Unraveling the regulatory network of flower coloration in soybean:Insights into roles of GmMYBA3 and GmMYBR1

Anthocyanins play crucial roles in pollen protection and pollinator attraction in flowering plants.However,the mechanisms underlying flower color determination and whether floral anthocyanin regulators participate in other processes remain largely unresolved in soybeans(Glycine max).In this study,we investigated the genetic components and mechanisms governing anthocyanin biosynthesis in soybean flowers.Molecular and genetic studies have characterized two antagonistic regulators,the positive activator GmMYBA3 and the negative repressor GmMYBR1,that modulate the gene expression of anthocyanin biosynthesis in soybean flowers.Further findings revealed a regulatory interplay between GmMYBA3 and GmMYBR1 bridged by GmTT8a,highlighting the complexity of anthocyanin regulation in different soybean organs.Exploration of additional soybean cultivars demonstrated the universality of GmMYBA3 and GmMYBR1 in regulating floral anthocyanin biosynthesis-related genes,with GmF3’5’H identified as a crucial determinant of white flower color.This study provides a molecular mechanism underlying soybean flower color determination,paving the way for the molecular modification of soybean flowers to probably enhance their resistance to abiotic stresses and attractiveness to pollinators.

Comprehensive Overview of Populus simonii Research in the Recent Years

As an important ecological tree species in northern China, Populus simonii plays a crucial role in maintaining ecological balance and promoting environmental sustainability. The academic community has conducted a series of in-depth studies on this species, covering key areas such as genomics, survival mechanisms, and genetic breeding. Through the analysis of the genomic structure and function of P. simonii, we have not only revealed the molecular basis for its adaptation to harsh environments but also identified key genes that promote its growth and resistance to pests and diseases. Furthermore, exploring the survival mechanisms of P. simonii has deepened our understanding of its stress resistance traits, including how it effectively copes with abiotic stresses such as drought, salinization, and heavy metal pollution. In genetic breeding, significant progress has been made through the application of modern biotechnology, improving the growth rate and wood quality of P. simonii and enhancing its environmental adaptability and disease resistance. These research findings have not only enriched our knowledge of the biological characteristics of P. simonii but also provided a solid scientific foundation for its application in ecological restoration, forestry production, and environmental management.

Geographic-genomic and geographic-phenotypic differentiation of the Aquilegia viridiflora complex

How species diverge into different lineages is a central issue in evolutionary biology.Despite the increasing evidence indicating that such divergences do not need geographic isolation,the correlation between lineage divergence and the adaptive ecological divergence of phenotype corresponding to distribution is still unknown.In addition,gene flow has been widely detected during and through such diverging processes.We used one widely distributed Aquilegia viridiflora complex as a model system to examine genomic differentiation and corresponding phenotypic variations along geographic gradients.Our phenotypic analyses of 20 populations from northwest to northeast China identified two phenotypic groups along the geographic cline.All examined traits are distinct from each other,although a few intermediate individuals occur in their contacting regions.We further sequenced the genomes of representative individuals of each population.However,four distinct genetic lineages were detected based on nuclear genomes.In particular,we recovered numerous genetic hybrids in the contact regions of four lineages.Gene flow is widespread and continuous between four lineages but much higher between contacting lineages than geographically isolated lineages.Gene flow and natural selection might result in inconsistency between heredity and phenotype.Moreover,many genes with fast lineage-specific mutations were identified to be involved in local adaptation.Our results suggest that both geographic isolation and local selection exerted by the environment and pollinators may together create geographic distributions of phenotypic variations as well as the underlying genomic divergences in numerous lineages.

Dip2a regulates stress susceptibility in the basolateral amygdala

Dysregulation of neurotransmitter metabolism in the central nervous system contributes to mood disorders such as depression, anxiety, and post–traumatic stress disorder. Monoamines and amino acids are important types of neurotransmitters. Our previous results have shown that disco-interacting protein 2 homolog A(Dip2a) knockout mice exhibit brain development disorders and abnormal amino acid metabolism in serum. This suggests that DIP2A is involved in the metabolism of amino acid–associated neurotransmitters. Therefore, we performed targeted neurotransmitter metabolomics analysis and found that Dip2a deficiency caused abnormal metabolism of tryptophan and thyroxine in the basolateral amygdala and medial prefrontal cortex. In addition, acute restraint stress induced a decrease in 5-hydroxytryptamine in the basolateral amygdala. Additionally, Dip2a was abundantly expressed in excitatory neurons of the basolateral amygdala, and deletion of Dip2a in these neurons resulted in hopelessness-like behavior in the tail suspension test. Altogether, these findings demonstrate that DIP2A in the basolateral amygdala may be involved in the regulation of stress susceptibility. This provides critical evidence implicating a role of DIP2A in affective disorders.

The genomic landscapes of histone H3-Lys9 modifications of gene promoter regions and expression profiles in human bone marrow mesenchymal stem cells

Mesenchymal stem cells （MSCs） of nonembryonic origins possess the proliferation and multi-lineage differentiation potentials. It has been established that epigenetic mechanisms could be critical for determining the fate of stem cells, and MSCs derived from different origins exhibited different expression profiles individually to a certain extent. In this study, ChiP-on-chip was used to generate genome-wide histone H3-Lys9 acetylation and dimethylation profiles at gene promoters in human bone marrow MSCs. We showed that modifications of histone H3-Lys9 at gene promoters correlated well with mRNA expression in human bone marrow MSCs. Functional analysis revealed that many key cellular pathways in human bone marrow MSC self-renewal, such as the canonical signaling pathways, cell cycle pathways and cytokine related pathways may be regulated by H3-Lys9 modifications. These data suggest that gene activation and silencing affected by H3-Lys9 acetylation and dimethylation, respectively, may be essential to the maintenance of human bone marrow MSC self-renewal and multi-potency.

Progress in in vitro culture and gene editing of porcine spermatogonial stem cells

Research on in vitro culture and gene editing of domestic spermatogonial stem cells (SSCs) is of considerable interest but remains a challenging issue in animal science. In recent years, some progress on the isolation, purification, and genetic manipulation of porcine SSCs has been reported. Here, we summarize the characteristics of porcine SSCs as well current advances in their in vitro culture, potential usage, and genetic manipulation. Furthermore, we discuss the current application of gene editing in pig cloning technology. Collectively, this commentary aims to summarize the progress made and obstacles encountered in porcine SSC research to better serve animal husbandry, improve livestock fecundity, and enhance potential clinical use.

Cloning and Functional Characterization of Chalcone Isomerase Genes Involved in Anthocyanin Biosynthesis in Clivia miniata

Chalcone isomerase(CHI),catalyzing isomerization of chalcones,is a crucial enzyme in flavonoid biosynthesis.Three CHI genes were isolated from Clivia miniata and designated as CmCHI1,CmCHI2 and CmCHI3,respectively.Multiple sequence alignments and phylogenetic analysis showed that CmCHI1 and CmCHI2 were members of type I CHI proteins,whereas CmCHI3 belonged to type IV CHI proteins.Subcellular localization analysis found that all three CmCHIs had diffused distribution in the cytoplasm similar to green fluorescent protein(GFP).Anthocyanin biosynthesis and gene expression analysis demonstrated that CmCHIs were highly expressed in anthocyanin accumulated tissues.To further functionally characterize the role of CmCHIs,an in vitro enzymatic activity assay was carried out using the purified recombinant proteins.Results showed that CmCHI1 and CmCHI2 could completely convert the substrate naringenin chalcone(NC)into the product naringenin(NA),whereas CmCHI3 seemed nonfunctional as no increment of NA was detected.Further genetic transformation of Arabidopsis tt5-1 mutant validated that CmCHI1 and CmCHI2 rather than CmCHI3 could complement the chi deficient phenotypes.In summary,CmCHI1 and CmCHI2 are the real active CHI genes in Clivia miniata.The results not only broaden our knowledge on flavonoid biosynthesis in C.miniata but also lay a new foundation for further flavonoid modification in C.miniata.

Dimethylsulfoniopropionate (DMSP) Increases Longevity and Mitochondrial Function in Caenorhabditis elegans: Implications for the Role of the Global Sulfur Cycle in Terrestrial Ecosystems

Dimethylsulfoniopropionate(DMSP)is a compound synthesized by marine phytoplankton that contributes to the oceanic sulfur cycle.Interestingly,DMSP has also been found in algal species and several terrestrial plants,forming part of the global sulfur cycle.However,compared to its role in the marine environment,the impact of DMSP on terrestrial ecosystems remains relatively unexplored.In this study,DMSP was shown to promote longevity and prevent age-associated functional decline in Caenorhabditis elegans(C.elegans),a soil-dwelling organism.DMSP decreased mitochondrial content and improved mitochondrial function in C.elegans at the old stage,which was via enhancing autophagy flux.It was demonstrated that DMSP significantly increased the expression of autophagy and mitophagy genes during aging.Furthermore,DMSP protected against Parkinson’s disease(PD)induced byα-synuclein(α-syn)aggregation via autophagy.Mechanistic studies showed that DMSP directly activated nuclear translocation of the Skinhead-1(SKN-1)transcription factor from the cytoplasm.Moreover,SKN-1 was involved in DMSP-induced autophagy and played a key role in lifespan extension andα-syn clearance in C.elegans.In conclusion,DMSP delays physiological aspects of aging in C.elegans,providing insights into the interplay between the global sulfur cycle and terrestrial organisms.

Molecular Cytogenetic Characterization of Wheat-Thinopyrum elongatum Addition,Substitution and Translocation Lines with a Novel Source of Resistance to Wheat Fusarium Head Blight

Thinopyrum elongatum （2n = 2x = 14, EE）, a wild relative of wheat, has been suggested as a potentially novel source of resistance to several major wheat diseases including Fusarium Head Blight （FHB）. In this study, a series of wheat （cv. Chinese Spring, CS） substitution and ditelosomic lines, including Th. elongatum additions, were assessed for Type II resistance to FHB. Results indicated that the lines containing chromosome 7E of Th. elongatum gave a high level of resistance to FHB, wherein the infection did not spread beyond the inoculated floret. Furthermore, it was determined that the novel resistance gene（s） of 7E was located on the short-ann （7ES） based on sharp difference in FHB resistance between the two 7E ditelosomic lines for each arm. On the other hand, Th. elongatum chromosomes 5E and 6E likely contain gene（s） for susceptibility to FHB because the disease spreads rapidly within the inoculated spikes of these lines. Genomic in situ hybridization （GISH） analysis revealed that the alien chromosomes in the addition and substitution lines were intact, and the lines did not contain discernible genomic aberrations. GISH and multicolor-GISH analyses were further performed on three trans- location lines that also showed high levels of resistance to FHB. Lines TA3499 and TA3695 were shown to contain one pair of wheat-Th. elongatum translocated chromosomes involving fragments of 7D plus a segment of the 7E, while line TA3493 was found to contain one pair of wheat-Th, elongatum translocated chromosomes involving the D- and A-genome chromosomes of wheat. Thus, this study has established that the short-arm of chromosome 7E of Th. elongatum harbors gene（s） highly resistant to the spreading of FHB, and chromatin of 7E introgressed into wheat chromosomes largely retained the resistance, implicating the feasibility of using these lines as novel material for breeding FHB-resistant wheat cultivars.

Valproic acid protects neurons and promotes neuronal regeneration after brachial plexus avulsion

Valproic acid has been shown to exert neuroprotective effects and promote neurite outgrowth in several peripheral nerve injury models. However, whether valproic acid can exert its beneficial effect on neurons after brachial plexus avulsion injury is currently unknown. In this study, brachial plexus root avulsion models, established in Wistar rats, were administered daily with valproic acid dis-solved in drinking water （300 mg/kg） or normal water. On days 1, 2, 3, 7, 14 and 28 after avulsion injury, tissues of the C 5-T 1 spinal cord segments of the avulsion injured side were harvested to in-vestigate the expression of Bcl-2, c-Jun and growth associated protein 43 by real-time PCR and western blot assay. Results showed that valproic acid significantly increased the expression of Bcl-2 and growth associated protein 43, and reduced the c-Jun expression after brachial plexus avulsion. Our findings indicate that valproic acid can protect neurons in the spinal cord and enhance neuronal regeneration fol owing brachial plexus root avulsion.

Rare tumors: a blue ocean of investigation

Advances in novel drugs,therapies,and genetic techniques have revolutionized the diagnosis and treatment of cancers,substantially improving cancer patients’prognosis.Although rare tumors account for a non-negligible number,the practice of precision medicine and development of novel therapies are largely hampered by many obstacles.Their low incidence and drastic regional disparities result in the difficulty of informative evidence-based diagnosis and subtyping.Sample exhaustion due to difficulty in diagnosis also leads to a lack of recommended therapeutic strategies in clinical guidelines,insufficient biomarkers for prognosis/efficacy,and inability to identify potential novel therapies in clinical trials.Herein,by reviewing the epidemiological data of Chinese solid tumors and publications defining rare tumors in other areas,we proposed a definition of rare tumor in China,including 515 tumor types with incidences of less than 2.5/100000 per year.We also summarized the current diagnosis process,treatment recommendations,and global developmental progress of targeted drugs and immunotherapy agents on the status quo.Lastly,we pinpointed the current recommendation chance for patients with rare tumors to be involved in a clinical trial by NCCN.With this informative report,we aimed to raise awareness on the importance of rare tumor investigations and guarantee a bright future for rare tumor patients.

Histone acetyltransferase p300 regulates the expression of human pituitary tumor transforming gene (hPTTG)

The human pituitary tumor transforming gene （hPTTG） serves as a marker for malignancy grading in several cancers, hPTTG is involved in multiple cellular pathways including cell transformation, apoptosis, DNA repair, genomic instability, mitotic control and angiogenesis induction. However, the molecular mechanisms underlying hPTTG regulation have not been fully explored. In this study, we found that overexpression of histone acetyltransferase （HAT） p300 upregulated hPTTG at the levels of promoter activity, mRNA and protein expression. Moreover, the HAT activity of p300 was critical for its regulatory function. Chromatin immunoprecipitation （CHIP） analysis revealed that overexpression of p300 elevated the level of histone H3 acetylation on the hPTTG promoter. Additionally, the NF-Y sites at the hPTTG promoter exhibited a synergistic effect on upregulation of hPTTG through interacting with p300. We also found that treatment of 293T cells with the histone deacetylase （HDAC） inhibitor Tfichostatin A （TSA） increased hPTTG promoter activity. Meanwhile, we provided evidence that HDAC3 decreased hPTTG promoter activity. These data implicate an important role of the histone acetylafion modification in the regulation of hPTTG.

Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome

Common wheat(Triticum aestivum,BBAADD)is a major staple food crop worldwide.The diploid progenitors of the A and D subgenomes have been unequivocally identified;that of B,however,remains ambiguous and controversial but is suspected to be related to species of Aegilops,section Sitopsis.Here,we report the assembly of chromosome-level genome sequences of all five Sitopsis species,namely Aegilops bicornis,Ae.longissima,Ae.searsii,Ae.sharonensis,and Ae.speltoides,as well as the partial assembly of the Amblyopyrum muticum(synonym Aegilops mutica)genome for phylogenetic analysis.Our results reveal that the donor of the common wheat B subgenome is a distinct,and most probably extinct,diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae.speltoides and Am.muticum belong.In addition,we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex.The five Sitopsis species have various assembled genome sizes(4.11-5.89 Gb)with high proportions of repetitive sequences(85.99%-89.81%);nonetheless,they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex.Differences in genome size were primarily due to independent post-speciation amplification of transposons.We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding.These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex,as well as for wheat improvement.

Habitat-induced reciprocal transformation in the root phenotype of Oriental ginseng is associated with alteration in DNA methylation

Oriental ginseng is an important medicinal plant that grows in 2 major forms or ecotypes,wild and domesticated.Each form differs conspicuously in root phenotype,but can be converted from one type to another by habitat.Here we show that the habi tat-induced transformation of ginseng root phenotype was accompanied by alteration in cytosine methylation at a large number of 5′-CCGG-3′sites detected by the methylation-sensitive polymorphism(MSAP)marker.The collective CG and CHG methylation levels of all 4 landraces of the domesticated form were significantly lower than those of the wild form.Interestingly,artificially transplanted ginseng plants recreated in both directions the methylation levels(at least in CHG)of their natural counterparts.The methylation differences between the 2 ginseng ecotypes were validated at 2 isolated MSAP loci bearing homology to a 5S rRNA gene or a copia retrotransposon.Our results implicate a link between epigenetic variation and habitat-induced phenotypic flexibility in Oriental ginseng.

Genetic and Epigenetic Diversities Shed Light on Domestication of Cultivated Ginseng （Panax ginseng）

Chinese ginseng （Panaxginseng） is a medically important herb within Panax and has crucial cultural values in East Asia. As the symbol of traditional Chinese medicine, Chinese ginseng has been used as a herbal remedy to restore stamina and capacity in East Asia for thousands of years. To address the evolutionary origin and domestication history of cultivated ginseng, we employed multiple molecular approaches to investigate the genetic structures of cultivated and wild ginseng across their distribution ranges in northeastern Asia. Phylogenetic and population genetic analyses revealed that the four cultivated ginseng landraces, COMMON, BIANTIAO, SHIZHU, and GAOLI （also known as Korean ginseng）, were not domesticated independently and Fusong Town is likely one of the primary domestication centers. In addition, our results from population genetic and epigenetic analyses demonstrated that cultivated ginseng maintained high levels of genetic and epigenetic diversity, but showed distinct cytosine methylation patterns compared with wild ginseng. The patterns of genetic and epigenetic variation revealed by this study have shed light on the domestication history of cultivated ginseng, which may serve as a framework for future genetic improvements.

HDAC Inhibitors:A Potential New Category of Anti-Tumor Agents

Over the past years, it has been found that the epigenetic silence of tumor suppressor genes induced by overexpression of histone deacetylases （HDACs） plays an important role in carcinogenesis. Thus, HDAC inhibitors have emerged as the accessory therapeutic agents for multiple human cancers, since they can block the activity of specific HDACs, restore the expression of some tumor suppressor genes and induce cell differentiation, growth arrest and apoptosis. To date, the precise mechanisms by which HDAC inhibitors induce cell death have not yet been fully elucidated and the roles of individual HDAC inhibitors have not been identified. Moreover, the practical uses of HDAC inhibitors in cancer therapy, as well as their synergistic effects with other therapeutic strategies are yet to be evaluated. In this review article, we discuss briefly the recent advances in studies of the developments of anti-cancer HDAC inhibitors and their potential clinical value.

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants.Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications.In the last two decades,how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied.Here,based on recent publications,we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought,abscisic acid,high salt,extreme temperature,nutrient deficiency or toxicity,and ultraviolet B exposure.We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory.We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or-resilient crops,which is essential for coping with global warming and extreme environments.

Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing

Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed ＂transcriptome shock＂. Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica （2n=2x=24, genome AA） and the tetraploid form of O. punctata （2n=4x =48, genome, BBCC）, and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico ＂hybrids＂ （parental mixtures）. We found that approximately 16% （2,541） of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the tran- scriptome response to interspecific hybridization and heterosis.

Nontoxic engineered virus nanofibers as an efficient agent for the prevention and detection of fungal infection

Candida albicans （C. albicans） infection has a high mortality rate in immunocompromised patients. Owing to the inefficiency of the current diagnostic system and the absence of licensed vaccines against candidiasis, the prevention of C. albicans infection remains a challenge. C. albicans infection can be evaluated and prevented by the anti-secreted aspartyl proteinase 2 antibody （anti-Sap2 IgG） and Hsp90 antibody （anti-Hsp90 IgG）. In this study, to explore a new agent for the improvement of the diagnosis and the prevention of C. albicans infection, an engineered fd bacteriophage, which is considered a human-safe virus nanofiber, was designed and prepared with two epitopes that could induce and capture anti-Sap2 IgG and anti-Hsp90 IgG. The dual-display phage was employed as a novel capture probe to develop a new enzyme-linked immunosorbent assay （ELISA） method, which significantly improved the detection rate compared with those of the ELISA in which recombinant protein Sap2 was used as coating antigen to capture the spedfic antibodies （rSap2-ELISA） and the ELISA in which recombinant protein Hsp90 was used as coating antigen to capture the specific antibodies （rHsp90-ELISA）. In addition, the nanofibers acted as a potential vaccine to immunize mice, as well as recombinant proteins, more efficiently mediated humoral and cellular immune responses, decreased levels of C. albicans colonization, and increased the survival rates in C. albicans-infected mice. Therefore, the phage dual-display nanofiber has been shown to be a powerful bifunctional agent for protection against and sensitive detection of clinical infections, which has the potential to be widely used in the life sciences, clinical medicine, and environmental sciences.

Genomic Rearrangement in Endogenous Long Terminal Repeat Retrotransposons of Rice Lines Introgressed by Wild Rice （Zizania latifolia Griseb.）

Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome. Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, lowcopy, and potentially active long terminal repeat （LTR） retrotransposons occurred in one or more of three rice lines studied that were introgressed by wild rice （Zizania latifolia Griseb.）. For nine retrotransposons in which both the reverse-transcriptase （RT） region and the LTR region were available, largely concordant rearrangements occurred at both regions in five elements and at the RT region only in the remaining four elements. A marked proportion of the genomic changes was shared by two or all three introgression lines that were derived from a single F~ plant. This indicates that most of the genomic changes occurred at early developmental stages of the F~ somatic cells, which then gave rise to germline cells, and, hence, ensured inheritance of the changes to later generations. Possible causes and potential implications of the introgression-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant genome evolution and breeding.