Publications by authors named "Francis Martin"

465 Publications

Diagnostic segregation of human breast tumours using Fourier-transform infrared spectroscopy coupled with multivariate analysis: Classifying cancer subtypes.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Mar 15;255:119694. Epub 2021 Mar 15.

School of Public Health, Guilin Medical University, Guilin, Guangxi, PR China. Electronic address:

The present study aimed to investigate whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with multivariate analysis could be applied to discriminate and classify among breast tumour molecular subtypes based on the unique spectral "fingerprints" of their biochemical composition. The different breast cancer tissues and normal breast tissues were collected and identified by pathology and ATR-FTIR spectroscopy respectively. The study indicates that the levels of the lipid-to-protein, nucleic acid-to-lipid, phosphate-to-carbohydrate and their secondary structure ratio, including RNA-to-DNA, Amide I-to-Amide II, and RNA-to-lipid ratios were significantly altered among the molecular subtype of breast tumour compared with normal breast tissues, which helps explain the changes in the biochemical structure of different molecular phenotypes of breast cancer. Tentatively-assigned characteristic peak ratios of infrared (IR) spectra reflect the changes of the macromolecule structure in different issues to a great extent and can be used as a potential biomarker to predict the molecular subtype of breast tumour. The present study acts as the first case study to show the successful application of IR spectroscopy in classifying subtypes of breast cancer with biochemical alterations. Therefore, the present study is likely to help to provide a new diagnostic approach for the accurate diagnosis of breast tumours and differential molecular subtypes and has the potential to be used for further intraoperative management.
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http://dx.doi.org/10.1016/j.saa.2021.119694DOI Listing
March 2021

Facultative symbiosis with a saprotrophic soil fungus promotes potassium uptake in American sweetgum trees.

Plant Cell Environ 2021 Mar 25. Epub 2021 Mar 25.

State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.

Several species of soil free-living saprotrophs can sometimes establish biotrophic symbiosis with plants, but the basic biology of this association remains largely unknown. Here, we investigate the symbiotic interaction between a common soil saprotroph, Clitopilus hobsonii (Agaricomycetes), and the American sweetgum (Liquidambar styraciflua). The colonized root cortical cells were found to contain numerous microsclerotia-like structures. Fungal colonization led to increased plant growth and facilitated potassium uptake, particularly under potassium limitation (0.05 mM K ). The expression of plant genes related to potassium uptake was not altered by the symbiosis, but colonized roots contained the transcripts of three fungal genes with homology to K transporters (ACU and HAK) and channel (SKC). Heterologously expressed ChACU and ChSKC restored growth of a yeast K -uptake-defective mutant. Upregulation of ChACU transcript under low K conditions (0 and 0.05 mM K ) compared to control (5 mM K ) was demonstrated in planta and in vitro. Colonized plants displayed a larger accumulation of soluble sugars under 0.05 mM K than non-colonized plants. The present study suggests reciprocal benefits of this novel tree-fungus symbiosis under potassium limitation mainly through an exchange of additional carbon and potassium between both partners. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1111/pce.14053DOI Listing
March 2021

Spectrochemical determination of effects on rat liver of binary exposure to benzo[a]pyrene and 2,2',4,4'-tetrabromodiphenyl ether.

J Appl Toxicol 2021 Mar 23. Epub 2021 Mar 23.

Department of Environmental Health and Occupational Medicine, School of Public Health, Guilin Medical University, Guilin, China.

Benzo[a]pyrene (B[a]P) and polybrominated diphenyl ethers (PBDEs) are persistent environmental contaminants. The effects in organisms of exposures to binary mixtures of such contaminants remain obscure. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy is a label-free, non-destructive analytical technique allowing spectrochemical analysis of macromolecular components, and alterations thereof, within tissue samples. Herein, we employed ATR-FTIR spectroscopy to identify biomolecular changes in rat liver post-exposure to B[a]P and BDE-47 (2,2',4,4'-tetrabromodiphenyl ether) congener mixtures. Our results demonstrate that significant separation occurs between spectra of tissue samples derived from control versus exposure categories (accuracy = 87%; sensitivity = 95%; specificity = 79%). Additionally, there is significant spectral separation between exposed categories (accuracy = 91%; sensitivity = 98%; specificity = 90%). Segregation between control and all exposure categories were primarily associated with wavenumbers ranging from 1600 to 1700 cm . B[a]P and BDE-47 alone, or in combination, induces liver damage in female rats. However, it is suggested that binary exposure apparently attenuates the toxic effects in rat liver of the individual contaminants. This is supported by morphological observations of liver tissue architecture on hematoxylin and eosin (H&E)-stained liver sections. Such observations highlight the difficulties in predicting the endpoint effects in target tissues of exposures to mixtures of environmental contaminants.
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http://dx.doi.org/10.1002/jat.4165DOI Listing
March 2021

Comparative analysis of genomes reveals oomycete pathogenesis in crops.

Heliyon 2021 Feb 23;7(2):e06317. Epub 2021 Feb 23.

Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen 518045, China.

The oomycete genus includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined species- and . Comparing these species and related genera allowed reconstruction of the phylogenetic relationships within the genus and revealed genomic features associated with infection and pathogenicity. We found that several hundred genes are putatively inherited from red algae, but does not have vestigial plastids originating from phototrophs. The horizontally-transferred genes are abundant transposons that "transmit" exogenous gene to species thus bring about the gene recombination possibility. Several expansion events of gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of evolution and will also be helpful for the design of phytopathological control strategies.
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http://dx.doi.org/10.1016/j.heliyon.2021.e06317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7907477PMC
February 2021

The evolving role of MUC16 (CA125) in the transformation of ovarian cells and the progression of neoplasia.

Carcinogenesis 2021 Feb 20. Epub 2021 Feb 20.

Biocel UK Ltd, Hull, UK.

MUC16 (the cancer antigen CA125) is the most commonly used serum biomarker in epithelial ovarian cancer, with increasing levels reflecting disease progression. It is a transmembrane glycoprotein with multiple isoforms, undergoing significant changes through the metastatic process. Aberrant glycosylation and cleavage with overexpression of a small membrane-bound fragment consist MUC16-related mechanisms that enhance malignant potential. Even MUC16 knockdown can induce an aggressive phenotype but can also increase susceptibility to chemotherapy. Variable MUC16 functions help ovarian cancer cells avoid immune cytotoxicity, survive inside ascites and form metastases. This review provides a comprehensive insight into MUC16 transformations and interactions, with description of activated oncogenic signalling pathways, and adds new elements on the role of its differential glycosylation. By following the journey of the molecule from pre-malignant states to advanced stages of disease it demonstrates its behaviour, in relation to the phenotypic shifts and progression of ovarian cancer. Additionally it presents proposed differences of MUC16 structure in normal/benign conditions and epithelial ovarian malignancy.
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http://dx.doi.org/10.1093/carcin/bgab010DOI Listing
February 2021

C-STABILITY an innovative modeling framework to leverage the continuous representation of organic matter.

Nat Commun 2021 02 5;12(1):810. Epub 2021 Feb 5.

INRAE, BEF, F-54000, Nancy, France.

The understanding of soil organic matter (SOM) dynamics has considerably advanced in recent years. It was previously assumed that most SOM consisted of recalcitrant compounds, whereas the emerging view considers SOM as a range of polymers continuously processed into smaller molecules by decomposer enzymes. Mainstreaming this new paradigm in current models is challenging because of their ill-adapted framework. We propose the C-STABILITY model to resolve this issue. Its innovative framework combines compartmental and continuous modeling approaches to accurately reproduce SOM cycling processes. C-STABILITY emphasizes the influence of substrate accessibility on SOM turnover and makes enzymatic and microbial biotransformations of substrate explicit. Theoretical simulations provide new insights on how depolymerization and decomposers ecology impact organic matter chemistry and amount during decomposition and at steady state. The flexible mathematical structure of C-STABILITY offers a promising foundation for exploring new mechanistic hypotheses and supporting the design of future experiments.
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http://dx.doi.org/10.1038/s41467-021-21079-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864906PMC
February 2021

Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.

Environ Microbiol 2021 Feb 4. Epub 2021 Feb 4.

INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.

Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
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http://dx.doi.org/10.1111/1462-2920.15423DOI Listing
February 2021

Hybrid genome assembly and gene repertoire of the root endophyte Clitopilus hobsonii QYL-10 (Entolomataceae, Agaricales, Basidiomycetes).

Mol Plant Microbe Interact 2021 Feb 1. Epub 2021 Feb 1.

No. 73, Daqiao RoadHangzhou, China, 311400;

Clitopilus hobsonii (Entolomataceae, Agaricales, Basidiomycetes) is a common soil saprotroph. There is also evidence that C. hobsonii can act as a root endophyte benefiting tree growth. Here, we report the genome assembly of C. hobsonii QYL-10 isolated from ectomycorrhizal root tips of Quercus lyrata. The genome size is 36.93 Mb, consisting of 13 contigs (N50=3.3 Mb) with 49.2% GC-content. Of them, 10 contigs approached the length of intact chromosomes, and 3 had telomeres at one end only. BUSCO analysis reported a completeness score of 98.4% using the Basidiomycota_odb10. Combining ab-initio, RNA-seq data, and homology-based predictions, we identified 12,710 protein-coding genes. Approximately, 1.43 Mb of Transposable elements (TEs) (3.88% of the assembly), 36 secondary metabolite biosynthetic gene clusters and 361 genes encoding putative CAZymes were identified. This genomic resource will allow functional studies aimed to characterize the symbiotic interactions between C. hobsonii and its host trees, but will also provide a valuable foundation for further research on comparative genomics of the Entolomataceae.
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http://dx.doi.org/10.1094/MPMI-11-20-0328-ADOI Listing
February 2021

Draft Genome Sequences of the Black Truffles Tuber brumale Vittad. and Tuber indicum Cook & Massee.

Microbiol Resour Announc 2021 Jan 28;10(4). Epub 2021 Jan 28.

Université de Lorraine, INRAE, IAM, Nancy, France

and (Pezizomycetes) are two edible black truffles establishing ectomycorrhizal symbiosis with trees and shrubs. is ubiquitous in Europe, and is mainly found in China. Here, we present the draft genome sequences of and .
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http://dx.doi.org/10.1128/MRA.00799-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7844066PMC
January 2021

An Updated Global Species Diversity and Phylogeny in the Forest Pathogenic Genus (Basidiomycota, Russulales).

Front Microbiol 2020 7;11:596393. Epub 2021 Jan 7.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.

species are amongst the most intensively studied polypores because several species are aggressive white rot pathogens of managed coniferous forests mainly in Europe and North America. In the present study, both morphological and multilocus phylogenetic analyses were carried out on samples from Asia, Oceania, Europe and North America. Three new taxa were found, i.e., , , and are from Asia and are described as new species. is treated as a synonym of . So far, six taxa in the species complex are recognized. , , and occur in Europe, , and in North America, and in East Asia. The North American was introduced to Italy during the Second World War. Species in the complex are pathogens of coniferous trees, except that seems to be a saprotroph. Ten species are found in the species complex, all of them are saprotrophs. The pathogenic species are distributed in Europe and North America; the Asian countries should consider the European and North American species as entry plant quarantine fungi. Parallelly, European countries should consider the American and as entry plant quarantine fungi although the latter species is already in Italy, while North America should treat , s.s., and as entry plant quarantine fungi. Eight species found in the Himalayas suggest that the ancestral species may have occurred in Asia.
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http://dx.doi.org/10.3389/fmicb.2020.596393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817714PMC
January 2021

Ultrarapid On-Site Detection of SARS-CoV-2 Infection Using Simple ATR-FTIR Spectroscopy and an Analysis Algorithm: High Sensitivity and Specificity.

Anal Chem 2021 02 22;93(5):2950-2958. Epub 2021 Jan 22.

Biocel UK Ltd., 15 Riplingham Road, West Ella, Hull HU10 6TS, U.K.

There is an urgent need for ultrarapid testing regimens to detect the severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] infections in real-time within seconds to stop its spread. Current testing approaches for this RNA virus focus primarily on diagnosis by RT-qPCR, which is time-consuming, costly, often inaccurate, and impractical for general population rollout due to the need for laboratory processing. The latency until the test result arrives with the patient has led to further virus spread. Furthermore, latest antigen rapid tests still require 15-30 min processing time and are challenging to handle. Despite increased polymerase chain reaction (PCR)-test and antigen-test efforts, the pandemic continues to evolve worldwide. Herein, we developed a superfast, reagent-free, and nondestructive approach of attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy with subsequent chemometric analysis toward the prescreening of virus-infected samples. Contrived saliva samples spiked with inactivated γ-irradiated COVID-19 virus particles at levels down to 1582 copies/mL generated infrared (IR) spectra with a good signal-to-noise ratio. Predominant virus spectral peaks are tentatively associated with nucleic acid bands, including RNA. At low copy numbers, the presence of a virus particle was found to be capable of modifying the IR spectral signature of saliva, again with discriminating wavenumbers primarily associated with RNA. Discrimination was also achievable following ATR-FTIR spectral analysis of swabs immersed in saliva variously spiked with virus. Next, we nested our test system in a clinical setting wherein participants were recruited to provide demographic details, symptoms, parallel RT-qPCR testing, and the acquisition of pharyngeal swabs for ATR-FTIR spectral analysis. Initial categorization of swab samples into negative versus positive COVID-19 infection was based on symptoms and PCR results ( = 111 negatives and 70 positives). Following training and validation (using = 61 negatives and 20 positives) of a genetic algorithm-linear discriminant analysis (GA-LDA) algorithm, a blind sensitivity of 95% and specificity of 89% was achieved. This prompt approach generates results within 2 min and is applicable in areas with increased people traffic that require sudden test results such as airports, events, or gate controls.
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http://dx.doi.org/10.1021/acs.analchem.0c04608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7857139PMC
February 2021

A tribute to Sally E. Smith.

New Phytol 2020 10;228(2):397-402

School of Agriculture, Food & Wine and the Waite Research Institute, The University of Adelaide, Urrbrae, SA, 5064, Australia.

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http://dx.doi.org/10.1111/nph.16895DOI Listing
October 2020

The Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicinal Sclerotium.

Genomics Proteomics Bioinformatics 2020 Dec 24. Epub 2020 Dec 24.

Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China. Electronic address:

Wolfiporia cocos (F. A. Wolf) has been praised as a food delicacy and medicine for centuries in China. Here, we present the genome and transcriptome of the Chinese strain CGMCC5.78 of W. cocos. High-confidence functional prediction was made for 9277 genes among the 10,908 total predicted gene models in the W. cocos genome. Up to 2838 differentially expressed genes (DEGs) were identified to be related to sclerotial development by comparing the transcriptomes of mycelial and sclerotial tissues. These DEGs are involved in mating processes, differentiation of fruiting body tissues, and metabolic pathways. A number of genes encoding enzymes and regulatory factors related to polysaccharide and triterpenoid production were strikingly regulated. A potential triterpenoid gene cluster including the signature lanosterol synthase (LSS) gene and its modified components were annotated. In addition, five nonribosomal peptide synthase (NRPS)-like gene clusters, eight polyketide synthase (PKS) gene clusters, and 15 terpene gene clusters were discovered in the genome. The differential expression of the velevt family proteins, transcription factors, carbohydrate-active enzymes, and signaling components indicated their essential roles in the regulation of fungal development and secondary metabolism in W. cocos. These genomic and transcriptomic resources will be valuable for further investigations of the molecular mechanisms controlling sclerotial formation and for its improved medicinal applications.
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http://dx.doi.org/10.1016/j.gpb.2019.01.007DOI Listing
December 2020

Applying Raman Microspectroscopy to Evaluate the Effects of Nutrient Cations on Alkane Bioavailability to ADP1.

Environ Sci Technol 2020 12 4;54(24):15800-15810. Epub 2020 Dec 4.

Biocel Ltd, Hull HU10 7TS, U.K.

Contamination with petroleum hydrocarbons causes extensive damage to ecological systems. On oil-contaminated sites, alkanes are major components; many indigenous bacteria can access and/or degrade alkanes. However, their ability to do so is affected by external properties of the soil, including nutrient cations. This study used Raman microspectroscopy to study how nutrient cations affect alkanes' bioavailability to ADP1 (a known degrader). Treated with Na, K, Mg, and Ca at 10 mM, was exposed to seven -alkanes (decane, dodecane, tetradecane, hexadecane, nonadecane, eicosane, and tetracosane) and one alkane mixture (mineral oil). Raman spectral analysis indicated that bioavailability of alkanes varied with carbon chain lengths, and additional cations altered the bacterial response to -alkanes. Sodium significantly increased the bacterial affinity toward decane and dodecane, and K and Mg enhanced the bioavailability of tetradecane and hexadecane. In contrast, the bacterial response was inhibited by Ca for all alkanes. Similar results were observed in mineral oil exposure. Our study employed Raman spectral assay to offer a deep insight into how nutrient cations affect the bioavailability of alkanes, suggesting that nutrient cations can play a key role in influencing the harmful effects of hydrocarbons and could be optimized to enhance the bioremediation strategy.
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http://dx.doi.org/10.1021/acs.est.0c04944DOI Listing
December 2020

A comparative analysis of different biofluids towards ovarian cancer diagnosis using Raman microspectroscopy.

Anal Bioanal Chem 2021 Jan 26;413(3):911-922. Epub 2020 Nov 26.

School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK.

Biofluids, such as blood plasma or serum, are currently being evaluated for cancer detection using vibrational spectroscopy. These fluids contain information of key biomolecules, such as proteins, lipids, carbohydrates and nucleic acids, that comprise spectrochemical patterns to differentiate samples. Raman is a water-free and practically non-destructive vibrational spectroscopy technique, capable of recording spectrochemical fingerprints of biofluids with minimum or no sample preparation. Herein, we compare the performance of these two common biofluids (blood plasma and serum) together with ascitic fluid, towards ovarian cancer detection using Raman microspectroscopy. Samples from thirty-eight patients were analysed (n = 18 ovarian cancer patients, n = 20 benign controls) through different spectral pre-processing and discriminant analysis techniques. Ascitic fluid provided the best class separation in both unsupervised and supervised discrimination approaches, where classification accuracies, sensitivities and specificities above 80% were obtained, in comparison to 60-73% with plasma or serum. Ascitic fluid appears to be rich in collagen information responsible for distinguishing ovarian cancer samples, where collagen-signalling bands at 1004 cm (phenylalanine), 1334 cm (CHCH wagging vibration), 1448 cm (CH deformation) and 1657 cm (Amide I) exhibited high statistical significance for class differentiation (P < 0.001). The efficacy of vibrational spectroscopy, in particular Raman spectroscopy, combined with ascitic fluid analysis, suggests a potential diagnostic method for ovarian cancer. Raman microspectroscopy analysis of ascitic fluid allows for discrimination of patients with benign gynaecological conditions or ovarian cancer.
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http://dx.doi.org/10.1007/s00216-020-03045-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7808972PMC
January 2021

The mutualism effector MiSSP7 of Laccaria bicolor alters the interactions between the poplar JAZ6 protein and its associated proteins.

Sci Rep 2020 11 23;10(1):20362. Epub 2020 Nov 23.

UMR 1136, Interactions Arbres/Microorganismes (IAM), Centre INRAE de Nancy, Université de Lorraine/INRAE, Champenoux, France.

Despite the pivotal role of jasmonic acid in the outcome of plant-microorganism interactions, JA-signaling components in roots of perennial trees like western balsam poplar (Populus trichocarpa) are poorly characterized. Here we decipher the poplar-root JA-perception complex centered on PtJAZ6, a co-repressor of JA-signaling targeted by the effector protein MiSSP7 from the ectomycorrhizal basidiomycete Laccaria bicolor during symbiotic development. Through protein-protein interaction studies in yeast we determined the poplar root proteins interacting with PtJAZ6. Moreover, we assessed via yeast triple-hybrid how the mutualistic effector MiSSP7 reshapes the association between PtJAZ6 and its partner proteins. In the absence of the symbiotic effector, PtJAZ6 interacts with the transcription factors PtMYC2s and PtJAM1.1. In addition, PtJAZ6 interacts with it-self and with other Populus JAZ proteins. Finally, MiSSP7 strengthens the binding of PtJAZ6 to PtMYC2.1 and antagonizes PtJAZ6 homo-/heterodimerization. We conclude that a symbiotic effector secreted by a mutualistic fungus may promote the symbiotic interaction through altered dynamics of a JA-signaling-associated protein-protein interaction network, maintaining the repression of PtMYC2.1-regulated genes.
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http://dx.doi.org/10.1038/s41598-020-76832-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7683724PMC
November 2020

ATR-FTIR spectroscopy in blood plasma combined with multivariate analysis to detect HIV infection in pregnant women.

Sci Rep 2020 11 19;10(1):20156. Epub 2020 Nov 19.

Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande Do Norte, Natal, RN, 5072-970, Brazil.

The primary concern for HIV-infected pregnant women is the vertical transmission that can occur during pregnancy, in the intrauterine period, during labour or even breastfeeding. The risk of vertical transmission can be reduced by early diagnosis. Therefore, it is necessary to develop new methods to detect this virus in a quick and low-cost fashion, as colorimetric assays for HIV detection tend to be laborious and costly. Herein, attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy combined with multivariate analysis was employed to distinguish HIV-infected patients from healthy uninfected controls in a total of 120 blood plasma samples. The best sensitivity (83%) and specificity (92%) values were obtained using the genetic algorithm with linear discriminant analysis (GA-LDA). These good classification results in addition to the potential for high analytical frequency, the low cost and reagent-free nature of this method demonstrate its potential as an alternative tool for HIV screening during pregnancy.
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http://dx.doi.org/10.1038/s41598-020-77378-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7677535PMC
November 2020

Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity.

Mol Biol Evol 2021 Apr;38(4):1428-1446

Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain.

As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates-namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose-methanol-choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases-we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
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http://dx.doi.org/10.1093/molbev/msaa301DOI Listing
April 2021

Intra-species genetic variability drives carbon metabolism and symbiotic host interactions in the ectomycorrhizal fungus Pisolithus microcarpus.

Environ Microbiol 2020 Nov 13. Epub 2020 Nov 13.

Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.

Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood. Here, we explore the extent of intra-species variation between four isolates of the ECM fungus Pisolithus microcarpus, in terms of gene regulation, carbon metabolism and growth, and interactions with a host, Eucalyptus grandis. We demonstrate that, while a core response to the host is maintained by all of the isolates tested, they have distinct patterns of gene expression and carbon metabolism, resulting in the differential expression of isolate-specific response pathways in the host plant. Together, these results highlight the importance of using a wider range of individuals within a species to understand the broader ecological roles of ECM fungi and their host interactions.
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http://dx.doi.org/10.1111/1462-2920.15320DOI Listing
November 2020

Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle.

New Phytol 2021 03 10;229(5):2917-2932. Epub 2020 Dec 10.

Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, Campus de Espinardo, Murcia, 30100, Spain.

Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the molecular mechanisms driving the ectendomycorrhizal interaction is lacking. Genomes of the highly appreciated edible desert truffles Terfezia claveryi Chatin and Tirmania nivea Trappe have been sequenced and compared with other Pezizomycetes. Transcriptomes of T. claveryi × Helianthemum almeriense mycorrhiza from well-watered and drought-stressed plants, when intracellular colonizations is promoted, were investigated. We have identified the fungal genes related to sexual reproduction in desert truffles and desert-truffles-specific genomic and secretomic features with respect to other Pezizomycetes, such as the expansion of a large set of gene families with unknown Pfam domains and a number of species or desert-truffle-specific small secreted proteins differentially regulated in symbiosis. A core set of plant genes, including carbohydrate, lipid-metabolism, and defence-related genes, differentially expressed in mycorrhiza under both conditions was found. Our results highlight the singularities of desert truffles with respect to other mycorrhizal fungi while providing a first glimpse on plant and fungal determinants involved in ecto to endo symbiotic switch that occurs in desert truffle under dry conditions.
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http://dx.doi.org/10.1111/nph.17044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7898904PMC
March 2021

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.

Nat Commun 2020 10 12;11(1):5125. Epub 2020 Oct 12.

Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l' environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.
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http://dx.doi.org/10.1038/s41467-020-18795-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7550596PMC
October 2020

Spectrochemical analysis of liquid biopsy harnessed to multivariate analysis towards breast cancer screening.

Sci Rep 2020 07 30;10(1):12818. Epub 2020 Jul 30.

Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil.

Mortality due to breast cancer could be reduced via screening programs where preliminary clinical tests employed in an asymptomatic well-population with the objective of identifying cancer biomarkers could allow earlier referral of women with altered results for deeper clinical analysis and treatment. The introduction of well-population screening using new and less-invasive technologies as a strategy for earlier detection of breast cancer is thus highly desirable. Herein, spectrochemical analyses harnessed to multivariate classification techniques are used as a bio-analytical tool for a Breast Cancer Screening Program using liquid biopsy in the form of blood plasma samples collected from 476 patients recruited over a 2-year period. This methodology is based on acquiring and analysing the spectrochemical fingerprint of plasma samples by attenuated total reflection Fourier-transform infrared spectroscopy; derived spectra reflect intrinsic biochemical composition, generating information on nucleic acids, carbohydrates, lipids and proteins. Excellent results in terms of sensitivity (94%) and specificity (91%) were obtained using this method in comparison with traditional mammography (88-93% and 85-94%, respectively). Additional advantages such as better disease prognosis thus allowing a more effective treatment, lower associated morbidity, fewer false-positive and false-negative results, lower-cost, and higher analytical frequency make this method attractive for translation to the clinical setting.
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http://dx.doi.org/10.1038/s41598-020-69800-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393361PMC
July 2020

A three-dimensional discriminant analysis approach for hyperspectral images.

Analyst 2020 Aug;145(17):5915-5924

School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK.

Raman hyperspectral imaging is a powerful technique that provides both chemical and spatial information of a sample matrix being studied. The generated data are composed of three-dimensional (3D) arrays containing the spatial information across the x- and y-axis, and the spectral information in the z-axis. Unfolding procedures are commonly employed to analyze this type of data in a multivariate fashion, where the spatial dimension is reshaped and the spectral data fits into a two-dimensional (2D) structure and, thereafter, common first-order chemometric algorithms are applied to process the data. There are only a few algorithms capable of working with the full 3D array. Herein, we propose new algorithms for 3D discriminant analysis of hyperspectral images based on a three-dimensional principal component analysis linear discriminant analysis (3D-PCA-LDA) and a three-dimensional discriminant analysis quadratic discriminant analysis (3D-PCA-QDA) approach. The analysis was performed in order to discriminate simulated and real-world data, comprising benign controls and ovarian cancer samples based on Raman hyperspectral imaging, in which 3D-PCA-LDA and 3D-PCA-QDA achieved far superior performance than classical algorithms using unfolding procedures (PCA-LDA, PCA-QDA, partial lest squares discriminant analysis [PLS-DA], and support vector machines [SVM]), where the classification accuracies improved from 66% to 83% (simulated data) and from 50% to 100% (real-world dataset) after employing the 3D techniques. 3D-PCA-LDA and 3D-PCA-QDA are new approaches for discriminant analysis of hyperspectral images multisets to provide faster and superior classification performance than traditional techniques.
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http://dx.doi.org/10.1039/d0an01328eDOI Listing
August 2020

Spectrochemical analysis in blood plasma combined with subsequent chemometrics for fibromyalgia detection.

Sci Rep 2020 07 16;10(1):11769. Epub 2020 Jul 16.

Postgraduation Program in Rehabilitation Sciences, Faculty of Health Science of Trairí, Federal University of Rio Grande do Norte, Trairí St., Santa Cruz, RN, 59200-000, Brazil.

Fibromyalgia is a rheumatologic condition characterized by multiple and chronic body pain, and other typical symptoms such as intense fatigue, anxiety and depression. It is a very complex disease where treatment is often made by non-medicated alternatives in order to alleviate symptoms and improve the patient's quality of life. Herein, we propose a method to detect patients with fibromyalgia (n = 252, 126 controls and 126 patients with fibromyalgia) through the analysis of their blood plasma using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy in conjunction with chemometric techniques, hence, providing a low-cost, fast and accurate diagnostic approach. Different chemometric algorithms were tested to classify the spectral data; genetic algorithm with linear discriminant analysis (GA-LDA) achieved the best diagnostic results with a sensitivity of 89.5% in an external test set. The GA-LDA model identified 24 spectral wavenumbers responsible for class separation; amongst these, the Amide II (1,545 cm) and proteins (1,425 cm) were identified to be discriminant features. These results reinforce the potential of ATR-FTIR spectroscopy with multivariate analysis as a new tool to screen and detect patients with fibromyalgia in a fast, low-cost, non-destructive and minimally invasive fashion.
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http://dx.doi.org/10.1038/s41598-020-68781-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366631PMC
July 2020

Paper Spray Ionization Mass Spectrometry as a Potential Tool for Early Diagnosis of Cervical Cancer.

J Am Soc Mass Spectrom 2020 Jul 20. Epub 2020 Jul 20.

Chemistry Institute, Federal University of Goiás, Goiánia, Brazil.

Squamous intraepithelial lesion is an abnormal growth of epithelial cells on the surface of the cervix that may lead to cervical cancer. Analytical protocols for the determination of squamous intraepithelial lesions are in high demand, since cervical cancer is the fourth most diagnosed cancer among women in the world. Here, paper spray ionization mass spectrometry (PSI-MS) is used to distinguish between healthy (negative for intraepithelial lesion or malignancy) and diseased (high-grade squamous intraepithelial lesion) blood plasmas. A total of 86 blood samples of different women (49 healthy samples, 37 diseased samples) were collected, and the plasmas were prepared. Then, 10 μL of each plasma sample was deposited onto triangular papers for PSI-MS analysis. No additional step of sample preparation was necessary. The interval-successive projection algorithm linear discriminant analysis (iSPA-LDA) was applied to the PSI mass spectra, showing six ions (mostly phospholipids) that were predictive of healthy and diseased plasmas. Values of 77% accuracy, 86% sensitivity, 80% positive predictive value (PPV), and 75% negative predictive value (NPV) were achieved. This study provides evidence that PSI-MS may potentially be used as a fast and simple analytical technique for the early diagnosis of cervical cancer.
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http://dx.doi.org/10.1021/jasms.0c00111DOI Listing
July 2020

A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions.

Mol Plant Microbe Interact 2020 Oct 17;33(10):1177-1188. Epub 2020 Aug 17.

Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.

Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry-based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo-assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar × 717-1B4 in interaction with the ectomycorrhizal basidiomycete . In total, we identified 1,660 and 2,870 and unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of . These PCPs mapped to 64 proteins and 69 proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.
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http://dx.doi.org/10.1094/MPMI-04-20-0082-TADOI Listing
October 2020

Mycorrhizal effector PaMiSSP10b alters polyamine biosynthesis in Eucalyptus root cells and promotes root colonization.

New Phytol 2020 10;228(2):712-727

Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.

Pathogenic microbes are known to manipulate the defences of their hosts through the production of secreted effector proteins. More recently, mutualistic mycorrhizal fungi have also been described as using these secreted effectors to promote host colonization. Here we characterize a mycorrhiza-induced small secreted effector protein of 10 kDa produced by the ectomycorrhizal fungus Pisolithus albus, PaMiSSP10b. We demonstrate that PaMiSSP10b is secreted from fungal hyphae, enters the cells of its host, Eucalyptus grandis, and interacts with an S-adenosyl methionine decarboxylase (AdoMetDC) in the polyamine pathway. Plant polyamines are regulatory molecules integral to the plant immune system during microbial challenge. Using biochemical and transgenic approaches we show that expression of PaMiSSP10b influences levels of polyamines in the plant roots as it enhances the enzymatic activity of AdoMetDC and increases the biosynthesis of higher polyamines. This ultimately favours the colonization success of P. albus. These results identify a new mechanism by which mutualistic microbes are able to manipulate the host´s enzymatic pathways to favour colonization.
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http://dx.doi.org/10.1111/nph.16759DOI Listing
October 2020

Tutorial: multivariate classification for vibrational spectroscopy in biological samples.

Nat Protoc 2020 07 17;15(7):2143-2162. Epub 2020 Jun 17.

School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK.

Vibrational spectroscopy techniques, such as Fourier-transform infrared (FTIR) and Raman spectroscopy, have been successful methods for studying the interaction of light with biological materials and facilitating novel cell biology analysis. Spectrochemical analysis is very attractive in disease screening and diagnosis, microbiological studies and forensic and environmental investigations because of its low cost, minimal sample preparation, non-destructive nature and substantially accurate results. However, there is now an urgent need for multivariate classification protocols allowing one to analyze biologically derived spectrochemical data to obtain accurate and reliable results. Multivariate classification comprises discriminant analysis and class-modeling techniques where multiple spectral variables are analyzed in conjunction to distinguish and assign unknown samples to pre-defined groups. The requirement for such protocols is demonstrated by the fact that applications of deep-learning algorithms of complex datasets are being increasingly recognized as critical for extracting important information and visualizing it in a readily interpretable form. Hereby, we have provided a tutorial for multivariate classification analysis of vibrational spectroscopy data (FTIR, Raman and near-IR) highlighting a series of critical steps, such as preprocessing, data selection, feature extraction, classification and model validation. This is an essential aspect toward the construction of a practical spectrochemical analysis model for biological analysis in real-world applications, where fast, accurate and reliable classification models are fundamental.
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http://dx.doi.org/10.1038/s41596-020-0322-8DOI Listing
July 2020

Towards screening Barrett's oesophagus: current guidelines, imaging modalities and future developments.

Clin J Gastroenterol 2020 Oct 3;13(5):635-649. Epub 2020 Jun 3.

Biocel Ltd, Hull, HU10 7TS, UK.

Barrett's oesophagus is the only known precursor to oesophageal adenocarcinoma (OAC). Although guidelines on the screening and surveillance exist in Barrett's oesophagus, the current strategies are inadequate. Oesophagogastroduodenoscopy (OGD) is the gold standard method in screening for Barrett's oesophagus. This invasive method is expensive with associated risks negating its use as a current screening tool for Barrett's oesophagus. This review explores current definitions, epidemiology, biomarkers, surveillance, and screening in Barrett's oesophagus. Imaging modalities applicable to this condition are discussed, in addition to future developments. There is an urgent need for an alternative non-invasive method of screening and/or surveillance which could be highly beneficial towards reducing waiting times, alleviating patient fears and reducing future costs in current healthcare services. Vibrational spectroscopy has been shown to be promising in categorising Barrett's oesophagus through to high-grade dysplasia (HGD) and OAC. These techniques need further validation through multicentre trials.
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http://dx.doi.org/10.1007/s12328-020-01135-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7519897PMC
October 2020