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1.
Proc Natl Acad Sci U S A ; 121(30): e2406993121, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39018189

ABSTRACT

Humans update their social behavior in response to past experiences and changing environments. Behavioral decisions are further complicated by uncertainty in the outcome of social interactions. Faced with uncertainty, some individuals exhibit risk aversion while others seek risk. Attitudes toward risk may depend on socioeconomic status; and individuals may update their risk preferences over time, which will feedback on their social behavior. Here, we study how uncertainty and risk preferences shape the evolution of social behaviors. We extend the game-theoretic framework for behavioral evolution to incorporate uncertainty about payoffs and variation in how individuals respond to this uncertainty. We find that different attitudes toward risk can substantially alter behavior and long-term outcomes, as individuals seek to optimize their rewards from social interactions. In a standard setting without risk, for example, defection always overtakes a well-mixed population engaged in the classic Prisoner's Dilemma, whereas risk aversion can reverse the direction of evolution, promoting cooperation over defection. When individuals update their risk preferences along with their strategic behaviors, a population can oscillate between periods dominated by risk-averse cooperators and periods of risk-seeking defectors. Our analysis provides a systematic account of how risk preferences modulate, and even coevolve with, behavior in an uncertain social world.


Subject(s)
Game Theory , Social Behavior , Humans , Uncertainty , Risk-Taking , Prisoner Dilemma , Cooperative Behavior
2.
Brief Bioinform ; 25(6)2024 Sep 23.
Article in English | MEDLINE | ID: mdl-39438078

ABSTRACT

Metagenomic analyses facilitate the exploration of the microbial world, advancing our understanding of microbial roles in ecological and biological processes. A pivotal aspect of metagenomic analysis involves assessing the quality of metagenome-assembled genomes (MAGs), crucial for accurate biological insights. Current machine learning-based methods often treat completeness and contamination prediction as separate tasks, overlooking their inherent relationship and limiting models' generalization. In this study, we present DeepCheck, a multitasking deep learning framework for simultaneous prediction of MAG completeness and contamination. DeepCheck consistently outperforms existing tools in accuracy across various experimental settings and demonstrates comparable speed while maintaining high predictive accuracy even for new lineages. Additionally, we employ interpretable machine learning techniques to identify specific genes and pathways that drive the model's predictions, enabling independent investigation and assessment of these biological elements for deeper insights.


Subject(s)
Deep Learning , Metagenome , Metagenomics , Metagenomics/methods , Genome, Microbial , Machine Learning , Software
3.
Plant Cell ; 35(5): 1386-1407, 2023 04 20.
Article in English | MEDLINE | ID: mdl-36748203

ABSTRACT

Plants undergo extended morphogenesis. The shoot apical meristem (SAM) allows for reiterative development and the formation of new structures throughout the life of the plant. Intriguingly, the SAM produces morphologically different leaves in an age-dependent manner, a phenomenon known as heteroblasty. In Arabidopsis thaliana, the SAM produces small orbicular leaves in the juvenile phase, but gives rise to large elliptical leaves in the adult phase. Previous studies have established that a developmental decline of microRNA156 (miR156) is necessary and sufficient to trigger this leaf shape switch, although the underlying mechanism is poorly understood. Here we show that the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE transcription factors with age promotes cell growth anisotropy in the abaxial epidermis at the base of the leaf blade, evident by the formation of elongated giant cells. Time-lapse imaging and developmental genetics further revealed that the establishment of adult leaf shape is tightly associated with the longitudinal cell expansion of giant cells, accompanied by a prolonged cell proliferation phase in their vicinity. Our results thus provide a plausible cellular mechanism for heteroblasty in Arabidopsis, and contribute to our understanding of anisotropic growth in plants.


Subject(s)
Arabidopsis Proteins , Arabidopsis , MicroRNAs , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Transcription Factors/metabolism , Plant Leaves/metabolism , Meristem/genetics , Meristem/metabolism , Cell Proliferation/genetics , Gene Expression Regulation, Plant/genetics , MicroRNAs/genetics , MicroRNAs/metabolism
4.
Proc Natl Acad Sci U S A ; 120(12): e2216218120, 2023 03 21.
Article in English | MEDLINE | ID: mdl-36927152

ABSTRACT

The concept of fitness is central to evolution, but it quantifies only the expected number of offspring an individual will produce. The actual number of offspring is also subject to demographic stochasticity-that is, randomness associated with birth and death processes. In nature, individuals who are more fecund tend to have greater variance in their offspring number. Here, we develop a model for the evolution of two types competing in a population of nonconstant size. The fitness of each type is determined by pairwise interactions in a prisoner's dilemma game, and the variance in offspring number depends upon its mean. Although defectors are preferred by natural selection in classical population models, since they always have greater fitness than cooperators, we show that sufficiently large offspring variance can reverse the direction of evolution and favor cooperation. Large offspring variance produces qualitatively new dynamics for other types of social interactions, as well, which cannot arise in populations with a fixed size or with a Poisson offspring distribution.


Subject(s)
Cooperative Behavior , Game Theory , Humans , Population Dynamics , Population Density , Selection, Genetic
5.
Syst Biol ; 2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39051673

ABSTRACT

Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex post-polyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this issue with the interesting case of subtribe Tussilagininae (Asteraceae: Senecioneae) and by developing HomeoSorter, a new pipeline for network inferences by phasing homeologs to parental subgenomes. The pipeline is based on the basic idea of a previous study but with major changes to address the scaling problem and implement some new functions. With simulated data, we demonstrate that HomeoSorter works efficiently on genome-scale data and has high accuracy in identifying polyploid patterns and assigning homeologs. Using HomeoSorter, the maximum pseudo-likelihood model of Phylonet, and genome-scale data, we further address the complex origin of Tussilagininae, a speciose group (ca. 45 genera and 710 species) characterized by having high base chromosome numbers (mainly x = 30, 40). In particular, the inferred patterns are strongly supported by the chromosomal evidence. Tussilagininae is revealed to comprise two large groups with successive allopolyploid origins: Tussilagininae s.s. (mainly x = 30) and the Gynoxyoid group (x = 40). Two allopolyploidy events first give rise to Tussilagininae s.s., with the first event occurring between the ancestor of subtribe Senecioninae (x = 10) and a lineage (highly probably with x = 10) related to the Brachyglottis alliance, and the resulting hybrid lineage crossing with the ancestor of Chersodoma (x = 10) and leading to Tussilagininae s.s. Then, after early diversification, the Central American group (mainly x = 30) of Tussilagininae s.s., is involved in a third allopolyploidy event with, again, the Chersodoma lineage and produces the Gynoxyoid group. Our study highlights the value of HomeoSorter and the homeolog-sorting approach in polyploid phylogenetics. With rich species diversity and clear evolutionary patterns, Tussilagininae s.s. and the Gynoxyoid group are also excellent models for future investigations of polyploidy.

6.
PLoS Genet ; 18(2): e1010071, 2022 02.
Article in English | MEDLINE | ID: mdl-35180223

ABSTRACT

The introduction of frameshifting non-3n indels enables the identification of gene-trait associations. However, it has been hypothesised that recovery of the original reading frame owing to usage of non-canonical splice forms could cause rescue. To date there is very little evidence for organism-level rescue by such a mechanism and it is unknown how commonly indels induce, or are otherwise associated with, frame-restoring splice forms. We perform CRISPR/Cas9 editing of randomly selected loci in rice to investigate these issues. We find that the majority of loci have a frame-restoring isoform. Importantly, three quarters of these isoforms are not seen in the absence of the indels, consistent with indels commonly inducing novel isoforms. This is supported by analysis in the context of NMD knockdowns. We consider in detail the two top rescue candidates, in wax deficient anther 1 (wda1) and brittle culm (bc10), finding that organismal-level rescue in both cases is strong but owing to different splice modification routes. More generally, however, as frame-restoring isoforms are low abundance and possibly too disruptive, such rescue we suggest to be the rare exception, not the rule. Nonetheless, assuming that indels commonly induce frame-restoring isoforms, these results emphasize the need to examine RNA level effects of non-3n indels and suggest that multiple non-3n indels in any given gene are advisable to probe a gene's trait associations.


Subject(s)
Oryza , INDEL Mutation/genetics , Oryza/genetics , Reading Frames
7.
J Am Chem Soc ; 146(7): 4402-4411, 2024 02 21.
Article in English | MEDLINE | ID: mdl-38329936

ABSTRACT

Fluorogenic RNA aptamers are valuable tools for cell imaging, but they still suffer from shortcomings such as easy degradation, limited photostability, and low fluorescence enhancement. Molecular crowding conditions enable the stabilization of the structure, promotion of folding, and improvement of activity of functional RNA. Based on artificial RNA condensates, here we present a versatile platform to improve fluorogenic RNA aptamer properties and develop sensors for target analyte imaging in living cells. Using the CUG repeat as a general tag to drive phase separation, various fluorogenic aptamer-based RNA condensates (FLARE) were prepared. We show that the molecular crowding of FLARE can improve the enzymatic resistance, thermostability, photostability, and binding affinity of fluorogenic RNA aptamers. Moreover, the FLARE systems can be modularly engineered into sensors (FLARES), which demonstrate enhanced brightness and sensitivity compared to free sensors dispersed in homogeneous solution. This scalable design principle provides new insights into RNA aptamer property regulation and cellular imaging.


Subject(s)
Aptamers, Nucleotide , RNA , RNA/chemistry , Aptamers, Nucleotide/chemistry , Fluorescent Dyes/chemistry , Fluorescence
8.
J Am Chem Soc ; 146(29): 19649-19653, 2024 Jul 24.
Article in English | MEDLINE | ID: mdl-38976364

ABSTRACT

The attractive electronic properties of metal-pyrazine materials─electrical conductivity, magnetic order, and strong magnetic coupling─can be tuned in a wide range depending on the metal employed, as well as its ligand-imposed redox environment. Using solvent-directed synthesis to control the dimensionality of such systems, a discrete tetranuclear chromium(III) complex, exhibiting a rare example of bridging radical pyrazine, has been prepared from chromium(II) triflate and neutral pyrazine. The strong antiferromagnetic interaction between CrIII (S = 3/2) and radical pyrazine (S = 1/2) spins, theoretically estimated at about -932 K, leads to a thermally isolated ST = 4 ground state, which remains the only populated state observable even at room temperature.

9.
Int J Cancer ; 2024 Oct 08.
Article in English | MEDLINE | ID: mdl-39377640

ABSTRACT

Brainstem gliomas (BSGs) are a class of clinically refractory malignant tumors for which there is no uniform and effective treatment protocol. Ultrasound and radiation can activate hematoporphyrin and produce sonodynamic and radiodynamic effects to kill cancer cells. Therefore, we conducted the first phase I clinical trial of sonodynamic therapy (SDT) combined with radiotherapy (RT) for the treatment of BSGs to verify its safety and efficacy. We conducted a study of SDT combined with RT in 11 patients with BSGs who received SDT and RT after hematoporphyrin administration. Magnetic resonance imaging was performed during this period to assess the tumor, and adverse events were recorded. All adverse events recorded were grade 1-2; no grade 3 or more serious adverse events were observed. Treatment was well tolerated, and no dose-limiting toxicities were observed. There were no treatment-related deaths during the course of treatment. 8 of 11 patients (72.7%) maintained stable disease, 2 (18.2%) achieved partial response, and the tumors were still shrinking as of the last follow-up date. The median progression-free survival (PFS) for patients was 9.2 (95% confidence interval [CI] 6.2-12.2) months, and the median overall survival (OS) was 11.7 (95% CI 9.6-13.8) months. Therefore, SDT combined with RT has a favorable safety and feasibility and shows a preliminary high therapeutic potential.

10.
J Hepatol ; 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38992769

ABSTRACT

BACKGROUND & AIMS: The changes in HBV-specific B cells in patients with chronic hepatitis B (CHB) undergoing pegylated interferon-α (PEG-IFNα) treatment and achieving functional cure remain unclear. We aimed to evaluate the alterations in HBV-specific B cells during treatment and therefore explored the mechanism of functional recovery of HBsAg-specific B cells. METHODS: We included 39 nucleos(t)ide analogue-treated patients with CHB who received sequential combination therapy with PEG-IFNα and eight treatment-naïve patients. HBV-specific B cells were characterized ex vivo using fluorescently labeled hepatitis B surface and core antigens (HBsAg and HBcAg). The frequency, phenotype, and subsets of HBV-specific B cells and follicular helper T cells (Tfh cells) were detected using flow cytometry. The functionality of HBV-specific B cells was quantified through ELISpot assays. RESULTS: During treatment, the fraction of activated memory B cells (MBCs) among HBsAg-specific B cells and the expression of IgG, CXCR3, and CD38 increased. The antibody-secretion capacity of HBsAg-specific B cells was only restored in patients achieving a functional cure after treatment and it positively correlated with serum hepatitis B surface antibody levels. The phenotype and function of HBsAg-specific B cells differed between patients with and without functional cure. Patients with functional cure exhibited IgG+ classical MBCs and plasmablasts among HBsAg-specific B cells. HBcAg-specific B cells displayed both attenuated antibody secretion with reduced IgG expression and an IgM+ atypical type of MBC after treatment, irrespective of functional cure. The number of CD40L+ Tfh cells increased after PEG-IFNα treatment and positively correlated with HBsAg-specific B-cell activation. CONCLUSIONS: After PEG-IFNα treatment, HBsAg- and HBcAg-specific B cells exhibit various changes in antibody secretion. Their functional differences are reflected in the alterations in phenotypes and subtypes. The presence of CD40L+ Tfh cells is associated with the active recovery of HBsAg-specific B cells. IMPACT AND IMPLICATIONS: HBV-related complications and hepatocellular carcinoma remain the leading causes of mortality from chronic liver disease worldwide, and a cure is rarely achieved with antiviral therapies. Elucidating the immunological mechanisms underlying the functional cure of patients with chronic hepatitis B offers a promising therapeutic strategy for viral clearance, e.g. via therapeutic vaccination. We analyzed the alterations in HBV-specific B cells in patients treated with pegylated interferon-α and identified novel pathways for immunotherapeutic boosting of B cell immunity.

11.
J Neuroinflammation ; 21(1): 241, 2024 Sep 27.
Article in English | MEDLINE | ID: mdl-39334486

ABSTRACT

BACKGROUND: Neuroinflammation is a vital pathogenic mechanism for neurodegenerative diseases such as Alzheimer's, schizophrenia, and age-related cognitive decline. Regulatory T cells (Tregs) exhibit potent anti-inflammatory properties and can modulate neurodegenerative diseases arising from central nervous system inflammatory responses. However, the role of Tregs in neuroinflammation-related cognitive dysfunction remains unclear. It is highly plausible that Htr7+ Tregs expressing unique genes associated with the nervous system, including the Htr7 gene encoding the serotonin receptor 5-HT7, play a pivotal role. METHODS: Mice were given a tryptophan-rich diet (with a tryptophan content of 0.6%) or a normal diet (with a tryptophan content of 0.16%). The neuroinflammation-mediated cognitive dysfunction model was established by intracerebroventricular injection of lipopolysaccharide (LPS) in 8-week-old C57BL/6J mice. The activation and infiltration of Tregs were measured using flow cytometry. Primary Tregs were cocultured separately with primary CD8+ T cells and primary microglia for in vitro validation of the impact of 5-HT and 5-HT7 receptor on Tregs. Prior to their transfer into recombination activating gene 1 (Rag1-/-) mice, Tregs were ex vivo transfected with lentivirus to knock down the expression of Htr7. RESULTS: In this study, the tryptophan-rich diet was found to reverse LPS-induced cognitive impairment and reduce the levels of 5-HT in peripheral blood. The tryptophan-rich diet led to increased levels of 5-HT in peripheral blood, which in turn promoted the proliferation and activation of Htr7+ Tregs. Additionally, the tryptophan-rich diet was also shown to attenuate LPS-mediated neuroinflammation by activating Htr7+ Tregs. Furthermore, 5-HT and 5-HT7 receptor were found to enhance the immunosuppressive effect of Tregs on CD8+ T cells and microglia. In Rag1-/- mice, Htr7+ Tregs were shown to alleviate LPS-induced neuroinflammation and cognitive impairment. CONCLUSIONS: Our research revealed the ability of Htr7+ Tregs to mitigate neuroinflammation and prevent neuronal damage by suppressing the infiltration of CD8+ T cells into the brain and excessive activation of microglia, thereby ameliorating LPS-induced cognitive impairment. These insights may offer novel therapeutic targets involving Tregs for neuroinflammation and cognitive impairment.


Subject(s)
Cognitive Dysfunction , Lipopolysaccharides , Mice, Inbred C57BL , Neuroinflammatory Diseases , Receptors, Serotonin , T-Lymphocytes, Regulatory , Tryptophan , Animals , Lipopolysaccharides/toxicity , Tryptophan/pharmacology , Mice , Cognitive Dysfunction/metabolism , Cognitive Dysfunction/chemically induced , T-Lymphocytes, Regulatory/metabolism , T-Lymphocytes, Regulatory/drug effects , T-Lymphocytes, Regulatory/immunology , Receptors, Serotonin/metabolism , Neuroinflammatory Diseases/metabolism , Neuroinflammatory Diseases/immunology , Male , Diet , Mice, Knockout
12.
Small ; 20(38): e2402651, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38747046

ABSTRACT

SnTe, as a potential medium-temperature thermoelectric material, reaches a maximum power factor (PF) usually above 750 K, which is not conducive to continuous high-power output in practical applications. In this study, PF is maintained at high values between 18.5 and 25 µW cm-1 K-2 for Sn0.99In0.01Te-x wt% tourmaline samples within the temperature range of 323 to 873 K, driving the highest PFeng of 1.2 W m-1 K-1 and PFave of 22.5 µW cm-1 K-2, over 2.5 times that of pristine SnTe. Such an extraordinary PF is attributed to the synergy of resonant levels and Sn vacancy suppression. Specifically, the Seebeck coefficient increases dramatically, reaching 88 µV K-1 at room temperature. Meanwhile, by Sn vacancy suppression, carrier concentration, and mobility are optimized to ≈1019 cm-3 and 740 cm2 V-1 s-1, respectively. With the tourmaline compositing, Sn vacancies are further suppressed and the thermal conductivity simultaneously decreases, with the minimum lattice thermal conductivity of 0.9 W m-1 K-1. Finally, the zT value ≈0.8 is obtained in the Sn0.99In0.01Te sample. The peak of the power output density reaches 0.89 W cm-2 at a temperature difference of 600 K. Such SnTe alloys with high and "temperature-independent" PF will offer an option for realizing high output power in thermoelectric devices.

13.
Ann Rheum Dis ; 83(7): 926-944, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38325908

ABSTRACT

OBJECTIVES: Single-cell and spatial transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome landscape and osteoarthritis (OA)-critical cell populations. METHODS: Single-cell RNA sequencing and spatially resolved transcriptomic technology have been applied to characterise the cellular heterogeneity of human knee articular cartilage which were collected from 8 OA donors, and 3 non-OA control donors, and a total of 19 samples. The novel chondrocyte population and marker genes of interest were validated by immunohistochemistry staining, quantitative real-time PCR, etc. The OA-critical cell populations were validated through integrative analyses of publicly available bulk RNA sequencing data and large-scale genome-wide association studies. RESULTS: We identified 33 cell population-specific marker genes that define 11 chondrocyte populations, including 9 known populations and 2 new populations, that is, pre-inflammatory chondrocyte population (preInfC) and inflammatory chondrocyte population (InfC). The novel findings that make this an important addition to the literature include: (1) the novel InfC activates the mediator MIF-CD74; (2) the prehypertrophic chondrocyte (preHTC) and hypertrophic chondrocyte (HTC) are potentially OA-critical cell populations; (3) most OA-associated differentially expressed genes reside in the articular surface and superficial zone; (4) the prefibrocartilage chondrocyte (preFC) population is a major contributor to the stratification of patients with OA, resulting in both an inflammatory-related subtype and a non-inflammatory-related subtype. CONCLUSIONS: Our results highlight InfC, preHTC, preFC and HTC as potential cell populations to target for therapy. Also, we conclude that profiling of those cell populations in patients might be used to stratify patient populations for defining cohorts for clinical trials and precision medicine.


Subject(s)
Cartilage, Articular , Chondrocytes , Osteoarthritis, Knee , Humans , Chondrocytes/pathology , Chondrocytes/metabolism , Osteoarthritis, Knee/pathology , Osteoarthritis, Knee/genetics , Cartilage, Articular/pathology , Cartilage, Articular/metabolism , Middle Aged , Male , Transcriptome , Genome-Wide Association Study , Female , Single-Cell Analysis/methods , Aged , Gene Expression Profiling/methods , Hypertrophy/genetics , Multiomics
14.
BMC Microbiol ; 24(1): 113, 2024 Apr 04.
Article in English | MEDLINE | ID: mdl-38575881

ABSTRACT

BACKGROUND: Cryptosporidium is a highly pathogenic parasite responsible for diarrhea in children worldwide. Here, the epidemiological status and genetic characteristics of Cryptosporidium in children with or without diarrhea were investigated with tracking of potential sources in Wenzhou City, China. METHODS: A total of 1032 children were recruited, 684 of whom had diarrhea and 348 without, from Yuying Children's Hospital in Wenzhou, China. Samples of stool were collected from each participant, followed by extraction of DNA, genotyping, and molecular identification of Cryptosporidium species and subtypes. RESULTS: Twenty-two of the 1032 (2.1%) children were infected with Cryptosporidium spp. with 2.5% (17/684) and 1.4% (5/348) in diarrhoeic and asymptomatic children, respectively. Four Cryptosporidium species were identified, including C. parvum (68.2%; 15/22), C. felis (13.6%; 3/22), C. viatorum (9.1%; 2/22), and C. baileyi (9.1%; 2/22). Two C. parvum subtypes named IIdA19G1 (n = 14) and IInA10 (n = 1), and one each of C. felis (XIXa) and C. viatorum (XVaA3g) subtype was found as well. CONCLUSIONS: This is the first research that identified Cryptosporidium in children of Wenzhou, China, using PCR. Identification of zoonotic C. parvum, C. felis, C. viatorum, and their subtypes indicate potential cross-species transmission of Cryptosporidium between children and animals. Additionally, the presence of C. baileyi in children suggests that this species has a wider host range than previously believed and that it possesses the capacity to infect humans.


Subject(s)
Cryptosporidiosis , Cryptosporidium , Child , Animals , Humans , Cryptosporidium/genetics , Cryptosporidiosis/epidemiology , Cryptosporidiosis/parasitology , Diarrhea/epidemiology , China/epidemiology , Feces/parasitology , Genotype , Probability
15.
New Phytol ; 244(3): 825-839, 2024 Nov.
Article in English | MEDLINE | ID: mdl-39169597

ABSTRACT

Plants frequently encounter adverse conditions and stress during their lives. Abscisic acid (ABA) plays a crucial role in response to salt stress, and dynamic regulation of ABA levels is essential for plant growth and stress resistance. In this study, we identified a transcription factor, OsSGL (Oryza sativa Stress tolerance and Grain Length), which acts as a negative regulator in salt stress, controlling ABA synthesis. OsSGL-overexpressing and mutant materials exhibited sensitivity and tolerance to salt stress, respectively. Notably, under salt treatment, several ABA-related genes, including the ABA synthesis enzyme OsNCED3 and the ABA response gene OsRAB21, were bound by OsSGL, leading to the inhibition of their transcription. Additionally, we found that a key enzyme involved in glycolysis, OsGAPC1, interacted with OsSGL and enhanced the inhibitory effect of OsSGL on OsNCED3. Upon salt stress, OsGAPC1 underwent acetylation and then translocated from the nucleus to the cytoplasm, partially alleviating the inhibitory effect of OsSGL on OsNCED3. Identification of the OsGAPC1-OsSGL module revealed a negative regulatory mechanism involved in the response of rice to salt stress. This discovery provides insight into the dynamic regulation of ABA synthesis in plants under salt stress conditions, highlighting the delicate balance between stress resistance and growth regulation.


Subject(s)
Abscisic Acid , Gene Expression Regulation, Plant , Oryza , Plant Proteins , Salt Tolerance , Oryza/genetics , Oryza/physiology , Oryza/drug effects , Oryza/metabolism , Abscisic Acid/metabolism , Plant Proteins/metabolism , Plant Proteins/genetics , Salt Tolerance/genetics , Salt Tolerance/drug effects , Gene Expression Regulation, Plant/drug effects , Salt Stress , Acetylation/drug effects , Protein Binding/drug effects , Transcription Factors/metabolism , Transcription Factors/genetics , Stress, Physiological/genetics , Stress, Physiological/drug effects , Plants, Genetically Modified
16.
Hepatology ; 77(1): 124-143, 2023 01 01.
Article in English | MEDLINE | ID: mdl-35429173

ABSTRACT

BACKGROUND AIMS: As a global health threat, NASH has been confirmed to be a chronic progressive liver disease that is strongly associated with obesity. However, no approved drugs or efficient therapeutic strategies are valid, mainly because its complicated pathological processes is underestimated. APPROACH RESULTS: We identified the RING-type E3 ubiquitin transferase-tripartite motif-containing protein 31 (TRIM31), a member of the E3 ubiquitin ligases family, as an efficient endogenous inhibitor of transforming growth factor-beta-activated kinase 1 (mitogen-activated protein kinase kinase kinase 7; MAP3K7), and we further confirmed that TRIM31 is an MAP3K7-interacting protein and promotes MAP3K7 degradation by enhancing ubiquitination of K48 linkage in hepatocytes. Hepatocyte-specific Trim31 deletion blocks hepatic metabolism homeostasis, concomitant with glucose metabolic syndrome, lipid accumulation, up-regulated inflammation, and dramatically facilitates NASH progression. Inversely, transgenic overexpression, lentivirus, or adeno-associated virus-mediated Trim31 gene therapy restrain NASH in three dietary mice models. Mechanistically, in response to metabolic insults, TRIM31 interacts with MAP3K7 and conjugates K48-linked ubiquitination chains to promote MAP3K7 degradation, thus blocking MAP3K7 abundance and its downstream signaling cascade activation in hepatocytes. CONCLUSIONS: TRIM31 may serve as a promising therapeutic target for NASH treatment and associated metabolic disorders.


Subject(s)
Non-alcoholic Fatty Liver Disease , Tripartite Motif Proteins , Ubiquitin-Protein Ligases , Animals , Mice , MAP Kinase Kinase Kinases/metabolism , Non-alcoholic Fatty Liver Disease/metabolism , Non-alcoholic Fatty Liver Disease/prevention & control , Ubiquitin-Protein Ligases/metabolism , Ubiquitination , Humans , Tripartite Motif Proteins/metabolism
17.
Plant Physiol ; 193(2): 1126-1141, 2023 09 22.
Article in English | MEDLINE | ID: mdl-37350495

ABSTRACT

Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5' tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.


Subject(s)
Arabidopsis , RNA, Transfer , RNA, Transfer/genetics , RNA, Transfer/metabolism , RNA/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Gene Expression
18.
Opt Express ; 32(10): 17499-17513, 2024 May 06.
Article in English | MEDLINE | ID: mdl-38858932

ABSTRACT

Over years of space laser communication technology advances, satellite optical networks (SONs) have emerged as a pivotal component in 6 G networks. Satellite services are transmitted from the global view, undergoing transmission through SONs, and being downloaded to the targeted areas. However, the transmission capacity of satellites passing through the areas where users are concentrated may be insufficient to download services transmitted worldwide. This problem exists in various kinds of satellite networks and may cause a large amount of service congestion. In this paper, we propose a multi-downlink delivery routing selection (MDD-RS) strategy to study the total utilization of transmission capacity of SONs. We construct an integer linear programming (ILP) model to establish an optimal case study for minimal network capacity occupation. Also, we design an online option, MDD-RS heuristic algorithm, dynamically calculating path routes, considering bandwidth allocation and resource constraints. A comparative analysis against the conventional single-downlink scheme reveals superior performance of the MDD-RS heuristic algorithm, with a reduction in blocking probability of 0.129 and an improvement in bandwidth utilization of 0.032.

19.
Clin Endocrinol (Oxf) ; 101(3): 234-242, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38606576

ABSTRACT

OBJECTIVE: Paragangliomas of the urinary bladder (UBPGLs) are rare neuroendocrine tumours and pose a diagnostic and surgical challenge. It remains unclear what factors contribute to a timely presurgical diagnosis. The purpose of this study is to identify factors contributing to missing the diagnosis of UBPGLs before surgery. DESIGN, PATIENTS AND MEASUREMENTS: A total of 73 patients from 11 centres in China, and 51 patients from 6 centres in Europe and 1 center in the United States were included. Clinical, surgical and genetic data were collected and compared in patients diagnosed before versus after surgery. Logistic regression analysis was used to identify clinical factors associated with initiation of presurgical biochemical testing. RESULTS: Among all patients, only 47.6% were diagnosed before surgery. These patients were younger (34.0 vs. 54.0 years, p < .001), had larger tumours (2.9 vs. 1.8 cm, p < .001), and more had a SDHB pathogenic variant (54.7% vs. 11.9%, p < .001) than those diagnosed after surgery. Patients with presurgical diagnosis presented with more micturition spells (39.7% vs. 15.9%, p = .003), hypertension (50.0% vs. 31.7%, p = .041) and catecholamine-related symptoms (37.9% vs. 17.5%, p = .012). Multivariable logistic analysis revealed that presence of younger age (<35 years, odds ratio [OR] = 6.47, p = .013), micturition spells (OR = 6.79, p = .007), hypertension (OR = 3.98, p = .011), and sweating (OR = 41.72, p = .013) increased the probability of initiating presurgical biochemical testing. CONCLUSIONS: Most patients with UBPGL are diagnosed after surgery. Young age, hypertension, micturition spells and sweating are clues in assisting to initiate early biochemical testing and thus may establish a timely presurgical diagnosis.


Subject(s)
Paraganglioma , Urinary Bladder Neoplasms , Humans , Middle Aged , Retrospective Studies , Urinary Bladder Neoplasms/diagnosis , Female , Male , Adult , Paraganglioma/diagnosis , Paraganglioma/surgery , Europe , United States , Aged , China
20.
Hum Reprod ; 39(2): 326-334, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38166353

ABSTRACT

STUDY QUESTION: Do prepregnancy peripheral leukocytes (PPLs) and their subsets influence the risk of spontaneous abortion (SAB)? SUMMARY ANSWER: PPLs and their subsets are associated with the risk of SAB. WHAT IS KNOWN ALREADY: Compelling studies have revealed the crucial role of maternal peripheral leukocytes in embryo implantation and pregnancy maintenance. Adaptive changes are made by PPLs and their subsets after conception. STUDY DESIGN, SIZE, DURATION: This population-based retrospective cohort study was based on data from the National Free Pre-pregnancy Check-up Project (NFPCP) in mainland China. Couples preparing for pregnancy within the next six months were provided with free prepregnancy health examinations and counseling services for reproductive health. The current study was based on 1 310 494 female NFPCP participants aged 20-49 who became pregnant in 2016. After sequentially excluding 235 456 participants lost to follow-up, with multiple births, and who failed to complete blood tests, a total of 1 075 038 participants were included in the primary analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS: PPLs and their subset counts and ratios were measured. The main outcome was SAB. A multivariable logistic regression model was used to estimate the odds ratio (OR) and 95% CI of SAB associated with PPLs and their subsets, and restricted cubic spline (RCS) was used to estimate the nonlinear exposure-response relationship. MAIN RESULTS AND ROLE OF CHANCE: Of the included pregnant participants, a total of 35 529 SAB events (3.30%) were recorded. Compared to participants with reference values of PPLs, the ORs (95% CIs) of leukopenia and leukocytosis for SAB were 1.14 (1.09-1.20) and 0.74 (0.69-0.79), respectively. The RCS result revealed a monotonous decreasing trend (Pnonlinear < 0.05). Similar relationships were observed for the neutrophil count and ratio, monocyte count, and middle-sized cell count and ratio. The lymphocyte ratio showed a positive and nonlinear relationship with the risk of SAB (Pnonlinear < 0.05). Both eosinophils and basophils showed positive relationships with the risk of SAB (eosinophil Pnonlinear > 0.05 and basophil Pnonlinear < 0.05). LIMITATIONS, REASONS FOR CAUTION: Chemical abortion events and the cause of SAB were not collected at follow-up. Whether women with abnormal PPLs had recovered during periconception was not determined. WIDER IMPLICATIONS OF THE FINDINGS: PPLs and their subsets are associated with the risk of SAB. Leukopenia and neutropenia screening in women preparing for pregnancy and developing a feasible PPL stimulation approach should be emphasized to utilize the immune window of opportunity to prevent SAB. STUDY FUNDING/COMPETING INTEREST(S): This study was approved by the Institutional Research Review Board of the National Health and Family Planning Commission. This study was supported by the National Key Research and Development Program of China (grants 2021YFC2700705 [Y.Y.] and 2016YFC100307 [X.M.]) and the National Natural Science Foundation of China (grant no. 82003472 [L.W.]). The funding source was not involved in the study design, data collection, analysis and interpretation of the data, writing the report, or the decision to submit this article for publication. No competing interests. TRIAL REGISTRATION NUMBER: N/A.


Subject(s)
Abortion, Induced , Abortion, Spontaneous , Leukopenia , Pregnancy , Animals , Female , Humans , Horses , Abortion, Spontaneous/etiology , Retrospective Studies , Abortion, Induced/adverse effects , Leukocytes , Leukopenia/complications
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