Publications by authors named "Jianping Xu"

363 Publications

Global patterns in culturable soil yeast diversity.

iScience 2021 Oct 9;24(10):103098. Epub 2021 Sep 9.

Department of Biology, McMaster University, Hamilton, ON, Canada.

Yeasts, broadly defined as unicellular fungi, fulfill essential roles in soil ecosystems as decomposers and nutrition sources for fellow soil-dwellers. Broad-scale investigations of soil yeasts pose a methodological challenge as metagenomics are of limited use for identifying this group of fungi. Here we characterize global soil yeast diversity using fungal DNA barcoding on 1473 yeasts cultured from 3826 soil samples obtained from nine countries in six continents. We identify mean annual precipitation and international air travel as two significant correlates with soil yeast community structure and composition worldwide. Evidence for anthropogenic influences on soil yeast communities, directly via travel and indirectly via altered rainfall patterns resulting from climate change, is concerning as we found common infectious yeasts frequently distributed in soil in several countries. Our discovery of 41 putative novel species highlights the continued need for culture-based studies to advance our knowledge of environmental yeast diversity.
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http://dx.doi.org/10.1016/j.isci.2021.103098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479693PMC
October 2021

Dynamic evolution of eukaryotic mitochondrial and nuclear genomes: a case study in the gourmet pine mushroom Tricholoma matsutake.

Environ Microbiol 2021 Sep 29. Epub 2021 Sep 29.

School of Life Science, Shanxi University, Taiyuan, 030006, China.

Fungi, as eukaryotic organisms, contain two genomes, the mitochondrial genome and the nuclear genome, in their cells. How the two genomes evolve and correlate to each other is debated. Herein, taking the gourmet pine mushroom Tricholoma matsutake as an example, we performed comparative mitogenomic analysis using samples collected from diverse locations and compared the evolution of the two genomes. The T. matsutake mitogenome encodes 49 genes and is rich of repetitive and non-coding DNAs. Six genes were invaded by up to 11 group I introns, with one cox1 intron cox1P372 showing presence/absence dynamics among different samples. Bioinformatic analyses suggested limited or no evidence of mitochondrial heteroplasmy. Interestingly, hundreds of mitochondrial DNA fragments were found in the nuclear genome, with several larger than 500 nt confirmed by PCR assays and read count comparisons, indicating clear evidence of transfer of mitochondrial DNA into the nuclear genome. Nuclear DNA of T. matsutake showed a higher mutation rate than mitochondrial DNA. Furthermore, we found evidence of incongruence between phylogenetic trees derived from mitogenome and nuclear DNA sequences. Together, our results reveal the dynamic genome evolution of the gourmet pine mushroom.
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http://dx.doi.org/10.1111/1462-2920.15792DOI Listing
September 2021

Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus in China.

Microorganisms 2021 Sep 9;9(9). Epub 2021 Sep 9.

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China.

Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol agent NTF are geographically and ecologically structured. A previous study reported evidence for ecological adaptation in the model NTF species . However, their large-scale geographic structure, patterns of gene flow, their potential phenotypic diversification, and host specialization remain largely unknown. In this study, we developed a new panel of 20 polymorphic short tandem repeat (STR) markers and analyzed 239 isolates of from 19 geographic populations in China. In addition, DNA sequences at six nuclear gene loci and strain mating types (MAT) were obtained for these strains. Our analyses suggest historical divergence within the population in China. The genetically differentiated populations also showed phenotypic differences that may be related to their ecological adaptations. Interestingly, our analyses identified evidence for recent dispersion and hybridization among the historically subdivided geographic populations in nature. Together, our results indicate a changing population structure of in China and that care must be taken in selecting the appropriate strains as biocontrol agents that can effectively reproduce in agriculture soil while maintaining their nematode-trapping ability.
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http://dx.doi.org/10.3390/microorganisms9091919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8465350PMC
September 2021

Abundant Genetic Diversity and Extensive Differentiation among Geographic Populations of the Citrus Pathogen in Southern China.

J Fungi (Basel) 2021 Sep 13;7(9). Epub 2021 Sep 13.

Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.

The fungal pathogen is a major cause of diseases in citrus. One common disease is melanose, responsible for large economic losses to the citrus fruit industry. However, very little is known about the epidemiology and genetic structure of . In this study, we analyzed 339 isolates from leaves and fruits with melanose symptoms from five provinces in southern China at 14 polymorphic simple sequence repeat (SSR) loci and the mating type idiomorphs. The genetic variations were analyzed at three levels with separate samples: among provinces, among orchards within one county, and among trees within one orchard. The five provincial populations from Fujian, Zhejiang, Jiangxi, Hunan, and Guizhou were significantly differentiated, while limited differences were found among orchards from the same county or among trees from the same orchard. STRUCTURE analysis detected two genetic clusters in the total sample, with different provincial subpopulations showing different frequencies of isolates in these two clusters. Mantel analysis showed significant positive correlation between genetic and geographic distances, consistent with geographic separation as a significant barrier to gene flow in in China. High levels of genetic diversity were found within individual subpopulations at all three spatial scales of analyses. Interestingly, most subpopulations at all three spatial scales had the two mating types in similar frequencies and with alleles at the 14 SSR loci not significantly different from linkage equilibrium. Indeed, strains with different mating types and different multilocus genotypes were frequently isolated from the same leaves and fruits. The results indicate that sexual reproduction plays an important role in natural populations of in southern China and that its ascospores likely represent an important contributor to citrus disease.
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http://dx.doi.org/10.3390/jof7090749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8468327PMC
September 2021

Development of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of .

Front Microbiol 2021 6;12:720485. Epub 2021 Sep 6.

Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.

Brown root rot caused by is a new destructive root disease on many plants such as Gingko, Citrus, kiwifruit, and ramie. The establishment of loop-mediated isothermal amplification (LAMP) technology for detecting can help monitor and control brown root rot quickly, efficiently, and accurately. LAMP technology is known for its simplicity, sensitivity, and speed; and it does not require any specialized equipment - a water bath or a thermoblock is sufficient for isothermal amplifications. LAMP products can be visualized by using hydroxy naphthol blue (HNB) dye or agarose gel electrophoresis. In this study, by searching and comparing the internal transcribed spacer (ITS) sequences of and the related species in oomycete genera , and , we designed specific primers targeting the ITS gene region of . Using HNB dye, we established a LAMP technique for rapid detection of by visible color change. In addition, we optimized the protocol to enhance both sensitivity and specificity for detection. Under the optimized condition, our protocol based on LAMP technology could detect as low as 24 copies of the genomic DNA, which is ∼100 times more sensitive than conventional PCR. This method can successfully detect using cell suspensions from - infected ramie root tissues.
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http://dx.doi.org/10.3389/fmicb.2021.720485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8450588PMC
September 2021

Does the primary tumour location affect the prognosis of patients with colorectal cancer peritoneal metastases treated with cytoreductive surgery and hyperthermic intraperitoneal chemotherapy?

World J Surg Oncol 2021 Aug 26;19(1):253. Epub 2021 Aug 26.

Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.

Background: The impact of primary tumour location on the prognosis of patients with peritoneal metastasis (PM) arising from colorectal cancer (CRC) after cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) is rarely discussed, and the evidence is still limited.

Methods: Patients with PM arising from CRC treated with CRS and HIPEC at the China National Cancer Center and Huanxing Cancer Hospital between June 2017 and June 2019 were systematically reviewed. Clinical characteristics, pathological features, perioperative parameters, and prognostic data were collected and analysed.

Results: A total of 70 patients were divided into two groups according to either colonic or rectal origin (18 patients in the rectum group and 52 patients in the colon group). Patients with PM of a colonic origin were more likely to develop grade 3-4 postoperative complications after CRS+HIPEC (38.9% vs 19.2%, P = 0.094), but this difference was not statistically significant. Patients with colon cancer had a longer median overall survival (OS) than patients with rectal cancer (27.0 vs 15.0 months, P = 0.011). In the multivariate analysis, the independent prognostic factors of reduced OS were a rectal origin (HR 2.15, 95% CI 1.15-4.93, P = 0.035) and incomplete cytoreduction (HR 1.99, 95% CI 1.06-4.17, P = 0.047).

Conclusion: CRS is a complex and potentially life-threatening procedure, and we suggest that the indications for CRS+HIPEC in patients with PM of rectal origin be more restrictive and that clinicians approach these cases with caution.
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http://dx.doi.org/10.1186/s12957-021-02374-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8393435PMC
August 2021

Genetic and Phenotypic Diversities in Experimental Populations of Diploid Inter-Lineage Hybrids in the Human Pathogenic .

Microorganisms 2021 Jul 24;9(8). Epub 2021 Jul 24.

Department of Biology, McMaster University, 1280 Main St West, Hamilton, ON L8S 4K1, Canada.

To better understand the potential factors contributing to genome instability and phenotypic diversity, we conducted mutation accumulation (MA) experiments for 120 days for 7 diploid cryptococcal hybrids under fluconazole (10 MA lines each) and non-fluconazole conditions (10 MA lines each). The genomic DNA content, loss of heterozygosity (LOH) rate, growth ability, and fluconazole susceptibility were determined for all 140 evolved cultures. Compared to that of their ancestral clones, the evolved clones showed: (i) genomic DNA content changes ranging from ~22% less to ~27% more, and (ii) reduced, similar, and increased phenotypic values for each tested trait, with most evolved clones displaying increased growth at 40 °C and increased fluconazole resistance. Aside from the ancestral multi-locus genotypes (MLGs) and heterozygosity patterns (MHPs), 77 unique MLGs and 70 unique MPHs were identified among the 140 evolved cultures at day 120. The average LOH rates of the MA lines in the absence and presence of fluconazole were similar at 1.27 × 10 and 1.38 × 10 LOH events per MA line per mitotic division, respectively. While LOH rates varied among MA lines from different ancestors, there was no apparent correlation between the genetic divergence of the parental haploid genomes within ancestral clones and LOH rates. Together, our results suggest that hybrids between diverse lineages of the human pathogenic can generate significant genotypic and phenotypic diversities during asexual reproduction.
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http://dx.doi.org/10.3390/microorganisms9081579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8398696PMC
July 2021

Genomic and Experimental Investigations of and Fungi Reveal New Insights into Pinecone Decomposition.

J Fungi (Basel) 2021 Aug 23;7(8). Epub 2021 Aug 23.

CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.

Saprophytic fungi (SPF) play vital roles in ecosystem dynamics and decomposition. However, because of the complexity of living systems, our understanding of how SPF interact with each other to decompose organic matter is very limited. Here we studied their roles and interactions in the decomposition of highly specialized substrates between the two genera and fungi-colonized fallen pinecones of the same plant sequentially. We obtained the genome sequences from seven fungal species with three pairs: -, - and -/ on cones of , and , respectively, and the organic profiles of substrate during decomposition. Our analyses revealed evidence for both competition and cooperation between the two groups of fungi during decomposition, enabling efficient utilization of substrates with complementary profiles of carbohydrate active enzymes (CAZymes). The fungi are highly effective at utilizing the primary organic carbon, such as lignin, and hemicellulose in freshly fallen cones, facilitated the invasion and colonization by fungi. The fungi have genes coding for abundant CAZymes to utilize the remaining organic compounds and for producing an arsenal of secondary metabolites such as strobilurins that can inhibit other fungi from colonizing the pinecones.
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http://dx.doi.org/10.3390/jof7080679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401616PMC
August 2021

Evidence for Persistent Heteroplasmy and Ancient Recombination in the Mitochondrial Genomes of the Edible Yellow Chanterelles From Southwestern China and Europe.

Front Microbiol 2021 14;12:699598. Epub 2021 Jul 14.

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China.

Mitochondrial genes and genomes have patterns of inheritance that are distinctly different from those of nuclear genes and genomes. In nature, the mitochondrial genomes in eukaryotes are generally considered non-recombining and homoplasmic. If heteroplasmy and recombination exist, they are typically very limited in both space and time. Here we show that mitochondrial heteroplasmy and recombination may not be limited to a specific population nor exit only transiently in the basidiomycete and related species. These edible yellow chanterelles are an ecologically very important group of fungi and among the most prominent wild edible mushrooms in the Northern Hemisphere. At present, very little is known about the genetics and population biology of these fungia cross large geographical distances. Our study here analyzed a total of 363 specimens of edible yellow chanterelles from 24 geographic locations in Yunnan in southwestern China and six geographic locations in five countries in Europe. For each mushroom sample, we obtained the DNA sequences at two genes, one in the nuclear genome and one in the mitochondrial genome. Our analyses of the nuclear gene, translation elongation factor 1-alpha () and the DNA barcode of and related species, suggested these samples belong to four known species and five potential new species. Interestingly, analyses of the mitochondrial ATP synthase subunit 6 () gene fragment revealed evidence of heteroplasmy in two geographic samples in Yunnan and recombination within the two new putative species in Yunnan. Specifically, all four possible haplotypes at two polymorphic nucleotide sites within the mitochondrial gene were found distributed across several geographic locations in Yunnan. Furthermore, these four haplotypes were broadly distributed across multiple phylogenetic clades constructed based on nuclear sequences. Our results suggest that heteroplasmy and mitochondrial recombination might have happened repeatedly during the evolution of the yellow chanterelles. Together, our results suggest that the edible yellow chanterelles represent an excellent system from which to study the evolution of mitochondrial-nuclear genome relationships.
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http://dx.doi.org/10.3389/fmicb.2021.699598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317506PMC
July 2021

CD8 T Cells Involved in Metabolic Inflammation in Visceral Adipose Tissue and Liver of Transgenic Pigs.

Front Immunol 2021 12;12:690069. Epub 2021 Jul 12.

State Key Laboratory of Animal Nutrition, Ministry of Agriculture Key Laboratory of Animal Genetics Breeding and Reproduction, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.

Anti-inflammatory therapies have the potential to become an effective treatment for obesity-related diseases. However, the huge gap of immune system between human and rodent leads to limitations of drug discovery. This work aims at constructing a transgenic pig model with higher risk of metabolic diseases and outlining the immune responses at the early stage of metaflammation by transcriptomic strategy. We used CRISPR/Cas9 techniques to targeted knock-in three humanized disease risk genes, , and . Transgenic effect increased the risk of metabolic disorders. Triple-transgenic pigs with short-term diet intervention showed early symptoms of type 2 diabetes, including glucose intolerance, pancreatic lipid infiltration, islet hypertrophy, hepatic lobular inflammation and adipose tissue inflammation. Molecular pathways related to CD8 T cell function were significantly activated in the liver and visceral adipose samples from triple-transgenic pigs, including antigen processing and presentation, T-cell receptor signaling, co-stimulation, cytotoxicity, and cytokine and chemokine secretion. The similar pro-inflammatory signaling in liver and visceral adipose tissue indicated that there might be a potential immune crosstalk between the two tissues. Moreover, genes that functionally related to liver antioxidant activity, mitochondrial function and extracellular matrix showed distinct expression between the two groups, indicating metabolic stress in transgenic pigs' liver samples. We confirmed that triple-transgenic pigs had high coincidence with human metabolic diseases, especially in the scope of inflammatory signaling at early stage metaflammation. Taken together, this study provides a valuable large animal model for the clinical study of metaflammation and metabolic diseases.
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http://dx.doi.org/10.3389/fimmu.2021.690069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8311854PMC
July 2021

Genetic Diversity and Azole Resistance Among Natural Aspergillus fumigatus Populations in Yunnan, China.

Microb Ecol 2021 Jul 19. Epub 2021 Jul 19.

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, Yunnan, People's Republic of China.

The emergence and spread of azole resistance alleles in clinical and environmental isolates of Aspergillus fumigatus is a global human health concern and endangers the "One Health" approach in our fight against antifungal resistance (AFR) in this pathogen. A major challenge to combat AFR in A. fumigatus is the massive aerial dispersal ability of its asexual spores. Our recent fine-scale survey of greenhouse populations of A. fumigatus near Kunming, Yunnan, China, suggested that the use of azole fungicides for plant protection was likely a major driver of the high-frequency azole-resistant A. fumigatus (ARAF) in greenhouses. Here, we investigated the potential spread of those ARAF and the structure of geographic populations of A. fumigatus by analyzing 452 isolates from 19 geographic locations across Yunnan. We found lower frequencies of ARAF in these outdoor populations than those in greenhouses near Kunming, but there were abundant new alleles and new genotypes, including those associated with azole resistance, consistent with multiple independent origins of ARAF across Yunnan. Interestingly, among the four ecological niches, the sediments of a large lake near Kunming were found to have the highest frequency of ARAF (~ 43%). While most genetic variations were observed within the 19 local populations, statistically significant genetic differentiations were found between many subpopulations within Yunnan. Furthermore, similar to greenhouse populations, these outdoor populations of A. fumigatus in Yunnan were significantly different from those in other parts of the world. Our results call for increased attention to local and regional studies of this fungal pathogen to help develop targeted control strategies against ARAF.
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http://dx.doi.org/10.1007/s00248-021-01804-wDOI Listing
July 2021

Global Temporal Patterns of Age Group and Sex Distributions of COVID-19.

Infect Dis Rep 2021 Jun 21;13(2):582-596. Epub 2021 Jun 21.

Department of Biology and Institute of Infectious Diseases Research, McMaster University, Hamilton, ON L8S 4K1, Canada.

Since the beginning of 2020, COVID-19 has been the biggest public health crisis in the world. To help develop appropriate public health measures and deploy corresponding resources, many governments have been actively tracking COVID-19 in real time within their jurisdictions. However, one of the key unresolved issues is whether COVID-19 was distributed differently among different age groups and between the two sexes in the ongoing pandemic. The objectives of this study were to use publicly available data to investigate the relative distributions of COVID-19 cases, hospitalizations, and deaths among age groups and between the sexes throughout 2020; and to analyze temporal changes in the relative frequencies of COVID-19 for each age group and each sex. Fifteen countries reported age group and/or sex data of patients with COVID-19. Our analyses revealed that different age groups and sexes were distributed differently in COVID-19 cases, hospitalizations, and deaths. However, there were differences among countries in both their age group and sex distributions. Though there was no consistent temporal change across all countries for any age group or either sex in COVID-19 cases, hospitalizations, and deaths, several countries showed statistically significant patterns. We discuss the potential mechanisms for these observations, the limitations of this study, and the implications of our results on the management of this ongoing pandemic.
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http://dx.doi.org/10.3390/idr13020054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293195PMC
June 2021

Diversity and Function of Appressoria.

Pathogens 2021 Jun 12;10(6). Epub 2021 Jun 12.

Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.

Endophytic, saprobic, and pathogenic fungi have evolved elaborate strategies to obtain nutrients from plants. Among the diverse plant-fungi interactions, the most crucial event is the attachment and penetration of the plant surface. Appressoria, specialized infection structures, have been evolved to facilitate this purpose. In this review, we describe the diversity of these appressoria and classify them into two main groups: single-celled appressoria (proto-appressoria, hyaline appressoria, melanized (dark) appressoria) and compound appressoria. The ultrastructure of appressoria, their initiation, their formation, and their function in fungi are discussed. We reviewed the molecular mechanisms regulating the formation and function of appressoria, their strategies to evade host defenses, and the related genomics and transcriptomics. The current review provides a foundation for comprehensive studies regarding their evolution and diversity in different fungal groups.
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http://dx.doi.org/10.3390/pathogens10060746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8231555PMC
June 2021

Current Practices for Reference Gene Selection in RT-qPCR of Aspergillus: Outlook and Recommendations for the Future.

Genes (Basel) 2021 06 24;12(7). Epub 2021 Jun 24.

Biology Department, McMaster University, 1280 Main St. W, Hamilton, ON L8S 4K1, Canada.

is a genus of filamentous fungi with vast geographic and ecological distributions. Species within this genus are clinically, agriculturally and biotechnologically relevant, leading to increasing interest in elucidating gene expression dynamics of key metabolic and physiological processes. Reverse-transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a sensitive and specific method of quantifying gene expression. A crucial step for comparing RT-qPCR results between strains and experimental conditions is normalisation to experimentally validated reference gene(s). In this review, we provide a critical analysis of current reference gene selection and validation practices for RT-qPCR gene expression analyses of . Of 90 primary research articles obtained through our PubMed query, 17 experimentally validated the reference gene(s) used. Twenty reference genes were used across the 90 studies, with beta-tubulin being the most used reference gene, followed by actin, 18S rRNA and glyceraldehyde 3-phosphate dehydrogenase. Sixteen of the 90 studies used multiple reference genes for normalisation. Failing to experimentally validate the stability of reference genes can lead to conflicting results, as was the case for four studies. Overall, our review highlights the need to experimentally validate reference genes in RT-qPCR studies of .
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http://dx.doi.org/10.3390/genes12070960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8307107PMC
June 2021

Genome-Wide Association Analysis for Triazole Resistance in .

Pathogens 2021 Jun 4;10(6). Epub 2021 Jun 4.

Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.

is a ubiquitous fungus and the main agent of aspergillosis, a common fungal infection in the immunocompromised population. Triazoles such as itraconazole and voriconazole are the common first-line drugs for treating aspergillosis. However, triazole resistance in has been reported in an increasing number of countries. While most studies of triazole resistance have focused on mutations in the triazole target gene , >70% of triazole-resistant strains in certain populations showed no mutations in . To identify potential non- mutations associated with triazole resistance in , we analyzed the whole genome sequences and triazole susceptibilities of 195 strains from 12 countries. These strains belonged to three distinct clades. Our genome-wide association study (GWAS) identified a total of six missense mutations significantly associated with itraconazole resistance and 18 missense mutations with voriconazole resistance. In addition, to investigate itraconazole and pan-azole resistance, Fisher's exact tests revealed 26 additional missense variants tightly linked to the top 20 SNPs obtained by GWAS, of which two were consistently associated with triazole resistance. The large number of novel mutations related to triazole resistance should help further investigations into their molecular mechanisms, their clinical importance, and the development of a comprehensive molecular diagnosis toolbox for triazole resistance in .
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http://dx.doi.org/10.3390/pathogens10060701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227032PMC
June 2021

Update on Pulmonary Cryptococcosis.

Mycopathologia 2021 Jun 28. Epub 2021 Jun 28.

Department of Biology, McMaster University, Hamilton, L8S 4K1, Canada.

Pulmonary cryptococcosis is a common but underdiagnosed opportunistic fungal infection in both immunocompromised and immunocompetent patients. The causal agents include at least eight evolutionary distinct haploid lineages as well as their hybrids of the human pathogenic Cryptococcus complex. In this update, we review recent advances in epidemiology, mode of transmission, risk factors, diagnostic methods, and therapy of pulmonary cryptococcosis. Our review suggests significant challenges and opportunities for research, from bedside to benchside and back to bedside.
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http://dx.doi.org/10.1007/s11046-021-00575-9DOI Listing
June 2021

Species Diversity and Antifungal Susceptibilities of Oral Yeasts from Patients with Head and Neck Cancer.

Infect Drug Resist 2021 18;14:2279-2288. Epub 2021 Jun 18.

Public Laboratory of Hainan Medical University, Haikou, 571199, Hainan, People's Republic of China.

Purpose: To investigate the colonization and susceptibility to antifungal drugs of oral yeasts in head and neck cancer patients in Hainan, China.

Methods: Oral mucosa samples from 211 head and neck cancer patients were collected. Oral yeasts were isolated and identified to species by rDNA ITS sequencing. The susceptibilities of all yeasts to amphotericin B, fluconazole, fluorocytosine, itraconazole, and ketoconazole were determined.

Results: Yeasts were isolated from 124 of the 211 oral swabs. The 124 yeast isolates were classified into following 10 species, from the most frequent to the least frequent, (53.2%), (22.6%), (6.5%), (5.6%), (4.8%), (2.4%), (1.6%), (1.6%), (0.8%), and (0.8%). The overall frequencies of resistance among the yeasts to amphotericin B, fluconazole, flucytosine, itraconazole, and ketoconazole were 4.8%, 8.1%, 16.1%, 9.7%, and 9.7%, respectively. One strain and one strain were tolerant/resistant to all five drugs.

Conclusion: Given the high prevalence of oral yeast colonization in head and neck cancer patients and the observed resistance of certain yeast isolates to the five antifungal drugs, our results suggest that rapid identification and susceptibility testing should be implemented before antifungal treatment is applied among patients with head and neck cancer in Hainan.
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http://dx.doi.org/10.2147/IDR.S316368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219225PMC
June 2021

Au nanoparticle-controlled formation of metallic and oxidized Pt nanoparticles on graphitic carbon nitride nanosheets for H evolution.

Dalton Trans 2021 Jul;50(27):9529-9539

School of Materials Science and Engineering, Institute of Material Physics, Key Laboratory of Display Materials and Photoelectric Devices, Ministry of Education, and Tianjin Key Laboratory for Photoelectric Materials and Devices, and National Demonstration Center for Experimental Function Materials Education, Tianjin University of Technology, Tianjin 300384, China.

Surface decoration of noble-metal cocatalysts on graphitic phase carbon nitride (g-C3N4) with high efficiency and trace content for water splitting is exciting but difficult to achieve. Herein, we report the anchoring of Au and metallic/oxidized Pt nanoparticles (NPs) on g-C3N4 as cocatalysts via a photoreduction process for enhancing photocatalytic H2 production. Au NPs are preferentially decorated on g-C3N4, which can control the formation of metallic/oxidized Pt complex species. The well dispersed Au and metallic/oxidized Pt NPs improved the light-harvesting and the photo-generated carrier separation of g-C3N4. G-C3N4 sequentially decorated with Au (0.3 wt%) and metallic/oxidized Pt (0.3 wt%) cocatalysts, exhibited the highest and stable H2 evolution rates of 2560 and 139 μmol h-1 g-1 under simulated sunlight and visible light (λ ≥ 420 nm) irradiation, respectively, compared to the samples that are simultaneously and sequentially decorated with the same content of Pt and Au on g-C3N4. The enhanced photocatalytic activity is attributed to the synergistic effect of Au and metallic/oxidized Pt cocatalysts, i.e., the effective localized surface plasma resonance coupling between Pt and Au NPs, as well as electron-sink function of metallic Pt, which promote the generation and transfer of more carriers from g-C3N4 to the Pt species, in addition to the superior hydrogen evolution capacity of metallic and oxidized Pt. This work maximizes the performance of noble-metal cocatalysts with minimized content and provides the possibility of realizing efficient solar-to-fuel conversion.
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http://dx.doi.org/10.1039/d1dt00910aDOI Listing
July 2021

Argo-Two Decades: Global Oceanography, Revolutionized.

Ann Rev Mar Sci 2021 Jun 8. Epub 2021 Jun 8.

Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China; email:

Argo, an international, global observational array of nearly 4,000 autonomous robotic profiling floats, each measuring ocean temperature and salinity from 0 to 2,000 m on nominal 10-day cycles, has revolutionized physical oceanography. Argo started at the turn of the millennium, growing out of advances in float technology over the previous several decades. After two decades, with well over 2 million profiles made publicly available in real time, Argo data have underpinned more than 4,000 scientific publications and improved countless nowcasts, forecasts, and projections. We review a small subset of those accomplishments, such as elucidating remarkable zonal jets spanning the deep tropical Pacific; increasing understanding of ocean eddies and the roles of mixing in shaping water masses and circulation; illuminating interannual to decadal ocean variability; quantifying, in concert with satellite data, contributions of ocean warming and ice melting to sea level rise; improving coupled numerical weather predictions; and underpinning decadal climate forecasts. Expected final online publication date for the , Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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http://dx.doi.org/10.1146/annurev-marine-022521-102008DOI Listing
June 2021

Phase I study of liposomal irinotecan (LY01610) in patients with advanced esophageal squamous cell carcinoma.

Cancer Chemother Pharmacol 2021 Sep 24;88(3):403-414. Epub 2021 May 24.

Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17 Panjiayuan Nanli, Chaoyang, 100021, Beijing, China.

Purpose: This phase I trial was performed to determine the maximum-tolerated dose (MTD), dose-limiting toxicities (DLTs), preliminary efficacy, and pharmacokinetics (PK) of LY01610, a novel liposome-encapsulated irinotecan, in patients with advanced esophageal squamous cell carcinoma (ESCC).

Methods: This trial was conducted in two stages. In the dose-escalation stage, patients with advanced ESCC refractory or intolerant to previous chemotherapy received escalating doses of LY01610. A recommended dose based on patient tolerance was then expanded in the second stage. LY01610 was administered intravenously every 2 weeks, except that the first cycle in dose escalation was 3 weeks to allow observation of DLTs.

Results: Twenty-four patients were enrolled across 4 dose levels (30, 60, 90 and 120 mg/m). The DLTs included vomiting and febrile neutropenia, and the MTD was 90 mg/m. The most common grade 3/4 adverse events were leukopenia in six patients (25.0%), anemia in six patients (25.0%) and neutropenia in five patients (20.8%). One patient achieved complete response, and four had partial response, including one patient receiving LY01610 at the starting dose of 30 mg/m. Compared with conventional irinotecan, the PK profile of LY01610 was characterized by increased and prolonged exposure of total irinotecan and the active metabolite SN-38 in plasma.

Conclusion: LY01610 demonstrated manageable toxicity and promising anti-tumor activity in patients with advanced ESCC. Future clinical development of LY01610 as single agent or in combination with other anti-cancer agents in treating ESCC patients is warranted.

Trial Registration: NCT04088604 at ClinicalTrials.gov.
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http://dx.doi.org/10.1007/s00280-021-04294-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143070PMC
September 2021

Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic .

Front Cell Infect Microbiol 2021 6;11:683670. Epub 2021 May 6.

Department of Biology, McMaster University, Hamilton, ON, Canada.

The human pathogenic species are the main agents of fungal meningitis in humans and the causes of other diseases collectively called cryptococcosis. There are at least eight evolutionary divergent lineages among these agents, with different lineages showing different geographic and/or ecological distributions. In this review, we describe the main strain typing methods that have been used to analyze the human pathogenic and discuss how molecular markers derived from the various strain typing methods have impacted our understanding of not only cryptococcal epidemiology but also its evolutionary histories. These methods include serotyping, multilocus enzyme electrophoresis, electrophoretic karyotyping, random amplified polymorphic DNA, restriction fragment length polymorphism, PCR-fingerprinting, amplified fragment length polymorphism, multilocus microsatellite typing, single locus and multilocus sequence typing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and whole genome sequencing. The major findings and the advantages and disadvantages of each method are discussed. Together, while controversies remain, these strain typing methods have helped reveal (i) the broad phylogenetic pattern among these agents, (ii) the centers of origins for several lineages and their dispersal patterns, (iii) the distributions of genetic variation among geographic regions and ecological niches, (iv) recent hybridization among several lineages, and (v) specific mutations during infections within individual patients. However, significant challenges remain. Multilocus sequence typing and whole genome sequencing are emerging as the gold standards for continued strain typing and epidemiological investigations of cryptococcosis.
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http://dx.doi.org/10.3389/fcimb.2021.683670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8134695PMC
July 2021

What Are the Best Parents for Hybrid Progeny? An Investigation into the Human Pathogenic Fungus .

Authors:
Man You Jianping Xu

J Fungi (Basel) 2021 Apr 15;7(4). Epub 2021 Apr 15.

Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.

Hybridization between more divergent organisms is likely to generate progeny with more novel genetic interactions and genetic variations. However, the relationship between parental genetic divergence and progeny phenotypic variation remains largely unknown. Here, using strains of the human pathogenic , we investigated the patterns of such a relationship. Twenty-two strains with up to 15% sequence divergence were mated. Progeny were genotyped at 16 loci. Parental strains and their progeny were phenotyped for growth ability at two temperatures, melanin production at seven conditions, and susceptibility to the antifungal drug fluconazole. We observed three patterns of relationships between parents and progeny for each phenotypic trait, including (i) similar to one of the parents, (ii) intermediate between the parents, and (iii) outside the parental phenotypic range. We found that as genetic distance increases between parental strains, progeny showed increased fluconazole resistance and growth at 37 °C but decreased melanin production under various oxidative and nitrosative stresses. Our findings demonstrate that, depending on the traits, both evolutionarily more similar strains and more divergent strains may be better parents to generate progeny with hybrid vigor. Together, the results indicate the enormous potential of hybrids in their evolution and adaptation to diverse conditions.
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http://dx.doi.org/10.3390/jof7040299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8071107PMC
April 2021

Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China, by DNA Barcoding.

J Fungi (Basel) 2021 Apr 17;7(4). Epub 2021 Apr 17.

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China.

Yunnan Province, China, is famous for its abundant wild edible mushroom diversity and a rich source of the world's wild mushroom trade markets. However, much remains unknown about the diversity of edible mushrooms, including the number of wild edible mushroom species and their distributions. In this study, we collected and analyzed 3585 mushroom samples from wild mushroom markets in 35 counties across Yunnan Province from 2010 to 2019. Among these samples, we successfully obtained the DNA barcode sequences from 2198 samples. Sequence comparisons revealed that these 2198 samples likely belonged to 159 known species in 56 different genera, 31 families, 11 orders, 2 classes, and 2 phyla. Significantly, 51.13% of these samples had sequence similarities to known species at lower than 97%, likely representing new taxa. Further phylogenetic analyses on several common mushroom groups including 1536 internal transcribed spacer (ITS) sequences suggested the existence of 20 new (cryptic) species in these groups. The extensive new and cryptic species diversity in wild mushroom markets in Yunnan calls for greater attention for the conservation and utilization of these resources. Our results on both the distinct barcode sequences and the distributions of these sequences should facilitate new mushroom species discovery and forensic authentication of high-valued mushrooms and contribute to the scientific inventory for the management of wild mushroom markets.
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http://dx.doi.org/10.3390/jof7040310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8074183PMC
April 2021

Highly efficient generation of bacterial leaf blight-resistant and transgene-free rice using a genome editing and multiplexed selection system.

BMC Plant Biol 2021 Apr 24;21(1):197. Epub 2021 Apr 24.

Syngenta Biotechnology (China) Co., Ltd, No.25, Life Science Park Road, Beijing, 102206, China.

Background: Rice leaf blight, which is a devastating disease worldwide, is caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The upregulated by transcription activator-like 1 (UPT) effector box in the promoter region of the rice Xa13 gene plays a key role in Xoo pathogenicity. Mutation of a key bacterial protein-binding site in the UPT box of Xa13 to abolish PXO99-induced Xa13 expression is a way to improve rice resistance to bacteria. Highly efficient generation and selection of transgene-free edited plants are helpful to shorten and simplify the gene editing-based breeding process. Selective elimination of transgenic pollen of T0 plants can enrich the proportion of T1 transgene-free offspring, and expression of a color marker gene in seeds makes the selection of T2 plants very convenient and efficient. In this study, a genome editing and multiplexed selection system was used to generate bacterial leaf blight-resistant and transgene-free rice plants.

Results: We introduced site-specific mutations into the UPT box using CRISPR/Cas12a technology to hamper with transcription-activator-like effector (TAL) protein binding and gene activation and generated genome-edited rice with improved bacterial blight resistance. Transgenic pollen of T0 plants was eliminated by pollen-specific expression of the α-amylase gene Zmaa1, and the proportion of transgene-free plants increased from 25 to 50% among single T-DNA insertion events in the T1 generation. Transgenic seeds were visually identified and discarded by specific aleuronic expression of DsRed, which reduced the cost by 50% and led to up to 98.64% accuracy for the selection of transgene-free edited plants.

Conclusion: We demonstrated that core nucleotide deletion in the UPT box of the Xa13 promoter conferred resistance to rice blight, and selection of transgene-free plants was boosted by introducing multiplexed selection. The combination of genome editing and transgene-free selection is an efficient strategy to accelerate functional genomic research and plant breeding.
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http://dx.doi.org/10.1186/s12870-021-02979-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8066475PMC
April 2021

Single-Handed Double Helix and Spiral Platelet Formed by Racemate of Dissymmetric Cages.

Angew Chem Int Ed Engl 2021 Jun 26;60(27):15080-15086. Epub 2021 May 26.

Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.

Spontaneous deracemization has been used to separate homochiral domains from the racemic system. However, homochirality can only be referred to when the scales of these domains and systems are specified. To clarify this, we report self-assembly of racemates of dissymmetric cages DC-1 with a cone-shape propeller geometry, forming a centrosymmetric columnar crystalline phase (racemic at crystallographic level). Owing to their anisotropic geometry, the two enantiomers are packed in a frustrated fashion in this crystalline phase; single-handed double helices are observed (single-handedness at supramolecular level). The frustrated packing (layer continuity break-up) in turn facilitates screw dislocation during the crystal growth, forming left- or right-handed spiral platelets (symmetry-breaking at morphological level), although each platelet is composed of DC-1 racemates. The symmetry correlation between DC-1 molecules, the crystalline phase and spiral platelets, all exhibit C symmetry.
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http://dx.doi.org/10.1002/anie.202103821DOI Listing
June 2021

Landscape Genetic Connectivity and Evidence for Recombination in the North American Population of the White-Nose Syndrome Pathogen, .

J Fungi (Basel) 2021 Mar 3;7(3). Epub 2021 Mar 3.

Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada.

White-Nose Syndrome is an ongoing fungal epizootic caused by epidermal infections of the fungus, Pseudogymnoascus destructans (), affecting hibernating bat species in North America. Emerging early in 2006 in New York State, infections of have spread to 38 US States and seven Canadian Provinces. Since then, clonal isolates of have accumulated genotypic and phenotypic variations in North America. Using microsatellite and single nucleotide polymorphism markers, we investigated the population structure and genetic relationships among isolates from diverse regions in North America to understand its pattern of spread, and to test hypotheses about factors that contribute to transmission. We found limited support for genetic isolation of populations by geographic distance, and instead identified evidence for gene flow among geographic regions. Interestingly, allelic association tests revealed evidence for recombination in the North American population. Our landscape genetic analyses revealed that the population structure of in North America was significantly influenced by anthropogenic impacts on the landscape. Our results have important implications for understanding the mechanism(s) of spread.
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http://dx.doi.org/10.3390/jof7030182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8001231PMC
March 2021

Application of hybrid electrocoagulation-filtration methods in the pretreatment of marine aquaculture wastewater.

Water Sci Technol 2021 Mar;83(6):1315-1326

Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Institute of Oceanology, Qingdao 266071, China E-mail: Center for Ocean Mega-Science Chinese Academy of Sciences, Qingdao 266071, China.

The aim of this study was to provide technical means and data support for enhancing the filtration pretreatment capacity of a recirculating aquaculture system. A continuous flow electrocoagulation (EC)-filtration system was designed and its application in the pretreatment of marine aquaculture wastewater was studied. The influences of anode combination modes, hydraulic retention times (HRTs) of the EC reactor and filter pore sizes on the water treatment capacity were investigated. Results showed that EC could significantly enhance the treatment efficiency of the filtration equipment used in subsequent steps. Al-Fe electrodes used as anode led to better processing capacity of this system, and the optimum anode was 3Al + Fe. With the increase of HRT and decrease of filter pore size, the enhanced effect of the EC process on the filter was more obvious. When the current density was 19.22 A/m, the anode was 3Al + Fe, the HRT was 4.5 min and the filter pore size was 45 μm, the removal efficiency of the system for Vibrio, chemical oxygen demand, total ammonia nitrogen, nitrite nitrogen (NO-N), nitrate nitrogen (NO-N) and total nitrogen was 69.55 ± 0.93%, 48.99 ± 1.42%, 57.06 ± 1.28%, 34.09 ± 2.27%, 18.47 ± 1.88% and 55.26 ± 1.42%, respectively, and the energy consumption was (26.25 ± 4.95) × 10kWh/m.
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http://dx.doi.org/10.2166/wst.2021.044DOI Listing
March 2021

Serum netrin-1 as a potential biomarker for functional outcome of traumatic brain injury.

Clin Chim Acta 2021 Jul 16;518:22-27. Epub 2021 Mar 16.

Liangzhu Hospital of Yuhang District of Hangzhou City, 1657 Moganshan Road, 311113 Hangzhou, China.

Background: Decreased serum netrin-1 concentrations have been found after acute brain injury. We investigated the role of serum netrin in prognosis of traumatic brain injury (TBI).

Methods: In this prospective and observational study, enzyme-linked immunosorbent assay was used to detect serum netrin-1 concentrations in 50 mild TBI patients (Glasgow coma scale (GCS) score, 13-15), 83 moderate TBI patients (GCS score, 9-12), 69 severe TBI patients (GCS score, 3-8) and 50 healthy controls. Glasgow outcome scale score of 1-3 at 6 months after trauma was defined as poor outcome.

Results: Serum netrin-1 concentrations were significantly lower in moderate or severe TBI patients than in controls and in severe TBI patients than in moderate TBI patients, while not in mild TBI patients than in controls. GCS score and Rotterdam computed tomography classification were closely correlated with serum netrin-1 concentrations among TBI patients. Forty-two (20.8%) patients had poor outcome. Receiver operating characteristic curve analysis revealed that serum netrin-1 concentrations could distinguish patients with poor outcome from the other remainders significantly. In addition, serum netrin-1 concentrations were independently associated with poor outcome.

Conclusions: Serum netrin-1 might serve as a potential biomarker for prognosis of TBI.
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http://dx.doi.org/10.1016/j.cca.2021.03.008DOI Listing
July 2021

Linking Plant Secondary Metabolites and Plant Microbiomes: A Review.

Front Plant Sci 2021 2;12:621276. Epub 2021 Mar 2.

Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.

Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.
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http://dx.doi.org/10.3389/fpls.2021.621276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7961088PMC
March 2021
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