Pathway-based prediction of the therapeutic effects and mode of action of custom-made multiherbal medicines.

Multiherbal medicines are traditionally used as personalized medicines with custom combinations of crude drugs; however, the mechanisms of multiherbal medicines are unclear. In this study, we developed a novel pathway-based method to predict therapeutic effects and the mode of action of custom-made multiherbal medicines using machine learning. This method considers disease-related pathways as therapeutic targets and evaluates the comprehensive influence of constituent compounds on their potential target proteins in the disease-related pathways. Our proposed method enabled us to comprehensively predict new indications of 194 Kampo medicines for 87 diseases. Using Kampo-induced transcriptomic data, we demonstrated that Kampo constituent compounds stimulated the disease-related proteins and a customized Kampo formula enhanced the efficacy compared with an existing Kampo formula. The proposed method will be useful for discovering effective Kampo medicines and optimizing custom-made multiherbal medicines in practice.

Decrease in purifying selection pressures on wheat homoeologous genes: tetraploidization versus hexaploidization.

A series of polyploidizations in higher-order polyploids is the main event affecting gene content in a genome. Each polyploidization event can lead to massive functional divergence because of the subsequent decrease in selection pressure on duplicated genes; however, the causal relationship between multiple rounds of polyploidization and the functional divergence of duplicated genes is poorly understood. We focused on the Triticum-Aegilops complex lineage and compared selection pressure before and after tetraploidization and hexaploidization events. Although both events led to decreased selection pressure on homoeologous gene pairs (compared with diploids and tetraploids), the initial tetraploidization had a greater impact on selection pressure on homoeologous gene pairs than did subsequent hexaploidization. Consistent with this, selection pressure on expression patterns for the initial event relaxed more than those for the subsequent event. Surprisingly, the decreased selection pressure on these homoeologous genes was independent of the existence of in-paralogs within the same subgenome. Wheat homoeologous pairs had different evolutionary consequences compared with orthologs related to other mechanisms (ancient allopolyploidization, ancient autopolyploidization, and small-scale duplication). Furthermore, tetraploidization and hexaploidization also seemed to have different evolutionary consequences. This suggests that homoeologous genes retain unique functions, including functions that are unlikely to be preserved in genes generated by the other duplication mechanisms. We found that their unique functions differed between tetraploidization and hexaploidization (e.g., reproductive and chromosome segregation processes). These findings imply that the substantial number of gene pairs resulting from multiple allopolyploidization events, especially initial tetraploidization, may have been a unique source of functional divergence.

Application of ethanol alleviates heat damage to leaf growth and yield in tomato.

Chemical priming has emerged as a promising area in agricultural research. Our previous studies have demonstrated that pretreatment with a low concentration of ethanol enhances abiotic stress tolerance in Arabidopsis and cassava. Here, we show that ethanol treatment induces heat stress tolerance in tomato (Solanum lycopersicon L.) plants. Seedlings of the tomato cultivar 'Micro-Tom' were pretreated with ethanol solution and then subjected to heat stress. The survival rates of the ethanol-pretreated plants were significantly higher than those of the water-treated control plants. Similarly, the fruit numbers of the ethanol-pretreated plants were greater than those of the water-treated ones. Transcriptome analysis identified sets of genes that were differentially expressed in shoots and roots of seedlings and in mature green fruits of ethanol-pretreated plants compared with those in water-treated plants. Gene ontology analysis using these genes showed that stress-related gene ontology terms were found in the set of ethanol-induced genes. Metabolome analysis revealed that the contents of a wide range of metabolites differed between water- and ethanol-treated samples. They included sugars such as trehalose, sucrose, glucose, and fructose. From our results, we speculate that ethanol-induced heat stress tolerance in tomato is mainly the result of increased expression of stress-related genes encoding late embryogenesis abundant (LEA) proteins, reactive oxygen species (ROS) elimination enzymes, and activated gluconeogenesis. Our results will be useful for establishing ethanol-based chemical priming technology to reduce heat stress damage in crops, especially in Solanaceae.

Expression profiles in knock-down transgenic plants of high and low diversified duplicate genes in Arabidopsis thaliana.

Duplicated genes show various degrees of functional diversification in plants. We previously identified 1,052 pairs of high diversified duplicates (HDDs) and 600 pairs of low diversified duplicates (LDDs) in Arabidopsis thaliana. Single knock-down of HDDs induced abnormal phenotypic changes because the other gene copy could not compensate for the knock-down effect, while single knock-down of LDDs did not induce abnormal phenotypic changes because of functional compensation by the copy gene. Here, focusing on one pair each of HDDs and LDDs, we performed transcriptome analyses in single-knock-down transgenic plants. The numbers of differentially expressed genes in single-knock-down transgenic plants were not different between HDDs and LDDs. Thus, functional compensation inferred by transcriptomics was similar between HDDs and LDDs. However, the trend of differentially expressed genes was similar in the pair of LDDs, while expression profiles were dissimilar in the pair of HDDs. This result indicates that a pair of LDDs tends to share similar functions but a pair of HDDs tends to have undergone functional divergence. Taking these findings together, as the reason for no phenotypic changes in single knock-down of LDDs but phenotypic changes in double knock-down of LDDs, we concluded that phenotypic changes of LDDs were induced by decreasing gene dosage.

Fully sequencing the cassava full-length cDNA library reveals unannotated transcript structures and alternative splicing events in regions with a high density of single nucleotide variations, insertions-deletions, and heterozygous sequences.

The primary transcript structure provides critical insights into protein diversity, transcriptional modification, and functions. Cassava transcript structures are highly diverse because of alternative splicing (AS) events and high heterozygosity. To precisely determine and characterize transcript structures, fully sequencing cloned transcripts is the most reliable method. However, cassava annotations were mainly determined according to fragmentation-based sequencing analyses (e.g., EST and short-read RNA-seq). In this study, we sequenced the cassava full-length cDNA library, which included rare transcripts. We obtained 8,628 non-redundant fully sequenced transcripts and detected 615 unannotated AS events and 421 unannotated loci. The different protein sequences resulting from the unannotated AS events tended to have diverse functional domains, implying that unannotated AS contributes to the truncation of functional domains. The unannotated loci tended to be derived from orphan genes, implying that the loci may be associated with cassava-specific traits. Unexpectedly, individual cassava transcripts were more likely to have multiple AS events than Arabidopsis transcripts, suggestive of the regulated interactions between cassava splicing-related complexes. We also observed that the unannotated loci and/or AS events were commonly in regions with abundant single nucleotide variations, insertions-deletions, and heterozygous sequences. These findings reflect the utility of completely sequenced FLcDNA clones for overcoming cassava-specific annotation-related problems to elucidate transcript structures. Our work provides researchers with transcript structural details that are useful for annotating highly diverse and unique transcripts and alternative splicing events.

Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution.

Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.

Regio- and stereoselective nickel-catalyzed homoallylation of aldehydes with 1,3-dienes.

Ni(acac)(2) catalyzes homoallylation of aldehydes with 1,3-dienes in the presence of triethylborane. Triethylborane serves as a reducing agent delivering a formal hydride to the C2 position of 1,3-dienes, thus generating a formal homoallyl anion species and enabling the novel homoallylation of aldehydes. The reaction proceeds smoothly at room temperature in the absence of any phosphane or nitrogen ligands and is highly regioselective and stereoselective for a wide variety combination of aldehydes and 1,3-dienes: e.g., isoprene and benzaldehyde combine to give a mixture of anti- and syn-1-phenyl-3-methyl-4-penten-1-ol (2.2) in a ratio of 15:1 in 90% yield. Under the conditions, sterically congested aliphatic aldehydes and ketones show low yields. In such cases, diethylzinc serves as a substitute for triethylborane and yields the expected products in good yields with similarly high regio- and stereoselectivity. 1,3-Cyclohexadiene is one exception among 24 kinds of dienes examined and undergoes allylation (not homoallylation) selectively.

Nickel-catalyzed addition of dimethylzinc to aldehydes across alkynes and 1,3-butadiene: an efficient four-component connection reaction.

In the presence of 10 mol % of Ni(acac)(2), four components comprising Me(2)Zn, alkynes, 1,3-butadiene, and carbonyl compounds combine in this order in 1:1:1:1 ratio to furnish (3E,6Z)-octadien-1-ols 1 in good yields. Similarly, the coupling reaction of Me(2)Zn, 1,omega-dienynes 5, and carbonyls furnishes 1-alkylidene-2-(4'-hydroxy-(1'E)-alkenyl)cyclopentanes and -cyclohexanes 6 and their oxygen and nitrogen heterocycle derivatives in good yield and an excellent level of 1,5-diastereoselectivity with respect to the cycloalkane methine carbon and the OH-bearing carbon of the C2 side chain. The reaction is completed in most cases within 1 h at room temperature under nitrogen, tolerates an ester, a hydroxy, an allyl and propargyl ethers, an allylamino, and a pyridyl functionalities, and accommodates a variety of aromatic and aliphatic alkynes and carbonyls (aldehydes and ketones).

Nickel-Catalyzed Homoallylation of Aldehydes and Ketones with 1,3-Dienes and Complementary Promotion by Diethylzinc or Triethylborane.

Regio- and stereoselective homoallylation of saturated aldehydes and ketones to give bishomoallyl alcohols 1,3-anti-1 is achieved with [Ni(acac)2 ] (cat.) and Et2 Zn [Eq. (a)]. This new catalyst system thus complements the previously reported combination of [Ni(acac)2 ] with Et3 B, which offers advantages in the homoallylation of unsaturated and aromatic aldehydes. acac=acetylacetonato.