Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae.

BACKGROUND: Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. RESULTS: The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia. CONCLUSION: Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.

Microglia sense and suppress epileptic neuronal hyperexcitability.

Microglia are the resident immune cells of the central nervous system, undertaking surveillance role and reacting to brain homeostasis and neurological diseases. Recent studies indicate that microglia modulate epilepsy-induced neuronal activities, however, the mechanisms underlying microglia-neuron communication in epilepsy are still unclear. Here we report that epileptic neuronal hyperexcitability activates microglia and drives microglial ATP/ADP hydrolyzing ectoenzyme CD39 (encoded by Entpd1) expression via recruiting the cAMP responsive element binding protein (CREB)-regulated transcription coactivator-1 (CRTC1) from cytoplasm to the nucleus and binding to CREB. Activated microglia in turn suppress epileptic neuronal hyperexcitability in a CD39 dependent manner. Disrupting microglial CREB/CRTC1 signaling, however, decreases CD39 expression and diminishes the inhibitory effect of microglia on epileptic neuronal hyperexcitability. Overall, our findings reveal CD39-dependent control of epileptic neuronal hyperexcitability by microglia is through an excitation-transcription coupling mechanism.

New DNA-hydrolyzing DNAs isolated from an ssDNA library carrying a terminal hybridization stem.

DNA-hydrolyzing DNAs represent an attractive type of DNA-processing catalysts distinctive from the protein-based restriction enzymes. The innate DNA property has enabled them to readily join DNA-based manipulations to promote the development of DNA biotechnology. A major in vitro selection strategy to identify these DNA catalysts relies tightly on the isolation of linear DNAs processed from a circular single-stranded (ss) DNA sequence library by self-hydrolysis. Herein, we report that by programming a terminal hybridization stem in the library, other than the previously reported classes (I & II) of deoxyribozymes, two new classes (III & IV) were identified with the old selection strategy to site-specifically hydrolyze DNA in the presence of Zn2+. Their representatives own a catalytic core consisting of ∼20 conserved nucleotides and a half-life of ∼15 min at neutral pH. In a bimolecular construct, class III exhibits unique broad generality on the enzyme strand, which can be potentially harnessed to engineer DNA-responsive DNA hydrolyzers for detection of any target ssDNA sequence. Besides the new findings, this work should also provide an improved approach to select for DNA-hydrolyzing deoxyribozymes that use various molecules and ions as cofactors.

Opening a door to the spatiotemporal history of plants from the tropical Indochina Peninsula to subtropical China.

The complexity of global biodiversity in the tropical Indochina Peninsula and subtropical China bioregions has fascinated biologists for decades, but little is known about the spatiotemporal patterns in these regions. Accordingly, the aims of present study were to investigate the evolutionary and distribution patterns of Engelhardia in these regions and establish a model for examining biogeographic patterns and geological events throughout the tropical Indochina Peninsula and subtropical China. The effects of geological events occurring in the area between the Indochina Peninsula and subtropical China bioregions on the two trees species (i.e., E. roxburghiana and E. fenzelii) were evaluated. A robust phylogenetic framework of 884 individuals from 79 populations was used to generate time-calibrated cytoplasmic and nuclear phylogenetic frameworks based on cpDNA, nrDNA, and nSSR data, respectively. When considered along with ancestral area reconstructions, the genetic data were also used to assess and reconstruct the species' population genetic structure and diversity. These analyses yielded important information about the (1) historical distribution relationships between the tropical and subtropical flora of China; (2) effects of the East Asian summer monsoon (EASM) on the evolutionary history of Asia's plants; and (3) importance of biogeography in conservation planning. Although cytoplasmic-nuclear discordance indicated cpDNA and nrDNA were subject to distinct evolutionary mechanisms that reflected respective evolutionary histories of the plastid and nuclear genomes of prior demographic and biogeographic events. The tropical elements of Engelhardia occupied the Indochina Peninsula during the early Eocene, whereas the subtropical elements were transformed from the tropical elements during Miocene cooling and the onset of the EASM at the Oligocene-Miocene boundary, intensified during the late Miocene and Pliocene, facilitating the transformation of Engelhardia from the tropical Indochina Peninsula to subtropical China. Demographic history provided insights into prominent planning frameworks in conservation biology, namely that subtropical China functioned as a refugium during past climate oscillations and will continue to serve in this capacity in the future.

Single-Atom Catalysts Supported on the Graphene/Graphdiyne Heterostructure for Effective CO2 Electroreduction.

Electrochemical reduction of CO2 to high-energy chemicals is a promising strategy for achieving carbon-neutral energy circulation. However, designing high-performance electrocatalysts for the CO2 reduction reaction (CO2RR) remains a great challenge. In this work, by means of density functional theory calculations, we systematically investigate the transition metal (TM) anchored on the nitrogen-doped graphene/graphdiyne heterostructure (TM-N4@GRA/GDY) as a single-atom catalyst for CO2 electroreduction applications. The computational results show that Co-N4@GRA/GDY exhibits remarkable activity with a low limiting potential of -0.567 V for the reduction of CO2 to CH4. When the charged Co-N4@GRA/GDY system is immersed in a continuum solvent, the reaction barrier decreases to 0.366 eV, which is ascribed to stronger electron transfer between GDY and transition metal atoms in the GRA/GDY heterostructure. In addition, the GRA/GDY heterostructure system significantly weakens the linear scaling relationship between the adsorption free energy of key CO2 reduction intermediates, which leads to a catalytic activity that is higher than that of the single-GRA system and thus greatly accelerates the CO2RR. The electronic structure analysis reveals that the appropriate d-π interaction will affect the d orbital electron distribution, which is directly relevant to the selectivity and activity of catalysis. We hope these computational results not only provide a potential electrocatalyst candidate but also open up an avenue for improving the catalytic performance for efficient electrochemical CO2RR.

Valproic acid suppresses cuprizone-induced hippocampal demyelination and anxiety-like behavior by promoting cholesterol biosynthesis.

Myelin consists of several layers of tightly compacted membranes that form an insulating sheath around axons. These membranes are highly enriched in cholesterol, which is essential for the myelination process. Proper myelination is crucial for various neurophysiological functions while demyelination may cause CNS disease, such as multiple sclerosis (MS). Recent studies demonstrated that demyelination occurs not only in the white matter but also in the grey matter, such as the hippocampus, which may cause cognitive deficits and mental disorders. Valproic acid (VPA) is an anticonvulsant agent prescribed for the treatment of epilepsy and seizure. Recently, VPA was reported to alter cholesterol metabolism in neural cells, suggesting that it may play an important role in myelin biogenesis. Here in this study, we found significant demyelination in the hippocampus of the mouse cuprizone model, which is accompanied by reduced cholesterol biosynthesis and increased anxiety-like behavior. VPA treatment, however, suppressed cuprizone-induced hippocampal demyelination and anxiety-like behavior by promoting cholesterol biosynthesis. These data identify an important role of VPA in the hippocampal demyelination process and the hippocampal demyelination-related behavior deficit via regulation of cholesterol biosynthesis, which provides new insights into the mechanisms of VPA as a protective agent against CNS demyelination.

Small DNAs that Bind Nickel(II) Specifically and Tightly.

Metal recognition by nucleic acids provides an intriguing route for biosensing of metal. Toward this goal, a key prerequisite is the acquisition of nucleic acids that can selectively respond to specific metals. Herein, we report for the first time the discovery of two small DNAs that can specifically bind Ni2+ and discriminate against similar ions, particularly, Co2+. Their minimal effective constructs are 60-70 nucleotides (nt) in length with Ni2+ binding even at harsh denaturing conditions of 8 M urea and 50 mM EDTA. Using isothermal titration calorimetry (ITC), we estimated the dissociation constant (KD) of a representative DNA to be 24.0 ± 4.5 µM, with a 9:1 stoichiometry of Ni2+ bound to DNA. As being engineered into nanosized particles, these DNAs can act like nanosponges to specifically adsorb Ni2+ from artificial wastewater, demonstrating their potential as a novel molecular tool for high-quality nickel enrichment and detection.

Horizontal Gene Transfer has Impacted cox1 Gene Evolution in Cassytha filiformis.

The gene cox1 is one of the most reported mitochondrial genes involved in horizontal gene transfer among angiosperms. However, whether different cox1 copies exist in different populations of a species and whether any other novel way except intron homing exists for cox1 intron acquisition is less understood. In this study, we chose Cassytha filiformis, a parasitic plant from the angiosperm family Lauraceae, as an example to study cox1 variation and evolution. We identified the stable and inheritable co-occurrence of two copies of cox1 genes, which were different in base composition and insertion/deletion among samples of a single species, C. filiformis. The bioinformatic analyses revealed that Type I copy had intact open reading frames, but type II copy had premature stop codons and was a pseudogene. Further INDEL characterization, phylogenetic analyses, and CCT comparisons consistently support two different origins for the two types of C. filiformis cox1 genes. Type I cox1 was likely vertically inherited within the magnoliids but it has captured an intron from another species, whereas the entire type II intron-containing cox1 has most likely been transferred integrally from Cuscuta or other Convolvulaceae species. The finding of the two independent horizontal gene transfer events associated with C. filiformis cox1 genes not only promotes our understanding of the evolutionary history of C. filiformis, but also leaves intriguing evolutionary questions that merits further efforts.

Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae).

Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.

Precise healing of oral and maxillofacial wounds: tissue engineering strategies and their associated mechanisms.

Precise healing of wounds in the oral and maxillofacial regions is usually achieved by targeting the entire healing process. The rich blood circulation in the oral and maxillofacial regions promotes the rapid healing of wounds through the action of various growth factors. Correspondingly, their tissue engineering can aid in preventing wound infections, accelerate angiogenesis, and enhance the proliferation and migration of tissue cells during wound healing. Recent years, have witnessed an increase in the number of researchers focusing on tissue engineering, particularly for precise wound healing. In this context, hydrogels, which possess a soft viscoelastic nature and demonstrate exceptional biocompatibility and biodegradability, have emerged as the current research hotspot. Additionally, nanofibers, films, and foam sponges have been explored as some of the most viable materials for wound healing, with noted advantages and drawbacks. Accordingly, future research is highly likely to explore the application of these materials harboring enhanced mechanical properties, reduced susceptibility to external mechanical disturbances, and commendable water absorption and non-expansion attributes, for superior wound healing.

Pomelo peel biomass derived highly active advanced-oxidation-process catalyst: Complete elimination of organic pollutants.

The advanced oxidation process (AOPs) is playing an important role in the elimination of hazardous organic pollutants, but the development of inexpensive and highly active advanced catalysts is facing challenges. In this study, a low-cost and readily available agricultural waste resource pomelo peel-flesh (PPF) biomass was used as the basic raw material, and the uniformly dispersed small cobalt nanoparticles were effectively anchored in the biochar derived from pomelo peel-flesh (BDPPF) by impregnation adsorption/complexation combined with heat treatment. Co/BDPPF (BDPPF embedded with Co) can effectively activate peroxymonosulfate (PMS) to SO4·-, ·OH and 1O2 reactive oxygen species, and achieve nearly 100% degradation of tetracycline persistent organic pollutant. Co/BDPPF can not only degrade tetracycline efficiently in complex water environment, but also degrade most organic pollutants universally, and has long-term stability, which solves the problem of poor universality and stability of heterogeneous catalysts to a certain extent. Importantly, Co/BDPPF derived from waste biomass was also innovatively designed as the core of an integrated continuous purification device to achieve continuous purification of organic wastewater. In this study, agricultural waste resources were selected as biomass raw materials to achieve efficient capture of Co2+, and finally developed advanced AOPs catalyst with excellent performance to achieve the purification of organic wastewater. It also provides a promising solution for the preparation of simple, low-cost, large-scale production of AOPs catalysts that can be put into actual production.

Local Embedding Learning via Landmark-Based Dynamic Connections.

Linear discriminant analysis (LDA) is one of the most effective and popular methods to reduce the dimensionality of data with Gaussian assumption. However, LDA cannot handle non-Gaussian data because the center point is incompetent to represent the distribution of data. Some existing methods based on graph embedding focus on exploring local structures via pairwise relationships of data for addressing the non-Gaussian issue. Due to massive pairwise relationships, the computational complexity is high as well as the locally optimal solution is hard to find. To address these issues, we propose a novel and efficient local embedding learning via landmark-based dynamic connections (LDC) in which we leverage several landmarks to represent different subclusters in the same class and establish the connections between each point and landmark. Furthermore, in order to explore the relationship of landmarks pairwise more precisely, the relationship between each point and their corresponding neighbor landmarks are found in the optimal subspace, rather than the original space, which can avoid the negative influence of the noises. We also propose an efficient iterative algorithm to deal with the proposed ratio minimization problem. Extensive experiments conducted on several real-world datasets have demonstrated the advantages of the proposed method.

Inhibition of neuronal nitric oxide synthase protects against hippocampal neuronal injuries by increasing neuropeptide Y expression in temporal lobe epilepsy mice.

Neuronal nitric oxide synthase (nNOS) plays a pivotal role in the pathological process of neuronal injury in the development of epilepsy. Our previous study has demonstrated that nitric oxide (NO) derived from nNOS in the epileptic brain is neurotoxic due to its reaction with the superoxide radical with the formation of peroxynitrite. Neuropeptide Y (NPY) is widely expressed in the mammalian brain, which has been implicated in energy homeostasis and neuroprotection. Recent studies suggest that nNOS may act as a mediator of NPY signaling. Here in this study, we sought to determine whether NPY expression is regulated by nNOS, and if so, whether the regulation of NPY by nNOS is associated with the neuronal injuries in the hippocampus of epileptic brain. Our results showed that pilocarpine-induced temporal lobe epilepsy (TLE) mice exhibited an increased level of nNOS expression and a decreased level of NPY expression along with hippocampal neuronal injuries and cognition deficit. Genetic deletion of nNOS gene, however, significantly upregulated hippocampal NPY expression and reduced TLE-induced hippocampal neuronal injuries and cognition decline. Knockdown of NPY abolished nNOS depletion-induced neuroprotection and cognitive improvement in the TLE mice, suggesting that inhibition of nNOS protects against hippocampal neuronal injuries by increasing neuropeptide Y expression in TLE mice. Targeting nNOS-NPY signaling pathway in the epileptic brain might provide clinical benefit by attenuating neuronal injuries and preventing cognitive deficits in epilepsy patients.

Two new species from Sulawesi and Borneo facilitate phylogeny and taxonomic revision of Engelhardia (Juglandaceae).

Engelhardia, a genus of Juglandaceae (the walnut family), is endemic to tropical and subtropical Asia. The rich Cenozoic fossil records and distinctive morphological characters of the living plants have been used to explore the evolutionary history and geographic distribution of Juglandaceae. However, the taxonomy of this genus has been suffered from a lack of in-depth investigation and good specimens across its distribution ranges. Species delimitation of Engelhardia was defined with seven species in 2020, but detailed information on the circumscription of the species still remains poorly understood. In this study, two new species are described from Sulawesi and Borneo, Engelhardia anminiana and E. borneensis. We also revised and reconstructed the phylogeny within Engelhardia using morphological, molecular (plastid and ribosomal), and distribution data. We sampled 787 individuals in 80 populations, and all the samples were genotyped using plastid regions, trnS-trnG, rps16, trnL-trnF, psbA-trnH, and rpl32-trnL; one ribosomal region, nuclear ribosomal internal transcribed spacer (nrITS). The all datasets were used to reconstruct the phylogenetic relationships. Then, the molecular analyses were combined for 738 sheets of specimens with 15 morphological characteristics to further explore the morphological clusters of Engelhardia. Cluster analysis using morphological data confirmed the delimitation of nine Engelhardia species. Also, phylogenetic analysis based on molecular data (i.e., plastid and ribosomal) supported the monophyly of Engelhardia and generated phylogenetic trees that included E. fenzelii, E. roxburghiana, E. borneensis, E. hainanensis, E. anminiana, E. serrata, E. villosa, E. apoensis and the varieties of E. spicata (i.e., E. spicata var. spicata, E. spicata var. rigida, E. spicata var. aceriflora, and E. spicata var. colebrookeana). Our comprehensive taxonomic revision of Engelhardia will provide an insight into understanding the plant diversity in tropical and subtropical Asia.

ADAM10 suppresses demyelination and reduces seizure susceptibility in cuprizone-induced demyelination model.

The metalloproteinase ADAM10 is the most important amyloid precursor protein (APP) α-secretase, preventing the deposit of neurotoxic amyloid ß (Aß) peptide and generating a soluble APP fragment (sAPPα) with neurotrophic functions. Recent studies have suggested that ADAM10 also play a role in the pathogenesis of inflammatory CNS diseases, such as multiple sclerosis (MS). Demyelination is the hallmarks of MS but the mechanisms involved remain unclear. Here in this study, we examined the role that ADAM10 might play in the cuprizone-induced demyelination model. Our results demonstrated that ADAM10 expression and sAPPα production were significantly reduced in the corpus callosum in response to cuprizone treatment. Overexpression of ADAM10 increased sAPPα production and suppressed demyelination as well as neuroinflammation and oxidative stress in cuprizone-induced demyelination model. Pharmacological inhibition of ADAM10 activity, however, abrogates the protective effect of ADAM10 against demyelination, neuroinflammation and oxidative stress. It has been reported that CNS demyelination may induce seizure activity. Here, we found that overexpression of ADAM10 reduced seizure susceptibility in cuprizone-induced demyelination model, suggesting that ADAM10-derived sAPPα suppresses demyelination and reduces seizure susceptibility via ameliorating neuroinflammation and oxidative stress in cuprizone-induced demyelination model.

Warming mediates the relationship between plant nutritional properties and herbivore functional responses.

Quantifying the per capita effects of invasive alien species is crucial for assessing their ecological impact. A major challenge to risk assessment of invasive species was to understand the factors that cause per capita effects to vary in different ecological contexts, particularly in a warming world. By conducting functional response experiments, we estimated the per capita effects (attack rate and maximum feeding rate) of an invasive herbivorous snail, Pomacea canaliculata, toward ten host plant species. We tested whether variation in these effects is related to plant nutritional and physical properties (total N and dry matter content (DMC)) and examined how increasing temperature can shift these relationships. We observed stronger per capita effects (i.e., higher attack rate and maximum feeding rate) by the snail on plants with higher total N, but no direct relationship was found with DMC. A significant interaction effect of total N and DMC on the attack rate indicated that DMC probably adjusted the feeding indirectly. Warmer temperatures reduced correlations between snail functional responses and host plant nutritional properties (total N) by increasing maximum feeding rate for plants of low nutrition, but there was no such effect on attack rates. However, given the nonreplacement design used in our study, the nonsignificant effect of temperature on the attack rate should be caveated. Our result suggests that characterizing the per capita effects of herbivores using functional responses can reveal the mechanisms by which climate change may alter herbivore-plant interactions and, thus, the ecological impacts of introduced herbivores.