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Homoeologous exchange (HE) is a major mechanism generating post-polyploidization genetic variation with important evolutionary consequences. However, the direct impacts of HE without entangling with additional evolutionary forces on gene expression remains to be fully understood. Here, we analyzed high-throughput RNA-seq data of young leaves from individuals of a synthetic allotetraploid wheat (AADD), which contain variable numbers of HEs. We aimed to investigate if and to which extent HE directly impacts gene expression and alternative splicing (AS). We found that HE impacts expression of genes located within HE regions primarily via cis-acting dosage effect, which led to significant changes in the total expression of homoeolog pairs, especially for homoeologs whose original expression was biased. In parallel, HE influences expression of a large amount of genes residing in non-HE regions by trans-regulation leading to convergent expression of homoeolog pairs. Intriguingly, when taking into account of the original relative homoeolog expression states, homoeolog pairs under trans-effect are more prone to showing convergent response to HE whereas those under cis-effect trended to show subgenome-specific expression. Moreover, HE induced quantitative, largely individual-specific, changes of alternative splicing (AS) events. Like homoeologs expression, homoeo-AS events which related to trans effect were more responsive to HE. HE therefore exerts multifaceted immediate effects on gene expression and, to a less extent, also transcript diversity in nascent allopolyploidy.

In recent years, immune checkpoint inhibitors (ICIs) have improved treatment for several types of cancer. However, the overall response rates remain low, and drug resistance can occur in patients after initial responses. This resistance is thought to be due in part to tumor-associated macrophages (TAMs), which can deploy a number of mechanisms to suppress anti-tumor immunity, resulting in tumor immune escape. Triggering receptor expressed on myeloid cells-2 (TREM2), a transmembrane receptor that is part of the immunoglobulin superfamily, is highly expressed on the surface of TAMs. Moreover, the expression level of TREM2 is reported to be higher in cancerous tissues vs normal tissues, with higher expression associated with poorer patient outcomes across multiple solid tumor types. Conversely, mice that lack Trem2 experience slower tumor cell expansion and are more responsive to anti-PD-1 immunotherapy, suggesting that TREM2 may be a promising therapeutic target for improving responses to ICI immunotherapies. To better assist the efficacy evaluation of anti TREM2 antibodies, Biocytogen has generated a humanized TREM2 mouse model. In these mice, exons 1-5 and the 3’UTR of mouse Trem2 gene, which encodes the full-length protein, were replaced by its human counterpart. In homozygous mice, human TREM2 protein expression is detected. The distribution of basal leukocyte subpopulations of blood, spleen, and lymph nodes in humanized B-hTREM2 mice were similar and comparable to those in wild-type C57BL/6 mice. Using the MC38 tumor model, we showed modest efficacy of an anti-human TREM2 antibody in inhibiting tumor growth in vivo. In summary, TREM2 humanized mice provide a powerful preclinical model for in vivo evaluation of anti-human TREM2 antibodies for cancer treatment. Citation Format: Ruili Lv, Jia Yu, Zhiyuan Shen, James Jin. Generation of humanized TREM2 mice for preclinical evaluation of therapeutics targeting tumor-associated macrophages. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5209.

During a survey of soil fungal diversity in a rocky desertification area in Yunnan Province, China, a new dematiaceous hyphomycete, Cordana yunnanensis was identified. Morphologically, this species is characterized by macronematous, mononematous conidiophores with discrete, polyblastic conidiogenous cells arranged in a whorl at the apices. Phylogenetic analysis of the combined sequences of the internal transcribed spacer and the large nuclear ribosomal RNA subunit confirmed the phylogenetic position of C. yunnanensis within the genus Cordana, in Cordanaceae.

The link between polyploidy and enhanced adaptation to environmental stresses could be a result of polyploidy itself harbouring higher tolerance to adverse conditions, or polyploidy possessing higher evolvability than diploids under stress conditions. Natural polyploids are inherently unsuitable to disentangle these two possibilities. Using selfed progenies of a synthetic allotetraploid wheat AT3 (AADD) along with its diploid parents, Triticum urartu TMU38 (AA) and Aegilops tauschii TQ27 (DD), we addressed the foregoing issue under abiotic salinity and hyper-osmotic (drought-like) stress. Under short duration of both stresses, euploid plants of AT3 showed intermediate tolerance of diploid parents; under life-long duration of both stresses, tolerant individuals to either stress emerged from selfed progenies of AT3, but not from comparable-sized diploid parent populations. Tolerance to both stresses were conditioned by the same two homoeologous exchanges (HEs; 2DS/2AS and 3DL/3AL), and at least one HE needed to be at the homozygous state. Transcriptomic analyses revealed that hyper-up-regulation of within-HE stress responsive genes of the A sub-genome origin is likely responsible for the dual-stress tolerant phenotypes. Our results suggest that HE-mediated inter-sub-genome rearrangements can be an important mechanism leading to adaptive evolution in allopolyploids as well as a promising target for genetic manipulation in crop improvement.

Allotetraploidization between A and S (closely related to B) genome species led to the speciation of allotetraploid wheat (genome BBAA). However, the immediate metabolic outcomes and adaptive changes caused by the allotetraploidization event are poorly understood. Here, we investigated how allotetraploidization affected salinity tolerance using a synthetic allotetraploid wheat line (genome S

Polyploidy, or whole genome duplication (WGD), is a driving evolutionary force across the tree of life and has played a pervasive role in the evolution of the plant kingdom. It is generally believed that a major genetic attribute contributing to the success of polyploidy is increased gene and genome dosage. The evolution of polyploid wheat has lent support to this scenario. Wheat has evolved at three ploidal levels: diploidy, tetraploidy, and hexaploidy. Ample evidence testifies that the evolutionary success, be it with respect to evolvability, natural adaptability, or domestication has dramatically increased with each elevation of the ploidal levels. A long-standing question is what would be the outcome if a further elevation of ploidy is superimposed on hexaploid wheat? Here, we characterized a spontaneously occurring nonaploid wheat individual in selfed progenies of synthetic hexaploid wheat and compared it with its isogenic hexaploid siblings at the phenotypic, cytological, and genome-wide gene-expression levels. The nonaploid manifested severe defects in growth and development, albeit with a balanced triplication of the three wheat subgenomes. Transcriptomic profiling of the second leaf of nonaploid, taken at a stage when phenotypic abnormality was not yet discernible, already revealed significant dysregulation in global-scale gene expression with ca. 25.2% of the 49,436 expressed genes being differentially expressed genes (DEGs) at a twofold change cutoff relative to the hexaploid counterpart. Both up- and downregulated DEGs were identified in the nonaploid vs. hexaploid, including 457 genes showing qualitative alteration, i.e., silencing or activation. Impaired functionality at both cellular and organismal levels was inferred from gene ontology analysis of the DEGs. Homoeologous expression analysis of 9,574 sets of syntenic triads indicated that, compared with hexaploid, the proportions showing various homeologous expression patterns were highly conserved in the nonaploid although gene identity showed moderate reshuffling among some of the patterns in the nonaploid. Together, our results suggest hexaploidy is likely the upper limit of ploidy level in wheat; crossing this threshold incurs severe ploidy syndrome that is preceded by disruptive dysregulation of global gene expression.

During a mycological survey of aquatic hyphomycetes on submerged decaying leaves in southwest China, a distinct new fungus was collected. The collection was cultured and sequenced and a BLAST search of its ITS and LSU sequence against data in GenBank revealed a dothideomycetous affiliation, with the closest related taxa in the genus Neodactylaria. Phylogenetic analyses of a multigene matrix containing sequences from four genes (LSU, SSU, rpb2, and tef1), representing broad groups of Dothideomycetes, revealed its placement within Dothideomycetes, but without a supported familial or ordinal affiliation. Based on further phylogenetic analyses and morphological investigations, the new fungus is described here as a new species of Neodactylaria, N. simaoensissp. nov., and placed in a new family Neodactylariaceaefam. nov. and a new order Neodactylarialesord. nov.

Although a distinct karyotype with defined chromosome number and structure characterizes each biological species, it is intrinsically labile. Polyploidy or whole-genome duplication has played a pervasive and ongoing role in the evolution of all eukaryotes, and is the most dramatic force known to cause rapid karyotypic reconfiguration, especially at the initial stage. However, issues concerning transgenerational propagation of karyotypic heterogeneity and its translation to phenotypic diversity in nascent allopolyploidy, at the population level, have yet to be studied in detail. Here, we report a large-scale examination of transgenerationally propagated karyotypic heterogeneity and its phenotypic manifestation in an artificially constructed allotetraploid with a genome composition of AADD, that is, involving two of the three progenitor genomes of polyploid wheat. Specifically, we show that 1) massive organismal karyotypic heterogeneity is precipitated after 12 consecutive generations of selfing from a single euploid founder individual, 2) there exist dramatic differences in aptitudes between subgenomes and among chromosomes for whole-chromosome gain and/or loss and structural variations, 3) majority of the numerical and structural chromosomal variations are concurrent due to mutual contingency and possible functional constraint, 4) purposed and continuous selection and propagation for euploidy over generations did not result in enhanced karyotype stabilization, and 5) extent of karyotypic variation correlates with variability of phenotypic manifestation. Together, our results document that allopolyploidization catalyzes rampant and transgenerationally heritable organismal karyotypic heterogeneity that drives population-level phenotypic diversification, which lends fresh empirical support to the still contentious notion that whole-genome duplication enhances organismal evolvability.

Background The BBAA subgenomes of hexaploid common wheat are structurally intact, which makes it possible to extract the BBAA subgenomes to constitute a novel plant type, namely, extracted tetraploid wheat (ETW). ETW displays multiple abnormal phenotypes such as massively reduced biomass and abnormal spike development, compared to extant tetraploid wheat with a BBAA genome. The genetic, biochemical and physiological basis underlying the phenotypic abnormality of ETW remains unknown. Results To explore the biochemical basis of these phenotypic abnormalities, we analysed the metabolomic and proteomic profiles and quantified 46 physiological traits of ETW in comparison with its common wheat donor (genome BBAADD), and a durum tetraploid wheat cultivar (genome BBAA). Among these three types of wheat, ETW showed a saliently different pattern of nutrient accumulation and seed quality, markedly lower concentrations of many metabolites involved in carbohydrate metabolism, and higher concentrations of many metabolites related to amino acids. Among the metabolites, changes in shikimate and sucrose were the most conspicuous. Higher levels of shikimate and lower levels of sucrose influence many metabolic processes including carbohydrate and amino acid metabolism, which may contribute to the phenotypic abnormalities. Gene expression assay showed downregulation of a shikimate degradation enzyme (5-enolpyruvylshikimate-3-phosphate synthase) coding gene and upregulation of several genes coding for the sucrose hydrolysis enzyme, which could explain the higher levels of shikimate and lower levels of sucrose, respectively. Conclusions Our results suggest that significant and irreversible biochemical changes have occurred in the BBAA subgenomes of common wheat during the course of its co-evolution with the DD subgenome at the hexaploid level. Electronic supplementary material The online version of this article (10.1186/s12870-019-1796-9) contains supplementary material, which is available to authorized users.

The inhibitor of apoptosis protein (IAP) family has been identified in a variety of organisms. All IAPs contain one to three baculoviral IAP repeat (BIR) domains, which are required for anti-apoptotic activity. Here, we identified a type II BIR domain-containing protein, MoBir1, in the rice blast fungus Magnaporthe oryzae. Expression of the MoBIR1 gene in Saccharomyces cerevisiae suppressed hydrogen peroxide-induced cell death and delayed yeast cell chronological aging. Delayed aging was found to require the carboxyl terminus of MoBir1. M. oryzae transformants overexpressing the MoBIR1 gene demonstrated increased growth rate and biomass, delayed mycelial aging, and enhanced resistance to hydrogen peroxide but reduced reactive oxygen species generation and virulence. Moreover, MoBIR1-overexpressing transformants exhibited anti-apoptotic activity. However, MoBIR1 silencing resulted in no obvious phenotypic changes, compared with the wild-type M. oryzae strain Guy11. Our findings broaden the knowledge on fungal type II BIR domain-containing proteins.

Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome-wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome-wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome-wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.

Figure S2. Frequency distribution of fold changes in protein abundance between extracted tetraploid wheat (ETW) and an extant tetraploid wheat line (AL, genome BBAA) and between ETW and a resynthesized allohexaploid wheat (XX329, genome BBAADD) obtained by crossing ETW (maternal parent) and TQ18 (paternal parent). (PDF 298 kb)

Hexokinases are conserved proteins functioning in glucose sensing and signaling. The rice blast fungus Magnaporthe oryzae contains several hexokinases, including MoHxk1 (hexokinase) and MoGlk1 (glucokinase) encoded respectively by MoHXK1 and MoGLK1 genes. The heterologous expression of MoGlk1 and MoHxk1 in Saccharomyces cerevisiae confirmed their conserved functions. Disruption of MoHXK1 resulted in growth reduction in medium containing fructose as the sole carbon source, whereas disruption of MoGLK1 did not cause the similar defect. However, the ΔMoglk1 mutant displayed decreased proton extrusion and a lower biomass in the presence of ammonium, suggesting a decline in the utilization of ammonium. Additionally, the MoGLK1 allele lacking catalytic activity restored growth to the ΔMoglk1 mutant. Moreover, the expression of MoPMA1 encoding a plasma membrane H(+)-ATPase decreased in the ΔMoglk1 mutant that can be suppressed by glucose and G-6-P. Thus, MoGlk1, but not MoHxk1, regulates ammonium utilization through a mechanism that is independent from its catalytic activity.

Magnaporthe oryzae is the causal agent of rice blast disease, leading to enormous losses of rice production. Here, we characterized a basic leucine zipper (bZIP) transcription factor, Moatf1, in M. oryzae, a homolog of Schizosaccharomyces pombe ATF/CREB that regulates the oxidative stress response. Moatf1 deletion caused retarded vegetative growth of mycelia, and the Moatf1 mutant exhibited higher sensitivity to hydrogen peroxide (H2O2) than did the wild-type strain. The mutant showed severely reduced activity of extracellular enzymes and transcription level of laccases and peroxidases and exhibited significantly reduced virulence on rice cultivar CO-39. On rice leaf sheath, most of the infectious hyphae of the mutant became swollen and displayed restricted growth in primary infected cells. Defense response was strongly activated in plants infected by the mutant. Diamino benzidine staining revealed an accumulation of H2O2 around Moatf1 mutant appressoria and rice cells with Moatf1 hyphae that was absent in the wild type. Inhibition of the plant NADPH oxidase by diphenyleneiodonium prevented host-derived H2O2 accumulation and restored infectious hyphal growth of the mutant in rice cells. Thus, we conclude that Moatf1 is necessary for full virulence of M. oryzae by regulating the transcription of laccases and peroxidases to impair reactive oxygen species–mediated plant defense.

The two multiple-antibiotic resistance (Mar) phenotypes (n = 8, respectively) and susceptible isolates (n = 4) of Shigella flexneri from China were characterized involving the efflux pump AcrAB-TolC. The accumulation of ciprofloxacin, acrAB-tolC PCR, and levels of mRNA with northern blots were performed in three groups. Sequencing of acrAB-tolC was performed in selected isolates. An efflux inhibition was performed with Phe-Arg-beta-naphthylamide. The accumulation of ciprofloxacin at steady state in susceptible isolates was significantly higher than that in the two Mar groups (p0.05). The level of accumulation in the Mar strains was increased upon the addition of the protonophore carbonyl cyanidem-chlorophenylhydrazone. The expression level of acrA mRNA in the Mar isolates was significantly higher than that in the susceptible isolates (p0.05). Mar strain H26 had a single-nucleotide substitution in locus 322(G--T) of acrA, and Mar 0008 in locus 171(C--A). The susceptible strain N15 had a base deletion in locus 36 (C) of tolC gene. The role of the inhibitors of efflux pumps was significant in some isolates with the high expression of Mar pump genes. In conclusion, overexpression of acrA gene leads to Mar in clinical isolates of S. flexneri, and ciprofloxacin acquired susceptible to S. flexneri with Phe-Arg-beta-naphthylamide.

OBJECTIVE: Extremely low-frequency magnetic field (ELF-MF) has been reported to be of potential pathogenetic relevance to Alzheimer's disease (AD) for years. However, evidence confirming this function remains inconclusive. Chronic Al treatment has been identified as a contributing factor to cognitive function impairment in AD. This study aims to examine whether or not ELF-MF and Al have synergistic effects toward AD pathogenesis by investigating the effects of ELF-MF with or without chronic Al treatment on SD rats. METHODS: Sprague-Dawley (SD) rats were subjected one of the following treatments: sham (control group), oral Al (Al group), ELF-MF (100 µT at 50 Hz) with oral Al (MF+Al group), or ELF-MF (100 µT at 50 Hz) without oral Al (MF group). RESULTS: After 12 wk of treatment, oral Al treatment groups (Al and MF+Al groups) showed learning and memory impairment as well as morphological hallmarks, including neuronal cell loss and high density of amyloid-β (Aβ) in the hippocampus and cerebral cortex. ELF-MF without Al treatment showed no significant effect on AD pathogenesis. ELF-MF+Al treatment induced no more damage than Al treatment did. CONCLUSIONS: Our results showed no evidence of any association between ELF-MF exposure (100 µT at 50 Hz) and AD, and ELF-MF exposure does not influence the pathogenesis of AD induced by Al overload.