bind IgE in the serum allergic to buckwheat and cross-react with pollen (w6). FtLTP1b is a novel allergenic member of the lipid-transfer protein 1 family found in Tartary buckwheat.

Self-attention enabled deep learning of dihydrouridine (D) modification on mRNAs unveiled a distinct sequence signature from tRNAs.

Dihydrouridine (D) is a modified pyrimidine nucleotide universally found in viral, prokaryotic, and eukaryotic species. It serves as a metabolic modulator for various pathological conditions, and its elevated levels in tumors are associated with a series of cancers. Precise identification of D sites on RNA is vital for understanding its biological function. A number of computational approaches have been developed for predicting D sites on tRNAs; however, none have considered mRNAs. We present here DPred, the first computational tool for predicting D on mRNAs in yeast from the primary RNA sequences. Built on a local self-attention layer and a convolutional neural network (CNN) layer, the proposed deep learning model outperformed classic machine learning approaches (random forest, support vector machines, etc.) and achieved reasonable accuracy and reliability with areas under the curve of 0.9166 and 0.9027 in jackknife cross-validation and on an independent testing dataset, respectively. Importantly, we showed that distinct sequence signatures are associated with the D sites on mRNAs and tRNAs, implying potentially different formation mechanisms and putative divergent functionality of this modification on the two types of RNA. DPred is available as a user-friendly Web server.

Zhuyeqing liquor promotes longevity through enhancing stress resistance via regulation of SKN-1 and HSF-1 transcription factors in Caenorhabditis elegans.

Zhuyeqing liquor (ZYQL) is well-known traditional functional liquor in China that contains twelve crude drugs. Studies have shown that ZYQL has many beneficial effects, but its anti-aging effect has not been reported. Here, we found that ZYQL had excellent antioxidant activity in vitro. In C. elegans, ZYQL could significantly extend the lifespan, and decreased aging related phenotype including accumulation of lipofuscin and the decrease of food intake and motility. Further, ZYQL significantly reduced ROS level and enhanced the antioxidant defense in C. elegans. ZYQL increased transcriptional activity of transcription factors HSF-1 and SKN-1, and ZYQL-mediated longevity was dependent on these factors. Taken together, the data suggested that ZYQL enhanced the transcriptional activity of transcription factors HSF-1 and SKN-1, which in turn increased oxidative/heat stress resistance to exert its anti-aging effect in C. elegans. Our results provide new insights into the beneficial effects and underlying mechanisms of ZYQL, which might be useful for further developing ZYQL into health or anti-aging beverages.

Exosomal circ-1199 derived from EPCs exposed to oscillating shear stress acts as a sponge of let-7g-5p to promote endothelial-mesenchymal transition of EPCs by increasing HMGA2 expression.

AIMS: Our previous study showed that oscillatory shear stress (OSS) induces endothelial progenitor cells (EPCs) to undergo endothelial to mesenchymal transition (EndoMT), which may contribute to the onset and progression of atherosclerosis (AS). However, the underlying mechanisms have not been elucidated. A recent study showed that exosomes (Exos) released from EPCs played a key role in various cardiovascular diseases. The purpose of this study was to identify the role and mechanism of Exos released by EPCs exposed to OSS in EPC EndoMT. MAIN METHODS: EPCs derived from the human umbilical cord blood were cultured and characterized. The Flexcell flow STR-4000 parallel plate flow chamber system was employed to apply OSS (±3.5 dyne/cm2, 1 Hz) to EPCs for 12 h. Then, Exos were extracted from the cellular supernatant (Static-Exos) or perfusate (OSS-Exos) by exoEasy Maxi Kit. Afterward, cellular intervention, angiogenesis assays, high-throughput sequencing and online database predictions were used to identify the role and mechanism of OSS-Exos in EPC EndoMT. KEY FINDINGS: OSS-Exos inhibited angiogenesis, promoted the proliferation of EPCs both in vivo and in vitro, and induced EPC EndoMT. In addition, the expression of circ-1199 in OSS-Exos was higher than that in Static-Exos. Moreover, circ-1199 induced EPC EndoMT. The dual-luciferase reporter gene assay showed that let-7g-5p was the direct target of circ-1199. Furthermore, OSS-Exos upregulated the expression of circ-1199 and then downregulated let-7g-5p, upregulating HMGA2, which activated p-Smad3/Smad3 and Snail. SIGNIFICANCE: OSS-Exos played an important role in the EndoMT of EPCs, which was mediated by the circ-1199/let-7g-5p/HMGA2 signaling pathway. These studies would have a high probability of revealing the mechanism of EPC EndoMT.

Controlled Self-assembly of Gold(I) Complexes by Multiple Kinetic Aggregation States with Nonlinear Optical and Waveguide Properties.

Introduction of multiple kinetic aggregation states (Aggs) into the self-assembly pathway could bring complexity and flexibility to the self-assemblies, which is difficult to realize due to the delicate equilibria established among different Aggs bonded by weak noncovalent interactions. Here, we describe a series of chiral and achiral d10 AuI bis(N-heterocyclic carbene, NHC) complexes, and the achiral complex could undergo self-assembly with multiple kinetic Aggs. Generation of multiple kinetic Aggs was realized by applying chiral or achiral seeds exhibiting large differences in elongation temperatures for their respective cooperative self-assembly processes. We further showed that the chiral AuI self-assemblies having non-centrosymmetric packing forms exhibit nonlinear optical response of second harmonic generation (SHG), while the SHG signal is absent in the achiral analogue. The crystalline achiral AuI self-assemblies could function as optical waveguides with strong emission polarization.