Multiple virulence factors regulated by AlgU contribute to the pathogenicity of Pseudomonas savastanoi pv. glycinea in soybean
Pseudomonas savastanoi pv. glycinea (Psg) causes bacterial blight of soybean. To identify candidate virulence factors, transposon-mediated mutational analysis of Psg was carried out. We syringe-inoculated soybean leaves with Psg transposon mutants and identified 28 mutants which showed reduced virulence from 1,000 mutants screened. Next, we spray-inoculated soybean leaves with these mutants and demonstrated that the algU mutant showed significantly reduced virulence together with reduced bacterial populations in planta. Expression profiles comparison between the Psg wild-type (WT) and algU mutant in HSC broth revealed that expression of coronatine (COR)-related genes (including cmaA and corR) were down-regulated in the algU mutant compared with Psg WT. Moreover, we also showed that COR production were reduced in the algU mutant compared with WT. We also demonstrated that algD, which is related to alginate biosynthesis, showed reduced expression and biofilm formation was significantly suppressed in the algU mutant. Furthermore, hrpL also showed less expression in the algU mutant. These results indicate that AlgU plays a critical role in promoting Psg pathogenesis by regulating multiple virulence factors.
Nguyen et al. (2021) Multiple virulence factors regulated by AlgU contribute to the pathogenicity of Pseudomonas savastanoi pv. glycinea in soybean. PeerJ 9:e12405 https://doi.org/10.7717/peerj.12405
Distribution and fractionation of rare earth elements in suspended particulate matter in a coastal river, Southeast China
Background In the river system, the geochemistry of rare earth elements (REEs, a series of elements from La to Lu) in suspended particulate matter (SPM) is generally controlled by rock weathering processes and hydrochemical characteristics, as well as being affected by anthropogenic activities. However, the variations of geochemical characteristics and behaviors of REEs in SPM with a salinity gradient from the inland river to the estuary have been short of a systematic understanding. Methods The REE concentrations, Post Archean Australia Shale (PAAS)-normalized REE, La/Yb, La/Sm, and Sm/Yb ratios of SPM were investigated in the Jiulongjiang River, which is a coastal river mainly flowing through granite rocks in Southeast China. The correlation relationships between physicochemical parameters (including water pH, total dissolved solids (TDS), HCO3– concentrations, and the concentrations of major elements of SPM) and PAAS-normalized REE ratios of SPM were analyzed to determine the factors that affect the REE concentration and fractionation of SPM in the different regions of Jiulongjiang River, including the main stream and tributary of Beixi River, Xixi River, Nanxi River, and estuary. Additionally, the Ce, Eu, and Gd anomalies of SPM were estimated. Results The average ∑REE concentration of SPM (352 mg/kg) in the granite rock basin was twice higher than the mean value (175 mg/kg) of the world’s rivers. The PAAS-normalized REE ratios of SPM in the main rivers including Beixi River (main stream), Xixi River, and Nanxi River were near due to the same lithologic distribution. In the tributary of Beixi River, the input of low-weathered carbonate minerals which contain very few REE caused the lower REE concentrations of SPM. The PAAS-normalized REE ratios of SPM in the estuary were significantly lower than those in the main rivers, which was mainly attributed to the significant REE removal with the increment of salinity. The enrichment of LREE relative to HREE in SPM increased with decreasing water pH in the main rivers. In the estuary, the preferential removal of dissolved LREE occurred compared to HREE with the increment of salinity. The negative Ce and Eu anomalies of SPM occurred in both the main rivers and estuary region and rare Gd pollution was present in the basin. Additionally, human activities caused the increment of REE concentrations and more negative Ce anomaly at some specific sites, such as dam effect and agricultural pollution. Conclusions The REE concentrations and fractionations of SPM in river water mainly depend on lithologic distribution and riverine pH, while they are affected by salinity in the estuary.
Environmental Contamination and Remediation
Liu et al. (2021) Distribution and fractionation of rare earth elements in suspended particulate matter in a coastal river, Southeast China. PeerJ 9:e12414 https://doi.org/10.7717/peerj.12414
Fusarium head blight in the Russian Far East: 140 years after description of the ‘drunken bread’ problem
The first appearance of Fusarium head blight (FHB)—and the beginning of scientific research of this disease—occurred the Far East region of Russia at the end of the 19th century. In the summer of 2019, in the Amur region, which comprises 60–70% of grain production in the Russian Far East, flooding caused a state of emergency. The quality of wheat and barley grains grown under natural conditions of FHB outbreaks, including grain infection, fungal species composition, DNA content of F. graminearum and chemotypes, and the presence of various mycotoxins, was studied. Fusarium infection rates reached extremely high percentages, 51–98%, the majority of which were F. graminearum infections. The amount of F. graminearum DNA in wheat grain samples was higher than in the barley grain samples and averaged 6.1 and 2.1 pg/ng, respectively. The content of deoxynivalenol (DON) in the wheat samples reached 13,343 ppb and in barley reached 7,755 ppb. A multilocus genotyping assay was conducted on the partially sequenced fragments of the translation elongation factor EF-1a, ammonium ligase gene, reductase gene, and 3-O-acetyltransferase gene in 29 Fusarium graminearum sensu lato strains from the grain harvested in the Amur region. All strains from the Far East region were characterized as F. graminearum sensu stricto; 70% were the 15-AcDON chemotype, while the other strains were the 3-AcDON chemotype. According to the results, after 140 years of study of FHB, we are still not very successful in controlling this disease if conditions are favorable for pathogen development. Even at present, some of the grain harvested must be destroyed, as high contamination of mycotoxins renders it unusable.
Gagkaeva et al. (2021) Fusarium head blight in the Russian Far East: 140 years after description of the ‘drunken bread’ problem. PeerJ 9:e12346 https://doi.org/10.7717/peerj.12346
The morphology and internal structure of dogwood (Cornus L.) endocarps in the taxonomy and phylogeny of the genus
The genus Cornus is known for its complicated taxonomy and extreme polymorphism. Currently, dogwoods are classified into four morphological groups reflected in four phylogenetic clades: blue- or white-fruited dogwoods (BW), cornelian cherries (CC), big-bracted dogwoods (BB), and dwarf dogwoods (DW). The present study is a continuation of a series of papers that started with the examination of the endocarp morphological diversity among BW species. The endocarps of 22 Cornus species were studied according to their morphology, internal structure, and sculpture; the aim was to evaluate the taxonomic importance of the examined characters and check whether endocarp differentiation supports the published phylogenies, according to which the relationships within the genus are indicated as (BW(CC(DW-BB))). Among the quantitative characters, the endocarp’s length, thickness, and width, its length/width ratio, and the number of vascular bundles on its surface were considered taxonomically important. Regarding the qualitative characters, the taxonomic significance of the stone shape, the endocarp apex and base outline, the position of vascular bundles on the endocarp surface, and the presence of the apical cavity and distinct furrow on the endocarp side walls was proved. Additionally, the uniform qualitative characters having a 100% share of a given character state were identified. Cornelian cherries and dwarf dogwoods were characterised by the presence of four uniform characters. In the big-bracted group, two uniform characters were found. Blue- or white-fruited species were the most heterogeneous, with no uniform characters. Regarding the endocarp’s internal structure, the presence of secretory cavities in the endocarp wall and in the septa, the presence of crystals in the outer endocarp, the number of cell layers in the transition sclereid zone, and the primary and secondary sculptures were found to be taxonomically significant. Additionally, the comparative analyses of dogwood endocarps found the following parameters to be useful: the germination valve thickness, the ratio of endocarp wall thickness to endocarp diameter, and the septum’s width and structure. Due to the great differentiation of the examined characters, it was difficult to verify the research hypothesis unambiguously. The calculated similarity coefficients of the endocarps’ qualitative and quantitative characters revealed the highest morphological similarity of endocarps between DW and BB groups, supporting the phylogenetic relationships based on molecular evidence. The number of vascular bundles on the endocarp surface was the character that supported this similarity the most. The similarity coefficients calculated separately for qualitative characters showed the closest similarity between groups CC-DW. However, these results do not directly reflect any of the published phylogenies.
Morozowska et al. (2021) The morphology and internal structure of dogwood (Cornus L.) endocarps in the taxonomy and phylogeny of the genus. PeerJ 9:e12170 https://doi.org/10.7717/peerj.12170
Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers
Background The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored. Methods We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan. Results A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. ‘Akikiki had a more diverse microbiome compared to ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki. Conclusion ʻAkikiki and ʻakekeʻe are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.
Costantini et al. (2021) Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers. PeerJ 9:e12291 https://doi.org/10.7717/peerj.12291
Obesity phenotypes and their relationships with atrial fibrillation
Background This study assessed the associations of metabolic obesity phenotypes with the risk of atrial fibrillation (Afib). Methods This prospective cohort study categorized Taiwanese adults according to their body mass index (BMI) and metabolic health status at baseline. We assigned the participants to the underweight (BMI < 18.5 kg/m2), normal weight (BMI = 18.5–23.9 kg/m2), and overweight/obesity groups (BMI ≥ 24 kg/m2). Metabolically healthy was defined as absence of hypertension, diabetes, and hyperlipidemia and the presence of healthy metabolic profiles. Results In total, 5,742 adults were included. During a median follow-up of 13.7 years, 148 patients developed Afib. Compared to the metabolically healthy normal weight group, the risk of Afib was significantly higher than those in the metabolically unhealthy overweight/obesity (hazard ratio = 2.20, 95% confidence interval [1.12–4.33]) and metabolically unhealthy normal weight groups (HR = 2.64, 95% CI [1.34–5.17]). Additionally, the point estimate suggested a 1.97-fold greater risk among the metabolically healthy overweight/obesity group, although this difference was not significant given the wide confidence interval (HR = 1.97, 95% CI [0.80–4.86]). Conclusion Our results demonstrated the relationships of metabolic health and weight regarding the risk of Afib in Taiwanese adults. The Afib risk among metabolic and obesity phenotypes is associated with a metabolically unhealthy status. A trend toward a higher Afib risk with obesity among metabolically healthy subjects was observed. However, the result was not robust and it still suggested further study.
Tsai et al. (2021) Obesity phenotypes and their relationships with atrial fibrillation. PeerJ 9:e12342 https://doi.org/10.7717/peerj.12342
The inconsistent microbiota of Budu, the Malaysian fermented anchovy sauce, revealed through 16S amplicon sequencing
Budu is a Malaysian fermented anchovy sauce produced by immersing small fishes into a brine solution for 6 to 18 months. Microbial enzymes are known to contribute to fermentation; however, not much is known about the microbial community in Budu. Therefore, a better understanding of the Budu microbiome is necessary to improve the quality, consistency, and safety of the Budu products. In this study, we collected 60 samples from 20 bottles of Budu produced by seven manufacturers. We analyzed their microbiota using V3–V4 16S rRNA amplicon sequencing when we first opened the bottle (month 0), as well as 3 and 7 months post-opening (months 3 and 7). Tetragenococcus was the dominant genus in many samples, reaching a maximum proportion of 98.62%, but was found in low abundance, or absent, in other samples. When Budu samples were not dominated by a dominant taxa, we observed a wider genera diversity such as Staphylococcus, Acinetobacter, Halanaerobium and Bacillus. While the taxonomic composition was relatively stable across sampling periods, samples from two brands showed a sudden increase in relative abundance of the genus Chromobacterium at month 7. Based on prediction of metagenome functions, non-Tetragenococcus-dominated samples were predicted to have enriched functional pathways related to amino acid metabolism and purine metabolism compared to Tetragenococcus-dominated samples; these two pathways are fundamental to fermentation quality and health attributes of fish sauce. Among the non-Tetragenococcus-dominated samples, contributions towards amino acid metabolism and purine metabolism were biased towards the dominant taxa when species evenness is low, while in samples with higher species evenness, the contributions towards the two pathways were predicted to be evenly distributed between taxa. Our results demonstrated that the utility of 16S sequencing to assess batch variation in fermented food production. The distinct microbiota was shown to correlate with characteristic metagenome function including functions potentially related to fermented food nutrition and quality.
Md Zoqratt et al. (2021) The inconsistent microbiota of Budu, the Malaysian fermented anchovy sauce, revealed through 16S amplicon sequencing. PeerJ 9:e12345 https://doi.org/10.7717/peerj.12345
In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit
The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.
Feng et al. (2021) In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit. PeerJ 9:e12348 https://doi.org/10.7717/peerj.12348
A novel role for apatinib in enhancing radiosensitivity in non-small cell lung cancer cells by suppressing the AKT and ERK pathways
Background Radioresistance is still the major cause of radiotherapy failure and poor prognosis in patients with non-small cell lung cancer (NSCLC). Apatinib (AP) is a highly selective inhibitor of vascular endothelial growth factor receptor 2 (VEGFR2). Whether and how AP affects radiosensitivity in NSCLC remains unknown. The present study aimed to explore the radiosensitization effect of AP in NSCLC and its underlying mechanism as a radiosensitizer. Methods The NSCLC cell lines A549 and LK2 were treated with AP, ionizing radiation (IR), or both AP and IR. Expression of VEGFR2 was analyzed by western blot and RT-PCR. Cell proliferation was measured using CCK-8 and colony formation assays. Apoptosis and cell cycle distribution in NSCLC cells were analyzed by flow cytometry. Nuclear phosphorylated histone H2AX foci immunofluorescence staining was performed to evaluate the efficacy of the combination treatment. Western blot was used to explore the potential mechanisms of action. Results AP inhibited cell proliferation in a dose- and time-dependent manner. Flow cytometry analysis indicated that AP significantly increased radiation-induced apoptosis. Colony formation assays revealed that AP enhanced the radiosensitivity of NSCLC cells. AP strongly restored radiosensitivity by increasing IR-induced G2/M phase arrest. AP effectively inhibited repair of radiation-induced DNA double-strand breaks. Western blot analysis showed that AP enhanced radiosensitivity by downregulating AKT and extracellular signal-regulated kinase (ERK) signaling. Conclusion Our findings suggest that AP may enhance radiosensitivity in NSCLC cells by blocking AKT and ERK signaling. Therefore, AP may be a potential clinical radiotherapy synergist and a novel small-molecule radiosensitizer in NSCLC. Our study fills a gap in the field of anti-angiogenic drugs and radiosensitivity.
Li et al. (2021) A novel role for apatinib in enhancing radiosensitivity in non-small cell lung cancer cells by suppressing the AKT and ERK pathways. PeerJ 9:e12356 https://doi.org/10.7717/peerj.12356
fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences
Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias (i.e., those termed ‘low-complexity’), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized ‘dark matter’ of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A ‘thorough’ option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper.
Harrison (2021) fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences. PeerJ 9:e12363 https://doi.org/10.7717/peerj.12363