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Semisupervised Dimension Reduction (SDR) Using Trace Ratio Criterion (TR-FSDA) is an effective iterative SDR algorithm, which introduces a flexible regularization term ‖ F − X T W ‖ 2 to relax such a hard linear constraint in SDA that the low-dimensional representation F is constrained to lie in the linear subspace spanned by the data matrix X . We, however, observe that TR-FSDA may take some meaningless features in the iteration and cannot be always guaranteed to converge. In this paper, we propose a novel method for SDR, referred to as Recursive Dimension Reduction for Semisupervised Learning (RDS). Instead of solving the non-trivial TR problem using the iterative algorithm of TR-FSDA, we solve the objective function of TR-FSDA using a newly-developed recursive procedure. In each iteration, only a projection vector and a one-dimensional data representation are produced by solving a standard Rayleigh Quotient problem. Our algorithm escapes from the convergence guarantee, since it directly solves the objective and requires no any iterative strategy in finding each of the projection vectors. The experiments on four face databases, one object database, one shape image database, and one Handwritten Digit database demonstrate the effectiveness of RDS. [ABSTRACT FROM AUTHOR]

The female‐specifically expressed response regulator (PdFERR) gene in Populus deltoides, a sex determination gene (an orthologous gene of ARR17 in Populus tremula), was found to promote femaleness in heterologous expression lines of Arabidopsis. None of the genes in the Arabidopsis genome seem to be orthologous to PdFERR. Although originating from two evolutionarily distant plants, the dioecious poplar FERR might promote femaleness in the hermaphroditic Arabidopsis through an evolutionary consistent regulatory pathway. However, there is no molecular evidence to support this viewpoint. In this study, to identify the shared downstream orthologous gene of PdFERR, we used yeast two‐hybrid assay to screen potential interactors of PdFERR in Arabidopsis. We identified the ethylene response factor 96 (AtERF96) and confirmed the interaction via in vivo and in vitro assays. The ERF96 orthologous gene in P. deltoides was also experimentally confirmed to interact with PdFERR. PdFERR could then promote femaleness in poplar or Arabidopsis through interactions with ERF96, which provide a new perspective for understanding the PdFERR gene regulating sex differentiation. [ABSTRACT FROM AUTHOR]

Background: The dioecious system is relatively rare in plants. Shrub willow is an annual flowering dioecious woody plant, and possesses many characteristics that lend it as a great model for tracking the missing pieces of sex determination evolution. To gain a global view of the genes differentially expressed in the male and female shrub willows and to develop a database for further studies, we performed a large-scale transcriptome sequencing of flower buds which were separately collected from two types of sexes. Results: Totally, 1,201,931 high quality reads were obtained, with an average length of 389 bp and a total length of 467.96 Mb. The ESTs were assembled into 29,048 contigs, and 132,709 singletons. These unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 291 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified 806 differentially expressed genes between the male and female flower buds. And 33 of them located on the incipient sex chromosome of Salicaceae, among which, 12 genes might involve in plant sex determination empirically. These genes were worthy of special notification in future studies. Conclusions: In this study, a large number of EST sequences were generated from the flower buds of a male and a female shrub willow. We also reported the differentially expressed genes between the two sex-type flowers. This work provides valuable information and sequence resources for uncovering the sex determining genes and for future functional genomics analysis of Salicaceae spp. [ABSTRACT FROM AUTHOR]

With the development of high-throughput sequencing techniques, transcriptome sequencing projects which provide valuable resources for designing simple sequence repeat (SSR) primers have been carried out for many plants. However, the utility of SSRs for molecular breeding depends on genome-wide distribution and coverage, as well as moderately high allelic variability, in the available SSR library. In this study, we characterized the exonic SSRs developed from the publicly available Populus genome as a case study to determine their value for molecular breeding. As expected, our results confirmed that microsatellites occurred approximately three times less often in coding regions than in non-coding regions. Mutability test also showed that exonic SSRs contained less allelic variability than intronic SSRs. More importantly, exonic SSRs were unevenly distributed both among and within chromosomes. Large exonic SSRs deserts were observed on several chromosomes. Differential selection between paralogous chromosomes, at the gene level, appears to be responsible for these SSR deserts, though the mechanisms that cause chromosome-specific SSR deserts are not known. This work provides ample evidence that the candidate gene approach based on unigenes identified from transcribed sequences may not be the best strategy to identify highly polymorphic SSRs. [ABSTRACT FROM AUTHOR]

We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and quantitative trait locus (QTL) identification.Key words: AFLP, Genetic map, poplar, RAPD, SSR.Les auteurs présentent des cartes génétiques moléculaires provenant de l'analyse d'une population hybride interspécifique chez le genre Populus, un système modèle en biologie forestière. Les hybrides ont été produits en croisant le P. deltoides (parent femelle) et le P. euramericana (parent mâle), ce dernier étant un hybride naturel entre le P. deltoides (grand-parent femelle) et le P. nigra (grand-parent mâle). Une analyse de liaison sur 93 des 450 individus « backcross » cultivés au champ pendant 15 ans a été réalisée à l'aide de marqueurs RAPD (ADN polymorphe amplifié au hasard), AFLP (polymorphisme de longueur des fragments amplifiés) et ISSR (intermicrosatellites). Des 839 marqueurs polymorphes identifiés, 560 (67 %) étaient des marqueurs testcross (hétérozygotes chez un parent mais absents chez l'autre et montrant une ségrégation 1 : 1), 206 (25 %) étaient des marqueurs dominants en ségrégation (hétérozygotes chez les deux parents et montrant une ségrégation de 3 : 1) et les 73 autres marqueurs (9 %) comprenaient 19 marqueurs RAPD absents chez les parents et en ségrégation 1 : 1 ainsi que 54 marqueurs AFLP codominants en ségrégation 1 : 1 : 1 : 1. Une combinaison de marqueurs testcross, de marqueurs RAPD non-parentaux et de marqueurs AFLP codominants a été employée afin de produire deux cartes de liaison, l'une représentant le génome du P. deltoides (D) et l'autre celui du P. euramericana (E). Les deux cartes couvrent presque complètement le génome, totalisant 3801 et 3452 cM respectivement. La disponibilité de marqueurs RAPD non-parentaux et de marqueurs AFLP codominants pour servir de locus orthologues a permis de comparer directement les taux de recombinaison méiotique chez les deux espèces parentales. Généralement, le taux de recombinaison méiotique était supérieur chez le parent mâle que chez le parent femelle chez les hybrides interspécifiques examinés ici. L'effet combiné du sexe et de l'espèce a pour conséquence que la distance entre locus orthologues était 11 % supérieure chez le parent mâle (P.euramericana; hybride interspécifique) que chez le parent femelle (P. deltoides; intraspécifique). Les groupes de liaison produits et la population hybride interspécifique du peuplier, pour laquelle des clones de génotypes individuels sont disponibles, constituent un fondement important pour de futures études génomiques et l'identification de locus de caractères quantitatifs (QTL).Mots clés : AFLP, carte génétique, peuplier, RAPD, SSR.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

We have constructed RAPD-based linkage maps for an interspecific cross between two species of the genus Populus (P. adenopoda and P. alba), based on a double pseudo-test-cross strategy. Of a total of 360 polymorphic fragments scored, 290 showed a test-cross configuration, corresponding to DNA polymorphisms heterozygous in one parent and null in the other. In the female parent, P. adenopoda, 82 markers were grouped in 19 different linkage groups (553 cM), whereas in the male parent P. alba, 197 markers established a much more complete framework map with an observed genome length of 2300 cM covering 87% of the total P. alba genome. The larger number of test-cross markers detected for the P. alba parent than for the P. adenopoda parent might be due to a higher level of heterozygosity in the former than in the latter. In this study, we detected only a small percentage (2%) of the intercross dominant markers heterozygous in both parents and segregating 3:1 in the progeny. The further focus in this mapping study should be on the identification of more intercross markers, to align the two parent-specific maps into a consensus map for mapping important genes causing species differentiation during long evolutionary divergences.Key words: interspecific hybrids, linkage map, poplar, pseudo-testcross mapping strategy.Les auteurs ont produit des cartes de liaison génétique à l'aide de marqueurs RAPD et d'une stratégie de double pseudo-testcross à partir d'un croisement interspécifique entre deux espèces du genre Populus : P. adenopoda et P. alba. D'un total de 360 fragments polymorphes examinés, 290 ont montré une configuration de type testcross, c'est-à-dire qu'ils étaient hétérozygotes chez un parent et absents chez l'autre. Chez le parent femelle, P. adenopoda, 82 marqueurs ont formé 19 groupes de liaison (553 cM) tandis que chez le parent mâle, P. alba, 197 marqueurs ont permis de produire une carte de référence beaucoup plus complète montrant une taille de 2300 cM et couvrant 87% du génome du P. alba. Le plus grand nombre de marqueurs de type testcross au sein du P. alba qu'au sein du P. adenopoda pourrait être dû à une plus grande hétérozygotie au sein de la première espèce. Dans ce travail, seule une faible proportion (2%) des marqueurs étaient hétérozygotes et dominants chez les deux parents et montraient une ségrégation 3 : 1 au sein de la progéniture. Les travaux à venir devraient viser à identifier davantage de marqueurs polymorphes chez les deux parents afin d'aligner les deux cartes spécifiques de chaque parent en une carte consensuelle dans le but de permettre la cartographie de gènes importants à l'origine de la différenciation des espèces au cours de l'évolution.Mots clés : hybrides interspécifiques, carte de liaison génétique, peuplier, stratégie de cartographie en pseudo-testcross.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology. A Populus super-pangenome is reconstructed from whole-genome assemblies for forest trees in this study. Based on this super-pangenome this study offers novel insights into the evolution of genomic landscape that underlies the widespread adaptation and high phenotypic diversity of long-lived trees, which advance our comprehension of tree biology and breeding. [ABSTRACT FROM AUTHOR]

Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis. [ABSTRACT FROM AUTHOR]

Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an f branch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix–Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera. [ABSTRACT FROM AUTHOR]

Colorectal cancer is a common malignancy and the second leading cause of cancer-related death. Emerging evidence suggests that the Wnt/β-catenin pathway has a significant role in cancer development. Shikonin is one of the main bioactive components of the plant, Lithospermum erythrorhizon, which possesses various biological properties. In this study, we identified a shikonin derivative, E5, as a novel suppressor of colorectal carcinoma that acted by inhibiting cell proliferation and migration, and promoting apoptosis. Mechanistically, the drug activated caspase-dependent pathways, negatively regulating the Wnt/β-catenin pathway, and inhibited epithelial–mesenchymal transition. The findings suggest the potential of β-catenin as a molecular target in colon carcinoma and propose E5 as a promising therapeutic strategy for targeting Wnt/β-catenin [Display omitted] ● A novel thioether shikonin derivative (E5), modified form of shikonin, acts as a novel inhibitor of β-catenin. ● E5 suppressed cancer cell proliferation and migration and promoted cell apoptosis via caspase-dependent pathways. ● E5 can be a drug candidate and has the potential to inhibit Wnt/β-catenin signaling pathway in the colon carcinoma. [ABSTRACT FROM AUTHOR]

3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), as the rate-limiting enzyme in the mevalonate pathway, is essential for the biosynthesis of shikonin in Lithospermum erythrorhizon. However, in the absence of sufficient data, the principles of a genome-wide in-depth evolutionary exploration of HMGR family members in plants, as well as key members related to shikonin biosynthesis, remain unidentified. In this study, 124 HMGRs were identified and characterized from 36 representative plants, including L. erythrorhizon. Vascular plants were found to have more HMGR family genes than nonvascular plants. The phylogenetic tree revealed that during lineage and species diversification, the HMGRs evolved independently and intronless LerHMGRs emerged from multi-intron HMGR in land plants. Among them, Pinus tabuliformis and L. erythrorhizon had the most HMGR gene duplications, with 11 LerHMGRs most likely expanded through WGD/segmental and tandem duplications. In seedling roots and M9 cultured cells/hairy roots, where shikonin biosynthesis occurs, LerHMGR1 and LerHMGR2 were expressed significantly more than other genes. The enzymatic activities of LerHMGR1 and LerHMGR2 further supported their roles in catalyzing the conversion of HMG-CoA to mevalonate. Our findings provide insight into the molecular evolutionary properties and function of the HMGR family in plants and a basis for the genetic improvement of efficiently produced secondary metabolites in L. erythrorhizon. [ABSTRACT FROM AUTHOR]

Expansins are a group of cell wall enzyme proteins that help to loosen cell walls by breaking hydrogen bonds between cellulose microfibrils and hemicellulose. Expansins are essential plant proteins that are involved in several key processes, including seed germination, the growth of pollen tubes and root hairs, fruit ripening and abscission processes. Currently, there is a lack of knowledge concerning the role of expansins in woody plants. In this study, we analyzed expansin genes using Populus genome as the study target. Thirty-six members of the expansin gene family were identified in Populus that were divided into four subfamilies (EXPA, EXPB, EXLA and EXLB). We analyzed the molecular structure, chromosome localization, evolutionary relationships and tissue specificity of these genes and investigated expression changes in responses to phytohormone and abiotic stresses of the expansin genes of Populus tremula L. (PtEXs). Molecular structure analysis revealed that each PtEX protein had several conserved motifs and all of the PtEXs genes had multiple exons. Chromosome structure analysis showed that the expansin gene family is distributed on 14 chromosomes. The PtEXs gene family expansion patterns showed segmental duplication. Transcriptome data of Populus revealed that 36 PtEXs genes were differently expressed in different tissues. Cis-element analysis showed that the PtEXs were closely associated with plant development and responses to phytohormone and abiotic stress. Quantitative real-time PCR showed that abscisic acid (ABA) and low-temperature treatment affected the expression of some PtEXs genes, suggesting that these genes are involved in responses to phytohormone and abiotic stress. This study provides a further understanding of the expansin gene family in Populus and forms a basis for future functional research studies. [ABSTRACT FROM AUTHOR]

Cytokinins have vital effects on various plant development-related processes. Type-A response regulators (RRs) are among the most important regulators in the cytokinin signaling pathway. Specifically, RR genes are the primary cytokinin-responsive genes, encode negative regulators of cytokinin signaling. Similar sex-determining mechanisms involving a type-A RR homolog have recently been identified in sister genera Populus and Salix. Here, we aimed to identify and characterize type-A RR gene family members in Populus deltoides. On the basis of the conserved receiver domain and phylogenetic analysis, we identified 9, 11, and 14 type-A RR genes were identified in P. deltoides , Populus trichocarpa , and Salix suchowensis , respectively. The exon-intron organization and chromosomal locations of these genes in P. deltoides as well as the characteristics of the encoded proteins were analyzed in detail. Gene duplication events, molecular evolution, and phylogenetic relationships were analyzed for all identified type-A RR genes along with 10 Arabidopsis thaliana homologs. These results indicated that the expansion of the type-A RR gene family was primarily due to whole-genome and segmental duplication events. The collinear type-A ARR pairs in A. thaliana were all derived from the α-whole-genome duplication (WGD) event, whereas those in the three Salicaceae species were divided into two groups, one comprising 10 pairs derived from the p -WGD event and the other consisting of 11 pairs derived from the γ-WGD event or a more ancient duplication event. All of the duplicated paralogous gene pairs had undergone purifying selection. Although different type-A RR paralogs experienced different selection pressures, convergent evolution was detected within the receiver domain-encoding sequence, indicative of the importance of this domain for the phosphorelay-related function of the encoded proteins. Three type-A RR genes (PdRR9 , PtRR11 , and SsRR12) associated with sex determination in Salicaceae species formed a small subclade that lacked A. thaliana counterparts. Evaluation of gene expression in vegetative tissues and at different floral developmental stages in P. deltoides revealed the specific spatiotemporal expression of each PdRR gene, with two (PdRR8 and PdRR9) of the nine PdRR genes exhibiting the opposite sex-biased expression patterns. Diverse expression levels were detected between all eight paralogous PdRR pairs. These findings support future research to elucidate the functional divergence of type-A RR genes. • Systematic genome-wide analysis of type-A RR genes was conducted in P. deltoides. • Expansion of the type-A RR gene family was primarily due to the WGD/segmental duplication events. • The PdRRs exhibited distinct developmental stage- and tissue-specific expression patterns. • This study will provide critical information to further elucidate the functional divergence of type-A RR genes. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) belong to a class of small, noncoding, and endogenous single-stranded RNAs that negatively regulate gene expression at the posttranscriptional level. Potential miRNAs can be identified based on sequence homology since miRNAs are highly conserved in plants. In this study, we aligned the expressed sequence tags derived from flower buds of male and female S. suchowensis to miRNAs in the miRBase, which enable us to identify 34 potential miRNAs from flower buds of the alternate sexes. Among them, 11 were from the female and 23 were from the male. Analyzing sequence complementarity led to identification of 124 and 55 miRNA targets in the male and female flower buds, respectively. By mapping the target genes of the predicted miRNAs to the sequence assemblies of S. suchowensis, a miR156 mediated gene was detected at the gender locus of willow, which was a transcription factor involved in flower development. It is noteworthy that this target is not expressed in male flower, while it is expressed fairly highly in female flower based on the transcriptome data derived from the alternate sexes of willows. This study provides new bioinformatic clue for further exploring the genetic mechanism underlying gender determination in willows. [ABSTRACT FROM AUTHOR]

Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) containing both AGP-like glycated domains and fasciclin (FAS) domains, which are involved in plant growth and development and synthesis of the cell wall. However, these proteins have not been identified or analyzed in willow, Salix, the sister genus of Populus. In this study, we performed a whole genome study of the FLA gene family of Salix suchowensis and compared it with the FLA gene family of Populus deltoides. The results showed the presence of 40 and 46 FLA genes in P. deltoides and S. suchowensis, distributed on 17 and 16 chromosomes, respectively. Four pairs of tandem repeat genes were found in willow, while poplar had no tandem repeat genes. Twelve and thirteen pairs of duplicated gene fragments were identified in poplar and willow, respectively. The multispecies phylogenetic tree showed that the FLA gene family could be divided into four groups (I–IV), with Group 1 showing significant expansion in woody plants. A gene expression analysis showed that PdeFLA19/27 in Group I of poplar was highly expressed, specifically during the secondary growth period of the stem and the rapid elongation of seed hairs. In the Group I genes of S. suchowensis, SsuFLA25/26/28 was also highly expressed during the secondary growth period, whereas increased expression of SsuFLA35 was associated with seed hair tissue. These results provide important clues about the differences in the FLA gene family during the evolution of herbs and woody plants, and suggest that the FLA gene family may play an essential role in regulating the secondary growth of woody plants. It also provides a reference for further studies on the regulation of secondary growth and seed hair development by FLA genes in poplar and willow. [ABSTRACT FROM AUTHOR]

Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in‐depth case studies still need to be carried out in a real‐world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate‐treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth‐promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen‐fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen‐fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron‐molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil–plant continuum largely control the composition and function of the root‐associated microbiome of triple transgenic soybean. [ABSTRACT FROM AUTHOR]

(A) The structural maps of pBI121-LeBAHD1/LeSAT1-eGFP overexpression vector and pYLCRISPR/Cas9-LeBAHD1/LeSAT1 knockout vectors. However, not all members of the BAHD acyltransferase gene family could be screened out from the I L. erythrorhizon i genome by only using AAT/SAT amino acid sequences as a query. Identification and Characterization of LeBAHD Genes in L. erythrorhizon Genome In order to have a comprehensive understanding of the characteristics and functions of BAHD family genes in I L. erythrorhizon i , 104 members were initially screened out from the I L. erythrorhizon i genome based on sequences homology and the conserved BAHD superfamily feature domain (Pfam: PF02458). [Extracted from the article]

Abiotic stresses such as drought and high salinity inhibit plant growth and productivity. NAC transcription factors play a variety of important roles in plant development and abiotic stress responses. To date, the transformation of NAC genes into poplar plants has not been reported. In this study, we introduced the CarNAC3 and CarNAC6 salinity and drought tolerant genes from Cicer arietinum (chickpea) into Populus deltoides × Populus euramericana 'Nanlin895' (poplar) plants using Agrobacterium tumefaciens-mediated transformation . We verified the integration of the two genes into the poplar genome using polymerase chain reaction (PCR) and their stable expression was confirmed at the transcript level using real-time (RT)-PCR. The growth rates of roots and shoots and the clawed root rate increased in transformed plants grown in agar medium or in soil and increased in response to drought and salt stress conditions. Proline and photoprotectant pigment accumulation and antioxidant enzyme activities increased in response to abiotic stress, but the accumulation of photosynthetic pigments and malondialdehyde (MDA) decreased in transgenic lines relative to wild-type control plants. The CarNAC3 transgene was expressed at higher levels than the CarNAC6 transgene. Our results showed that the CarNAC3 and CarNAC6 genes enhanced the capacity for osmotic adjustment and increased antioxidant enzyme activity and suggest that these genes could play a significant role in improving drought and salt tolerance when expressed in poplar plants. [ABSTRACT FROM AUTHOR]

The paper optimizes the design for the needle head by mechanical analysis, the experiments of the needle head, structural improvements. The purpose is to design the best structure of the needle head, reduce the trunk fibre squeezed by the outer surface of the needle head. Extrusion capacity just is the thickness of the needle head's wall, which decreases splitting of wood fibres, thus ensuring the sealing effect and improving the injection efficiency of the trunk injector. According to the theory and experiments, it is obtained the range of the needle head's best size: the outer diameter is 6-8 mm, the thickness of the wall is 0.5-1mm. There are some relationships between the resistance and sizes of the needle heads. If the head needle's outer diameter is same, the larger the needle head's aperture is, the smaller the resistance of the needle head entering the trunk is. If the thickness of the wall is the same, the larger the needle head's outer diameter is, the larger the needle head's aperture is, the larger the resistance of the needle head entering the trunk is. Comparing the new needle head with the old needle head, the resistance of the needle head has been reduced. It can enhance strength and avoid fracture. It makes the wood core exist in the grooves of both sides without squeezing trunks and has good sealing effect. [ABSTRACT FROM AUTHOR]

Compared to linear discriminant analysis (LDA), its orthogonalized version is a more effective statistical learning tool for dimension reduction, which devotes to better separating the data points from different classes in the lower-dimensional subspace. However, existing orthogonalized LDA techniques suffer from various drawbacks, including the requirement for expensive computing time. This paper develops an efficient orthogonal dimension reduction approach, referred to as fast orthogonal linear discriminant analysis (FOLDA), which is based on existing orthogonal linear discriminant analysis (OLDA) algorithms. However, different from previous efforts, the new approach applies the QR decomposition and the regression to solve for a new orthogonal projection vector at each iteration, leading to the by far cheaper computational cost. FOLDA achieves comparable recognition rate to existing OLDA algorithms due to the incorporation of the idea and spirit behind the latter ones. Experimental results on image databases, such as MINST, COIL20, MEPG-7 and OUTEX, show the effectiveness and efficiency of our algorithm. [ABSTRACT FROM AUTHOR]

12-Oxophytodienoate reductase (OPR) enzymes in dicots are categorized as flavin mononucleotide (FMN)–dependent oxidoreductases and are divided into two subgroups. Although subgroup II OPRs have been identified as being involved in a critical step in the production of jasmonic acid (JA), the functions of subgroup I OPRs are uncertain. In this study, we cloned a potential subgroup I OPR gene, EpOPR1, from Echium plantagineum using comparative transcriptome analysis. EpOPR1 expression was found to be significantly increased in root samples containing secondary metabolites such as shikonin and its derivatives. Using a transgenic hairy root system, we further explored the role of EpOPR1 in the production of these secondary metabolites. The results indicated that although the chemical profile of EpOPR1 overexpressing hairy roots (OPRO) is similar to that of the empty vector hairy roots (EV), the EpOPR1 overexpressing line considerably increased the yield of acetylshikonin by around two-fold. Our findings shed light on the potential role of subgroup I OPRs in E. plantagineum secondary metabolism regulation. [ABSTRACT FROM AUTHOR]

Elucidating the genetic factors underlying long-term biological processes remains challenging since the relevant genes and their effects may vary across different developmental stages. In this study, we carried out a large-scale field trial of the progeny of an F1 full-sib pedigree of Salix suchowensis and measured plant height and ground diameter periodically over a time course of 240 days. With the obtained data, we characterized plant growth rhythms and performed time-sequential analyses of quantitative trait loci underlying the dynamic growth of the plants. The dynamic mapping of quantitative trait loci revealed that stem height and ground diameter were under the control of four quantitative trait loci, and the effects of these quantitative trait loci varied greatly throughout the growth process, in which two quantitative trait loci were found to exert a pleiotropic effect determining the correlation between stem height and ground diameter. The analysis of candidate genes in the target genetic intervals showed that the pleiotropic effect of the two quantitative trait loci arises from the colocalization of genes with independent effects on stem height and ground diameter. Further examination of the expression patterns of the candidate genes indicated that height and circumference growth involve different activities of leaf and cambium tissues. This study provides unprecedented information to help us understand the dynamic growth of plants and presents an applicable strategy for elucidating the genetic mechanism underlying a long-term biological process by using plant growth as an example. [ABSTRACT FROM AUTHOR]

Highlights: [•] For get more satisfactory results, EMVSVM enlarges the rank of the between-class scatter matrix. [•] EMVSVM gets multiple weight vectors for each class by defining a new criterion. [•] EMVSVM shows the more promising classification accuracy than other multisurface classifiers. [•] From the statistical viewpoint, the analysis of EMVSVM is done. [Copyright &y& Elsevier]

Shikonin and its derivatives are the main components of traditional Chinese medicine, Zicao. The pharmacological potential of shikonin and its derivatives have been extensively studied. Yet, less is known about the microbial assemblages associated with shikonin producing Borage plants. We studied microbial profiles of two Borage species, Echium plantagineum (EP) and Lithospermum erythrorhizon (LE), to identify the dynamics of microbial colonization pattern within three rhizo-compatments and two distinct soil types. Results of α and β-diversity via PacBio sequencing revealed significantly higher microbial richness and diversity in the natural soil along with a decreasing microbial gradient across rhizosphere to endosphere. Our results displayed genotype and soil type–dependent fine-tuning of microbial profiles. The host plant was found to exert effects on the physical and chemical properties of soil, resulting in reproducibly different micro-biota. Analysis of differentially abundant microbial OTUs displayed Planctomycetes and Bacteroidetes to be specifically enriched in EP and LE rhizosphere while endosphere was mostly prevailed by Cyanobacteria. Network analysis to unfold co-existing microbial species displayed different types of positive and negative interactions within different communities. The data provided here will help to identify microbes associated with different rhizo-compartments of potential host plants. In the future, this might be helpful for manipulating the keystone microbes for ecosystem functioning. [ABSTRACT FROM AUTHOR]

Short-rotation coppice willows, which are commonly propagated with cuttings, are promising bioenergy resource crops. In this study, a field trial with a completely randomized block design was carried out with 787 clones from three full-sib pedigrees involving two shrub willow species. A total of 7083 cuttings were planted in the field, and the mass of each cutting was recorded correspondingly. The mortality rate, growth traits, and wood property traits of each cutting-propagated plant were measured throughout a complete growing season. The obtained data showed that heavier cuttings produced shoots with lower mortality rate, higher height, thicker ground diameter, and larger biomass production than lighter cuttings. The cutting mass significantly improved plant performance, especially at the early developmental stages. However, the cutting mass had no effect on the basic density and the main chemical composition (i.e., cellulose, hemicellulose, and lignin) of willow wood. This study provided essential information for improving the establishment of short-rotation coppice willow plantations. [ABSTRACT FROM AUTHOR]

SUMMARY: Sex differences and evolutionary differences are critical biological issues. Ginkgo is an ancient lineage of dioecious gymnosperms with special value for studying the mechanism of sex determination in plants. However, the major genetic basic underlying sex chromosomes remains to be uncovered. In this study, we identify the sex‐determining region of Ginkgo and locate it to the area from megabases 48 to 75 on chromosome 2. We find that the male sex‐determining region of Ginkgo contains more than 200 genes, including four MADS‐box genes, demonstrating that the Ginkgo sex determination system is of the XY type. We also find that genetic sex differences result in specialized flavonoid metabolism and regulation in each sex. These findings establish a foundation for revealing the molecular mechanism of sexual dimorphism and promoting the development of the Ginkgo industry. [ABSTRACT FROM AUTHOR]

SUMMARY: Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high‐quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole‐genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long‐chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27‐Mb region of pseudochromosome 4. Our chromosome‐scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids. Significance Statement: Here, we provide the first report on the Acer truncatum genome. Our work provides extensive genetic resources necessary for very long‐chain monounsaturated fatty acid biosynthesis. [ABSTRACT FROM AUTHOR]

Podophyllotoxin is a potent cytotoxic agent and serves as a useful lead compound for development of anticancer agents. Tubulin is known as an attractive target for drug discovery and cancer therapies. There are few studies on the treatment of breast cancer with podophyllotoxin and its derivatives targeting tubulin. Here, a series of novel aryl 1,3,4‐oxadiazole/1,3,4‐thiadiazole acid podophyllotoxin ester derivatives (D1–D16) were synthesized. Among these compounds, D9 exhibited excellent antiproliferation activity against MCF‐7 cells (IC50=2.46±0.12 μM). Furthermore, D9 caused cell cycle arrest at the G2/M phase and induced cell apoptosis. Confocal microscopy showed that D9 inhibited microtubule polymerization by causing cancer cell growth inhibition. Molecular docking results suggested D9 could bind to the active binding site of tubulin. In a mouse model, compound D9 suppressed malignant growth without causing significant toxicity to normal tissues. Our findings support the utility of D9 as a novel compound for the development of anticancer agent. [ABSTRACT FROM AUTHOR]

The presence of thousands of independent origins of dioecy in angiosperms provides a unique opportunity to address the parallel evolution of the molecular pathways underlying unisexual flowers. Recent progress towards identifying sex determination genes has identified hormone response pathways, mainly associated with cytokinin and ethylene response pathways, as having been recruited multiple times independently to control unisexuality. Moreover, transcriptomics has begun to identify commonalities among intermediate sections of signal transduction pathways. These recent advances set the stage for development of a comparative evolutionary development research program to identify the shared and unique aspects of the genetic pathways of unisexual flower development in angiosperms. [ABSTRACT FROM AUTHOR]

Summary: Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere.We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence.We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance.Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies. [ABSTRACT FROM AUTHOR]

1-Deoxy-D-xylulose-5-phosphate synthasse (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) are key enzymes in terpenoid biosynthesis. DXS catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate (DXP) from pyruvate and D-glyceraldehyde-3-phosphate. DXR catalyzes the formation of 2-C-methyl-D-erythritol 4-phosphate (MEP) from DXP. Previous studies of the DXS and DXR genes have focused on herbs, such as Arabidopsis thaliana , Salvia miltiorrhiza , and Amomum villosum , but few studies have been conducted on woody plants. For that reason, we chose Populus trichocarpa as a model woody plant for investigating the DXS and DXR genes. PtDXS exhibited the highest expression level in leaves and the lowest expression in roots. PtDXR showed maximum expression in young leaves, and the lowest expression in mature leaves. The expression profiles revealed by RT-PCR following different elicitor treatments such as abscisic acid, NaCl, PEG 6000 , H 2 O 2 , and cold stress showed that PtDXS and PtDXR were elicitor-responsive genes. Our results showed that the PtDXS gene exhibited diurnal changes, but PtDXR did not. Moreover, overexpression of PtDXR in transgenic poplars improved tolerance to abiotic and biotic stresses. Those results showed that the PtDXR encoded a functional protein, and widely participates in plant growth and development, stress physiological process. [ABSTRACT FROM AUTHOR]

[Display omitted] • A novel series of dual-target benzenesulfonyl shikonin derivative has been designed and synthesized. • Z10 could activate activity of PKM2 and inhibit activity against PDK1 by direct intereaction. • Z10 showed significant anticancer activity in colorectal cancer in comparison with shikonin, PKM2 or PDK1 target agent. • Z10 exhibited lower toxicity than shikonin at 4 μM in vitro and at a dosage of 4.2 mg/kg in vivo. • Z10 could significantly induce apoptosis in colorectal cells and in xenograft mice models. Warburg effect provides energy and material essential for tumor proliferation, the reverse of Warburg effect provides insights into the development of a novel anti-cancer strategy. Pyruvate kinase 2 (PKM2) and pyruvate dehydrogenase kinase 1 (PDK1) are two key enzymes in tumor glucose metabolism pathway that not only contribute to the Warburg effect through accelerating aerobic glycolysis, but also serve as druggable target for colorectal cancer (CRC). Considering that targeting PKM2 or PDK1 alone does not seem to be sufficient to remodel abnormal glucose metabolism and achieve significant antitumor activity, a series of novel benzenesulfonyl shikonin derivatives were designed to regulate PKM2 and PDK1 simultaneously. By means of molecular docking and antiproliferative screen, we found that compound Z10 could act as the combination of PKM2 activator and PDK1 inhibitor, thereby significantly inhibited glycolysis that reshaping tumor metabolism. Moreover, Z10 could inhibit proliferation, migration and induce apoptosis in CRC cell HCT-8. Finally, the in vivo anti-tumor activity of Z10 was evaluated in a colorectal cancer cell xenograft model in nude mice and the results demonstrated that Z10 induced tumor cell apoptosis and inhibited tumor cell proliferation with lower toxicity than shikonin. Our findings indicated that it is feasible to alter tumor energy metabolism through multi-target synergies, and the dual-target benzenesulfonyl shikonin derivative Z10 could be a potential anti-CRC agent. [ABSTRACT FROM AUTHOR]

The SnRK (sucrose non-fermenting-1 related protein kinase) families respond to salt tolerance, nutritional stress, disease stress, and carbon metabolic regulation. In this study, the SnRK2.8 gene was cloned from Arabidopsis thaliana and nominated AtSnRK2.8. Bioinformatics characterization of AtSnRK2.8 showed that it contained an ATP binding site and a serine/threonine protein kinase binding site at the N-terminal catalytic domain. In addition, the AtSnRK2.8 protein contained special domain I at the C-terminal catalytic domain. Real-time polymerase chain reaction (PCR) results showed that the AtSnRK2.8 gene was expressed in all tested tissues and was highly expressed in seeds. Our analyses proved that the AtSnRK2.8 gene expression was upregulated by salt and drought stresses. The recombinant AtSnRK2.8 protein was expressed using a pET-28a system and purified with HisTrap HP affinity columns. The recombinant AtSnRK2.8 protein has the properties of a protein kinase. The results of overexpressing AtSnRK2.8 in Nanlin895 poplar showed that the transgenic poplar plants had a better ability to resist drought and salt stress compared to the wild type, and adapted well to drought and a high-salt environment. [ABSTRACT FROM AUTHOR]

The placenta in fruits of most plants either desiccate and shrink as the fruits mature or develop further to form the fleshy tissues. In poplars, placental epidermal cells protrude collectively to produce catkin fibers. In this study, three carpel limited MIXTA genes, PdeMIXTA02, PdeMIXTA03, PdeMIXTA04 , were find to specifically expressed in carpel immediately after pollination. Heterologous expression of the three genes in Arabidopsis demonstrated that PdeMIXTA04 significantly promoted trichomes density and could restore trichomes in the trichomeless mutant. By contrast, such functions were not observed with PdeMIXTA02, PdeMIXTA03. In situ hybridization revealed that PdeMIXTA04 was explicitly expressed in poplar placental epidermal cells. We also confirmed trichome-specific expression of the PdeMIXTA04 promoter. Multiple experimental proofs have confirmed the interaction between PdeMIXTA04, PdeMYC and PdeWD40, indicating PdeMIXTA04 functioned through the MYB-bHLH-WD40 ternary complex. Our work provided distinctive understanding of the molecular mechanism triggering differentiation of poplar catkins. [ABSTRACT FROM AUTHOR]

There are concerns that the innovation of genetically modified herbicide-tolerant (GMHT) plants, as well as the application of herbicide to such GMHT plants, could have an impact on ecological interactions and unintentionally harm non-targeted organisms. Consequently, we intend to use full-length 16 S rDNA amplicon sequencing to examine changes in the bacterial community in the rhizosphere of GMHT soybean (Z106) harboring 5-enolpyruvylshikimate-3-phosphate synthase and Glyphosate N-acetyltransferase genes and GMHT soybean treated with glyphosate (Z106G). Glyphosate application significantly impacted bacterial alpha diversity (species richness, and Shannon diversity). Permutational multivariate analysis of variance of beta diversity demonstrated that soil compartments and growth stages had a substantial impact on soybean rhizobacterial communities (soil compartments, growth stages, P = 0.001). Community composition revealed that Z106G soils were abundant in Taibaiella and Arthrobacter pascens at maturity, while Chryseobacterium joostei and Stenotrophomonas maltophilia predominated in Z106 soils during flowering. Nitrogen-fixing and phosphate-solubilizing microbes were found in higher proportions in the rhizosphere than in bulk soil, with Sinorhizobium being more abundant in Z106 and Bacillus and Stenotrophomonas being more prevalent in Z106G rhizosphere soils. Collectively, our findings suggest glyphosate application and glyphosate-tolerant soybean as potential regulators of soybean rhizobacterial composition. [Display omitted] • Glyphosate application had an impact on bacterial alpha diversity (species richness, and Shannon diversity). • Sinorhizobium fredii, a nitrogen fixer, was more abundant in the glyphosate-tolerant soybean line. • Neither glyphosate nor transgenic soybean line affected the relative abundance of the pathogenic fungus Fusarium. • Glyphosate spraying and soybean carrying EPSPS and GAT transgenes both positively regulate rhizobacterial composition. [ABSTRACT FROM AUTHOR]

Epigenetic modification by DNA methylation is necessary for all cellular processes, including genetic expression events, DNA repair, genomic imprinting and regulation of tissue development. It occurs almost exclusively at the C5 position of symmetric CpG and asymmetric CpHpG and CpHpH sites in genomic DNA. The RNA-directed DNA methylation ( RDM1 ) gene is crucial for heterochromatin and DNA methylation. We overexpressed PtRDM1 gene from Populus trichocarpa to amplify transcripts of orthologous RDM1 in ‘Nanlin895’ ( P. deltoides  ×  P. euramericana ‘Nanlin895’). This overexpression resulted in increasing RDM1 transcript levels: by ∼150% at 0 mM NaCl treatment and by ∼300% at 60 mM NaCl treatment compared to WT (control) poplars. Genomic cytosine methylation was monitored within 5.8S rDNA and histone H3 loci by bisulfite sequencing. In total, transgenic poplars revealed more DNA methylation than WT plants. In our results, roots revealed more methylated CG contexts than stems and leaves whereas, histone H3 presented more DNA methylation than 5.8S rDNA in both WT and transgenic poplars. The NaCl stresses enhanced more DNA methylation in transgenic poplars than WT plants through histone H3 and 5.8 rDNA loci. Also, the overexpression of PtRDM1 resulted in hyper-methylation, which affected plant phenotype. Transgenic poplars revealed significantly more regeneration of roots than WT poplars via NaCl treatments. Our results proved that RDM1 protein enhanced the DNA methylation by chromatin remodeling (e.g. histone H3 ) more than repetitive DNA sequences (e.g. 5.8S rDNA). [ABSTRACT FROM AUTHOR]

Gene knockdown and gene-silencing pathways in eukaryotic organisms are associated with small RNAs 20 to 25 nucleotides in length, which include microRNAs (miRNAs) and small interfering RNAs (siRNAs). These small RNAs are recruited to repress gene expression upstream or downstream of the transcription pathway. RNA interference (RNAi) is a biological inhibitor of gene expression that results in the destruction of messenger RNAs (mRNAs), leading to the inhibition of protein production. Indeed, RNA silencing plays a key role in plant development in terms of the plant’s response to both biotic and abiotic stresses. Conversely, Viral Suppressors of RNA silencing (VSRs) are proteins that hamper antiviral RNAi activation in plants, lead to suppress plant RNA-silencing. These VSR proteins prevent the induction of the plant antiviral RNAi immune response. This review focuses on small RNAs in plants and their roles in the responses of plants to biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

Recent works have proposed two L1-norm distance measure-based linear discriminant analysis (LDA) methods, L1-LD and LDA-L1, which aim to promote the robustness of the conventional LDA against outliers. In LDA-L1, a gradient ascending iterative algorithm is applied, which, however, suffers from the choice of stepwise. In L1-LDA, an alternating optimization strategy is proposed to overcome this problem. In this paper, however, we show that due to the use of this strategy, L1-LDA is accompanied with some serious problems that hinder the derivation of the optimal discrimination for data. Then, we propose an effective iterative framework to solve a general L1-norm minimization–maximization (minmax) problem. Based on the framework, we further develop a effective L1-norm distance-based LDA (called L1-ELDA) method. Theoretical insights into the convergence and effectiveness of our algorithm are provided and further verified by extensive experimental results on image databases. [ABSTRACT FROM PUBLISHER]

The prior knowledge plays an important role in increasing the performance of the support vector machines (SVMs). Traditional SVMs do not consider any prior knowledge of the training set. In this paper, the neighbors' distribution knowledge is incorporated into SVMs. The neighbors' distribution can be measured by the sum of the cosine value of the angle, which is between the difference between the sample and its corresponding neighbor, and the difference between the sample and the mean of corresponding neighbors. The neighbors' distribution knowledge reflects the sample's importance in the training processing. It can be explained as the relative margin or instance weight. In this paper, the neighbors' distribution knowledge is regarded as the relative margin and incorporated into the framework of density-induced margin support vector machines whose relative margin is measured by relative density degree. The results of the experiments, performed on both artificial synthetic datasets and real-world benchmark datasets, demonstrate that SVMs performs better after incorporating neighbors' distribution. Furthermore, experimental results also show that neighbors' distribution are more suitable than relative density degree to represent the relative margin. [ABSTRACT FROM AUTHOR]

Nucleoside diphosphate kinases (NDPKs) are multifunctional proteins that regulate a variety of eukaryotic cellular activities, including cell proliferation, development, and differentiation. NDPK2 regulates the expression of antioxidant genes in plants. In a previous study, the Arabidopsis thaliana NDPK2 gene ( AtNDPK2 ) was found to be associated with H 2 O 2 -mediated mitogen-activated protein kinase signaling in Arabidopsis thaliana . Proteins from transgenic plants overexpressing AtNDPK2 showed higher levels of autophosphorylation and NDPK activity and lower levels of reactive oxygen species (ROS) than those of wild-type (WT) plants. Therefore, constitutive overexpression of AtNDPK2 in Arabidopsis plants conferred enhanced tolerance to multiple environmental stresses that elicit ROS accumulation in situ . In this study, we cloned the Populus trichocarpa NDPK2 gene and analyzed its molecular structure and function. We generated and evaluated transgenic poplar plants expressing the PtNDPK2 gene under the control of the 35S promoter to achieve enhanced tolerance to various abiotic stresses. Transgenic poplar plants showed enhanced tolerance to salt and drought stress at the whole-plant level. The transgenic poplar plants showed significantly greater tolerance to 200 mM NaCl and drought stresses than WT poplar plants. In addition, the transgenic plants exhibited better growth due to increased expression of auxin-related indole acetic acid genes under normal growth conditions compared with WT plants. Our results suggest that induction of PtNDPK2 overexpression in poplars will be useful for increasing biomass production in the presence of various abiotic stresses. [ABSTRACT FROM AUTHOR]

Pyruvate kinase 2 (PKM2) and pyruvate dehydrogenase kinase 1 (PDK1) are two key enzymes in tumor glucose metabolism pathway that not only promote tumor growth and proliferation through accelerating aerobic glycolysis, but also contribute to drug resistance of non-small cell lung cancer (NSCLC). Considering that targeting PKM2 or PDK1 alone seems insufficient to remodel abnormal glucose metabolism to achieve significant antitumor activity, we proposed a "two-step approach" that regulates PKM2 and PDK1 synchronously. Firstly, we found that the combination of ML265 (PKM2 activator) and AZD7545 (PDK1 inhibitor) could synergistically inhibit proliferation and induce apoptosis in H1299 cells. Base on this, we designed a series of novel shikonin (SK) thioether derivatives as PKM2/PDK1 dual-target agents, among which the most potent compound E5 featuring a 2-methyl substitution on the benzene ring exerted significantly increased inhibitory activity toward EGFR mutant NSCLC cell H1975 (IC 50 = 1.51 μmol/L), which was 3 and 17-fold more active than the lead compound SK (IC 50 = 4.56 μmol/L) and the positive control gefitinib (IC 50 = 25.56 μmol/L), respectively. Additionally, E5 also showed good anti-tumor activity in xenografted mouse models, with significantly lower toxicity side effects than SK. Moreover, E5 also inhibited the entry of PKM2 into nucleus to regulate the transcriptional activation of oncogenes, thus restoring the sensitivity of H1975 cell to gefitinib. Collectively, these data demonstrate that E5 , a dual inhibitor of PKM2/PDK1, may be a promising adjunct to gefitinib in the treatment of EGFR-TKIs resistant NSCLC, deserving further investigation. [Display omitted] • A synergistic effect of PKM2 activation and PDK1 inhibition was first demonstrated. • A series of PKM2/PDK1 dual-target shikonin thioether derivatives were developed. • The most active compound E5 significantly inhibit tumor growth in vitro and in vivo. • The most active compound E5 enhance the sensitivity of H1975 cells to gefitinib. [ABSTRACT FROM AUTHOR]

Polyploid breeding is an important means for creating elite willow cultivars, and therefore provokes an active demand for discriminating the ploidy levels of natural willow stands. In this study, we established an analytical toolkit for polyploid willow identification by combining molecular markers and flow cytometry (FCM). A total of 10 single-copy fully informative SSRs were chosen for marker-aided selection based on a segregation test with a full-sib willow pedigree and a mutability test with a collection of natural willow stands. Aided by these molecular markers, we performed polyploid selection in two tree species and two shrub species of the genus Salix. The ploidy levels of the investigated samples were further examined using a flow cytometer. It was previously shown that results from marker-aided selection were consistent with those from FCM measurements. Based on ploidy level assessment in different willow species, it was found that tree willows were dominantly tetraploid, whereas shrub willows were most frequently diploid. With this analytical toolkit, polyploids can be rapidly screened from a large number of natural stands; thereafter, the exact ploidy levels of the polyploid candidates can be efficiently confirmed by FCM. This analytical toolkit will greatly enhance polyploid breeding programs for willows. [ABSTRACT FROM AUTHOR]

Many willow species, especially the short-rotation coppice willows, are suitable for development into renewable bioenergy crops. In this study, we conducted high-throughput transcriptome sequencing of a shrub willow, S. suchowensis, to generate expressed sequence tags ( ESTs) for gene discovery and molecular marker development. Totally, 136.1 million clean reads were generated from five different tissues of S. suchowensis using Illumina RNA-seq technology. De novo sequence assembly produced 90 269 unigenes, among which 64 127 unigenes were annotated in one or more of the NR, Swiss-Prot, GO, COG and KEGG databases. A total of 21 052 simple sequence repeats were identified in the expressed sequence assemblies, and a primer database containing 36 912 EST- SSR markers were developed for 12 304 SSR loci. Subsequently, 25 primers were randomly selected for experimental test. Among which, 24 primers succeeded in PCR amplification and 21 produced amplicons in expected sizes, suggesting that the sequence assemblies were of high quality. The established sequence database and marker resource are useful for different aspects of genetic studies on Salix spp., and particularly valuable for marker-assisted breeding of willows. [ABSTRACT FROM AUTHOR]

Unlike two-class (multi-class) support vector machines, massive targets and few outliers are available in one-class support vector machine. The strategies to select useful data for two-class (multi-class) support vector machines are not suitable for one-class support vector machine. In this paper, relative density degree is introduced to select useful data for one-class support vector machine. These data would become support vectors after training and locate near the boundary of the data distribution. The relative density degree of the data near the boundary of the training set is smaller than that of the data in the interior of the training set. Thus, the data near the boundary of training set can be preserved and the others can be disposed through relative density degree. Experimental results show that merely preserving about 20 % of the training set, the performance will not decrease and be better than previous related method. But the model is simpler and the training process is faster. [ABSTRACT FROM AUTHOR]

The antimicrobial peptide ABP-dHC-cecropin A is a small cationic peptide with potent activity against a wide range of bacterial species. Evidence of antifungal activity has also been suggested; however, evaluation of this peptide has been limited due to the low expression of cecropin proteins in Escherichia coli . To improve the expression level of ABP-dHC-cecropin A in E. coli , tandem repeats of the ABP-dHC-cecropin A gene were constructed and expressed as fusion proteins (SUMO-nABP-dHC-cecropin, n = 1, 2, 3, 4) via pSUMO-nABP-dHC-cecropin A vectors ( n = 1, 2, 3, 4). Comparison of the expression levels of soluble SUMO-nABP-dHC-cecropin A fusion proteins ( n = 1, 2, 3, 4) suggested that BL21 (DE3)/pSUMO-3ABP-dHC-cecropin A is an ideal recombinant strain for ABP-dHC-cecropin A production. Under the selected conditions of cultivation and isopropylthiogalactoside (IPTG) induction, the expression level of ABP-dHC-cecropin A was as high as 65 mg/L, with ∼21.3% of the fusion protein in soluble form. By large-scale fermentation, protein production reached nearly 300 mg/L, which is the highest yield of ABP-dHC-cecropin A reported to date. In antibacterial experiments, the efficacy was approximately the same as that of synthetic ABP-dHC-cecropin A. This method provides a novel and effective means of producing large amounts of ABP-dHC-cecropin A. [ABSTRACT FROM AUTHOR]

PDK1 is one of the key enzymes in the glucose metabolism pathway, which is abnormally high expressed in breast cancer tissues and can promote tumor proliferation and metastasis. PDK1 and the PDHC/PDK axis are important targets for regulating glucose metabolism and anti-tumor activity. In this study, we evaluated the anti-tumor activities of a series of semi-synthesized shikonin (SK) derivatives against human breast cancer cells. The anti-proliferation activity of SK derivatives against human breast cancer cell lines was tested by CCK-8 and EdU assay. Flow cytometry was utilized to evaluate cell apoptosis, reactive oxygen species and cell cycle distribution. Cell migration ability was determined by wound healing and trans-well assay. PDK1 targeting effect was confirmed by western bolting, molecular docking, bio-layer interferometry and PDK1 enzyme activity assay. Nude-mouse transplanted tumor model was used to evaluate their anti-tumor effect in vivo. Findings revealed that SK derivatives had good anti-proliferation ability against MDA-MB-231 cell. They induced cell apoptosis by regulating the mitochondrial apoptosis and death receptor pathway. They also inhibited cell migration by suppressing EMT progression. Molecular docking, PDK1 affinity and enzyme activity demonstrated their PDK1 targeting. In vivo antitumor experiment showed that E2 could significantly inhibit tumor growth with lower side-effect on mice than SK. In conclusion, the novel SK derivatives E2 and E5 inhibited tumor glycolysis by targeting PDK1 and ultimately induced apoptosis. Our data demonstrated that E2 would be a good lead compound for the treatment of human TNBC as a novel PDK1 inhibitor. [ABSTRACT FROM AUTHOR]

[Display omitted] • SK and acetyl-SK relieve colonic injuries inAOM / DSS -induced colitis-associated colorectal cancer (CAC) model of C57BL/6J mice. • SK and acetyl-SK remodel the gut microbial communities of CAC mice models. • SK and acetyl-SK rescued the increased Ileibacterium valens and g_norank_f_norank_o_Clostridia_UCG-014 in CAC mice. • SK downregulated the expression of ACTN2, FGG and PKM2 in CAC mice. • SK upregulated the expression of Aldh1a1 and Aldh1b1 which involved in the Wnt/ β -catenin pathway in CAC mice. Colorectal cancer (CRC) and inflammatory bowel disease (IBD) are the most common diseases of human digestive system. Nowadays, the influence of the inflammatory microenvironment on tumorigenesis has become a new direction, and the exploration of relative molecular mechanism will facilitate the discovery and identification of novel potential anti-cancer molecules. Natural shikonin (SK) and acetyl-shikonin (acetyl-SK) was administered to azoxymethane (AOM)/dextran sodium sulphate (DSS)-induced colitis-associated colorectal cancer (CAC) mice model by gavage to investigate their therapeutic effects. Moreover, fresh feces and colon tissues were collected for determining the function of SK and acetyl-SK on the gut microbes and protein expression, respectively. Both SK and acetyl-SK decreased AOM/DSS-induced CAC, and regulated the intestinal flora structure in CAC mouse model. They, especially SK, improved species richness, evenness and diversity of intestinal flora, recovered the upregulated ratio of Firmicutes to Bacteroidota (F/B ratio) which symbolizes gut microbiota dysbiosis. SK and its derivative increased the beneficial bacteria g__norank_f__Muribaculaceae, Lactobacillus, Lachnospiraceae_NK4A136_Group, and reduced those harmful ones including Ileibacterium and Coriobacteriaceae UCG–002. Notably, AOM/DSS caused significant increase in the abundance of Ileibaterium valens and g__norank_f__norank_o__Clostridia_UCG-014 , which were not previously reported in studies of colonic inflammation or cancer, and the disorder was reversed by 20 mg/kg of SK. In our current study, the action of SK and acetyl-SK is dose-dependent, and 20 mg/kg SK exhibited the most effective functions, even better than the positive drug mesalazine. Moreover, differential proteomics and ELISA results showed that SK could recover the increase of pro-inflammatory cytokines (including IL-1β, IL-6 and TNF-α), the upregulation of pyruvate kinase isozyme type M2 (PKM2) and some other proteins (mainly concentrated in transcriptional mis-regulation in cancer and IL-17 signaling pathways), and the downregulation of Aldh1b1-Acc3-Maoa and Μgt2b34-Aldh1a1-Aldh1a7 involved in Wnt/ β -catenin signaling pathway. Our study identified SK and acetyl-SK, especially SK, as potential preventive agents for CAC through regulating both gut microbes and pathways involved in inflammation and cancer such as Wnt/ β -catenin signaling pathway. [ABSTRACT FROM AUTHOR]