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Although there is accumulating evidence for the role of foreign genes in plant development and adaptation, many issues remain. A recent study by Wang et al. on a gene of fungal origin in wheatgrass disease resistance highlights the potential application of fungal genes in crop improvement and related areas., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Seed germination is a vital developmental process that is tightly controlled by environmental signals, ensuring germination under favorable conditions. High temperature (HT) suppresses seed germination. This process, known as thermoinhibition, is achieved by activating abscisic acid and inhibiting gibberellic acid biosynthesis. The zinc-finger protein SOMNUS (SOM) participates in thermoinhibition of seed germination by altering gibberellic acid/abscisic acid metabolism, but the underlying regulatory mechanism is poorly understood. In this study, we report that SOM binds to its own promoter and activates its own expression in Arabidopsis ( Arabidopsis thaliana ) and identify the MADS-box transcription factor AGAMOUS-LIKE67 (AGL67) as a critical player in SOM function, based on its ability to recognize CArG-boxes within the SOM promoter and mediate the trans-activation of SOM under HTs. In addition, AGL67 recruits the histone mark reader EARLY BOLTING IN SHORT DAY (EBS), which recognizes H3K4me3 at SOM chromatin. In response to HTs, AGL67 and EBS are highly enriched around the SOM promoter. The AGL67-EBS complex is also necessary for histone H4K5 acetylation, which activates SOM expression, ultimately inhibiting seed germination. Taken together, our results reveal an essential mechanism in which AGL67 cooperates with the histone mark reader EBS, which bridges the process of H3K4me3 recognition with H4K5 acetylation, thereby epigenetically activating SOM expression to suppress seed germination under HT stress., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Ligustilide (LIG), a main lipophilic component isolated from Cnidii Rhizoma (Cnidium officinale, rhizome) and Angelicae Gigantis Radix (Angelica gigas Nakai, root), has been shown to alleviate cerebral ischemia injury and paly a neuroprotective role. We investigated mechanisms underlying the antiapoptotic effects of LIG in vitro and in vivo , respectively, using cultured primary hippocampal neurons under oxygen-glucose deprivation/reperfusion (OGD/R) and rats under cerebral ischemia reperfusion(I/R) conditions. In vitro studies revealed that the suppressed apoptosis in hippocampal neurons upon LIG treatment was associated with reduced calcium influx and generation of reactive oxygen species. The LIG-treated hippocampal neurons exhibited decreased the ratio of Bax/Bcl-2, and the release of CytC from mitochondria as well as the expression of cleaved caspase-3, which were accompanied with enhanced the phosphorylation of Akt protein, in a PI3K-dependent manner. In vivo studies demonstrated a neuroprotective role of LIG in attenuating cerebral infarction volume, neurological injury and hippocampal neuron injury, suggesting that LIG could reverse ischemia reperfusion(I/R)-induced apoptosis of hippocampal neurons. These results together suggest that LIG may be considered as a neuroprotectant in the treatment of ischemia stroke., (Copyright © 2020 Wu, Mao, Liu, Huang and Wang.)

Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

The emergence of antibiotic-resistant Salmonella through mutations led to mismatch repair (MMR) deficiency that represents a potential hazard to public health. Here, four representative MMR-deficient Salmonella hypermutator strains and Salmonella Typhimurium LT2 were used to comprehensively reveal the influence of MMR deficiency on antibiotic resistance among Salmonella . Our results indicated that the mutation frequency ranged from 3.39 × 10 -4 to 5.46 × 10 -2 in the hypermutator. Mutation sites in MutS, MutL, MutT, and UvrD of the four hypermutators were all located in the essential and core functional regions. Mutation frequency of the hypermutator was most highly correlated with the extent of mutation in MutS. Mutations in MMR genes ( mut S, mut T, mut L, and uvr D) were correlated with increased mutation in antibiotic resistance genes, and the extent of antibiotic resistance was significantly correlated with the number of mutation sites in MutL and in ParC. The number of mutation sites in MMR genes and antibiotic resistance genes exhibited a significant positive correlation with the number of antibiotics resisted and with expression levels of mut S, mut T, and mut L. Compared to Salmonella Typhimurium LT2, a total of 137 differentially expressed and 110 specifically expressed proteins were identified in the four hypermutators. Functional enrichment analysis indicated that the proteins significantly overexpressed in the hypermutators primarily associated with translation and stress response. Interaction network analysis revealed that the ribosome pathway might be a critical factor for high mutation frequency and multidrug resistance in MMR-deficient Salmonella hypermutators. These results help elucidate the mutational dynamics that lead to hypermutation, antibiotic resistance, and activation of stress response pathways in Salmonella ., (Copyright © 2020 Sheng, Huang, Han, Liu, Lü, Zhang, Zhang, Yang, Cui and Yang.)

Plant colonization of land has been intimately associated with mycorrhizae or mycorrhizae-like fungi. Despite the pivotal role of fungi in plant adaptation, it remains unclear whether and how gene acquisition following fungal interaction might have affected the development of land plants. Here we report a macro2 domain gene in bryophytes that is likely derived from Mucoromycota, a group that includes some mycorrhizae-like fungi found in the earliest land plants. Experimental and transcriptomic evidence suggests that this macro2 domain gene in the moss Physcomitrella patens, PpMACRO2, is important in epigenetic modification, stem cell function, cell reprogramming and other processes. Gene knockout and over-expression of PpMACRO2 significantly change the number and size of gametophores. These findings provide insights into the role of fungal association and the ancestral gene repertoire in the early evolution of land plants.

Cytokinin oxidase/dehydrogenase (CKX) is a key enzyme responsible for the degradation of endogenous cytokinins. However, the origins and roles of CKX genes in angiosperm evolution remain unclear. Based on comprehensive bioinformatic and transgenic plant analyses, we demonstrate that the CKX s of land plants most likely originated from an ancient chlamydial endosymbiont during primary endosymbiosis. We refer to the CKX s retaining evolutionarily ancient characteristics as "ancient CKX s" and those that have expanded and functionally diverged in angiosperms as "non-ancient CKX s". We show that the expression of some non-ancient CKX s is rapidly inducible within 15 min upon the dehydration of Arabidopsis , while the ancient CKX ( AtCKX7 ) is not drought responsive. Tobacco plants overexpressing a non-ancient CKX display improved oxidative and drought tolerance and root growth. Previous mutant studies have shown that non-ancient CKX s regulate organ development, particularly that of flowers. Furthermore, ancient CKXs preferentially degrade cis -zeatin ( c Z)-type cytokinins, while non-ancient CKXs preferentially target N 6 -(Δ 2 -isopentenyl) adenines (iPs) and trans -zeatins ( t Zs). Based on the results of this work, an accompanying study (Wang et al. 10.1038/s41438-019-0211-x) and previous studies, we hypothesize that non-ancient CKXs and their preferred substrates of iP/ t Z-type cytokinins regulate angiosperm organ development and environmental stress responses, while ancient CKXs and their preferred substrates of c Zs play a housekeeping role, which echoes the conclusions and hypothesis described in the accompanying report (Wang, X. et al. Evolution and roles of cytokinin genes in angiosperms 1: Doancient IPTs play housekeeping while non-ancient IPTs play regulatory roles? Hortic Res 7 , (2020). 10.1038/s41438-019-0211-x)., Competing Interests: Conflict of interestThe authors declare that they have no conflict of interest., (© The Author(s) 2020.)

Pickled ready-to-eat meat (PRTEM) is a meat product that is treated with various seasonings and then cooked. PRTEM is a popular food consumed mostly in China and some Asian countries. Since this food is considered 'ready to eat', once it is contaminated by foodborne pathogens such as Salmonella , the prospect for significant morbidity, mortality, and immeasurable economic losses can occur. Here we investigated the prevalence and concentration of Salmonella in 107 PRTEM samples collected from Shaanxi, China during 2015-2016. Furthermore, we analyzed the serotype, antibiotic susceptibility, and presence of antibiotic resistance genes and amino acid mutations in 219 Salmonella isolates, followed by subtyping of 115 representative isolates. The average detection rate of Salmonella -positive PRTEM was 58.9%, and the average most probable number (MPN) of Salmonella in positive samples was 2.27 logMPN per gram of sample (range: 2.10-2.43). Ten serotypes were identified from the 219 Salmonella isolates, with S. Thompson (37.9%) and S . Indiana (20.5%) being predominant. The remaining serotypes were S . Typhi (7.8%), S . Typhimurium (7.3%), S . Mbandaka (6.9%), S . Albany (6.4%), S . Blockley (5.5%), S . Infantis (4.1%), S . Escanaba (3.2%), and S . Dusseldorf (0.5%). All isolates were resistant to ceftiofur (100%), while most of them were resistant to ciprofloxacin (99.1%), amoxicillin-clavulanic acid (97.7%), trimethoprim-sulfamethoxazole (96.4%), ampicillin (92.3%), sulfisoxazole (92.2%), tetracyclines (90.4%), and nalidixic acid (90.4%), respectively. A single mutation of Ser83Phe (27.1%) and double mutations of Ser83Phe-Asp87Gly (25.9%) in GyrA were detected in 85 isolates, whereas mutations of Thr57Ser (63.9%) and Ser80Arg (36.1%) in ParC were detected in 122 isolates. qnr B, oqx AB, aac(6')-Ib , and qnr A were present in 50 (22.8%), 48 (21.9%), 26 (11.9%), and 1 (0.5%) isolate(s), respectively. Pulse field gel electrophoresis results revealed that those isolates recovered from the same type of PRTEM or the same sampling place shared identical or similar DNA profiles, antibiotic resistance phenotypes, and even plasmid-mediated quinolone resistance encoding genes. The findings indicate that Salmonella is commonly prevalent in PRTEMs at high concentrations in Shaanxi, China. More attention should be paid to the processing and storage of this ready-to-eat food to prevent bacterial contamination and foodborne outbreaks., (Copyright © 2019 Wang, Sheng, Xu, Huang, Meng, Cao, Zeng, Meng and Yang.)

Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies., (© The Author(s) 2019. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)

Crucihimalaya himalaica , a close relative of Arabidopsis and Capsella , grows on the Qinghai-Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata , from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica 's adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica , might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

ABI5-BINDING PROTEIN2 (AFP2) negatively regulates the abscisic acid signal by accelerating ABI5 degradation during seed germination in Arabidopsis ( Arabidopsis thaliana ). The abscisic acid signal is reported to delay flowering by up-regulating Flowering Locus C expression, but the role of AFP2 in regulating flowering time is unknown. Here, we found that flowering time was markedly delayed and CONSTANS ( CO ) expression was reduced in a transgenic Arabidopsis line overexpressing AFP2 under LD conditions. Conversely, the loss-of-function afp2 mutant showed slightly earlier flowering, with higher CO expression. These data suggest that AFP2 negatively regulates photoperiod-dependent flowering time by modulating the CO signal. We then found that AFP2 exhibited circadian expression rhythms that peaked during the night. Furthermore, the C-terminus of AFP2 interacted with CO, while its N-terminal ethylene response factor-associated amphiphilic repression motif interacted with the transcriptional corepressor TOPLESS-related protein2 (TPR2). Thus, AFP2 bridges CO and TPR2 to form the CO-AFP2-TPR2 complex. Biochemical and genetic analyses showed that AFP2 mediated CO degradation during the night. AFP2 also recruited histone deacetylase activity at Flowering Locus T chromatin through its interaction with TPR2. Taken together, our results reveal an elaborate mechanism by which AFP2 modulates flowering time through coordinating the activity and stability of CO., (© 2019 American Society of Plant Biologists. All Rights Reserved.)

In the establishment and continuation of a successful pregnancy, the proliferation, migration, and invasion of trophoblast cells play essential roles. Impaired trophoblast function has been reported to be involved in recurrent spontaneous abortion (RSA) but the potential mechanisms are still unknown. CD44 variant domain 6 (CD44v6) is a transmembrane glycoprotein that has been known for decades to be expressed in the placenta. In this study, we investigated the effect of CD44v6 on proliferation and migration of trophoblast cells. Our results show that CD44v6 expression in the villi is lower in RSA patients than in women with normal pregnancies. Furthermore, downregulation of CD44v6 leads to a reduction in proliferation and migration in the human trophoblast cell line HTR-8/SVneo, along with decreased expression and nuclear translocation of NF-κB. These results suggest that decreased expression of CD44v6 may cause miscarriage by downregulating trophoblast cell proliferation via the NF-κB pathway., Competing Interests: None., (IJCEP Copyright © 2018.)

Within the interleukin-17 (IL-17) family of cytokines, IL-17A is known to be critical in the host defense against fungal infections; however, the function of the other IL-17 family members in anti-fungal immunity remains largely unknown. Here, we show that IL-17C expression was highly induced in kidney epithelial cells after fungal infection. Mice that lacked IL-17C exhibited increased survival and attenuated kidney tissue damage, although they had similar fungal loads. IL-17C deficiency resulted in decreased pro-inflammatory cytokine expression compared with wild-type control mice. Additionally, IL-17C directly acted on renal epithelial cells in vitro to promote pro-inflammatory cytokine production. Taken together, our data demonstrate that IL-17C is a critical factor that potentiates inflammatory responses and causes host injury during fungal infection.

Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the 'true' evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

Although horizontal gene transfer (HGT) is often considered as a disruptive force in reconstructing organismal phylogeny, it can also be a valuable phylogenetic tool. A gene in the net of life is often horizontally transferred to the ancestor of a major lineage. If the gene is retained in the recipient and its descendants, it will constitute a shared derived character and mark the recipient and all descendants as a monophyletic group. Additionally, phylogenetically informative HGTs also provide information about the sequence of emergence of involved taxa, because the donor organism must have emerged at least as early as the recipient. Here we review the recent applications of ancient HGT events in reconstructing organismal phylogeny as well as the promise and potential pitfalls of this approach.

The purpose of current study was to investigate the potential repeated dosed toxicity of ZnPcP(2)S(2)-based photodynamic therapy (ZnPc-PDT) in Beagle dogs. Twenty-four Beagle dogs were randomly allocated to four groups, in which they were administered ZnPcS(2)P(2) preparation intravenously at dosages of 0, 0.5, 1.5, and 4.5mg/kg body weight and then were irradiated with 670nm laser for 6min at subsequent 48 and 72h, once every four days for successively 10 times. There were no abnormal changes in clinical observations. After the administration most animals showed dysphoria and several had light edema on their faces. The results showed no mortality and no abnormity in ophthalmoscopy, electrocardiography, hematology, blood biochemistry and urinalysis, except that some statistical changes in specific indexes such as APTT in 1.5 and 4.5mg/kg groups, and these changes disappeared at the end of recovery. Histopathological examination showed hepatic spotty and lytic necrosis in Beagle dogs of 4.5mg/kg group, and at the end of recovery the damages alleviated. Additionally, some Kelly and Khaki granules presented in liver, spleen, lungs, kidneys, ovaries, lymph nodes, marrows and injection points. These drug pigmentations will provide valuable information about distribution of ZnPcP(2)S(2). Based on the results; the NOAEL was considered to be 1.5mg/kg and ZnPc-PDT appears to be a safety and promising approach in clinic.

Phosphonate utilization by microbes provides a potential source of phosphorus for their growth. Homologous genes for both C-P lyase and phosphonatase degradative pathways are distributed in distantly related bacterial species. The phn gene clusters for the C-P lyase pathway show great structural and compositional variation among organisms, but all contain phnG-phnM genes that are essential for C-P bond cleavage. In the gamma-proteobacterium Erwinia carotovora, genes common to phosphonate biosyntheses were found in neighboring positions of those for the C-P lyase degradative pathway and in the same transcriptional direction. A gene encoding a hypothetical protein DUF1045 was found predominantly associated with the phn gene cluster and was predicted functionally related to C-P bond cleavage. Genes for phosphonate degradation are frequently located in close proximity of genes encoding transposases or other mobile elements. Phylogenetic analyses suggest that both degradative pathways have been subject to extensive lateral gene transfers during their evolution. The implications of plasmids and transposition in the evolution of phosphonate degradation are also discussed.

Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity. Parallel Monte Carlo methods for a maximum likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a simulated Monte Carlo algorithm. A two-tier parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the simulated Monte Carlo algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a network of shared-memory symmetric multiprocessors (SMPs) are presented.