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Fulltext Multigene phylogeny and morphological descriptions of five species of Agaricus sect. Minores from subtropical climate zones of Pakistan

Bashir H, Asif M, Ghafoor A, Niazi AR, Khalid AN, Parveen G, et al.

PLoS One, 2024;19(7):e0302222.
PMID: 38990811 DOI: 10.1371/journal.pone.0302222

The genus Agaricus includes more than 500 species mostly containing the edible and cultivated species worldwide. As part of the ongoing studies on the biodiversity of genus Agaricus in Pakistan, our objective was to focus on A. sect. Minores which is the largest section of the genus. In the first phylogenetic analyses based on the ITS region of the nuclear ribosomal DNA, our sample included specimens of 97 named species, 27 unnamed species, and 31 specimens (29 newly generated sequences in this study) from subtropical climate zones of Pakistan that likely belong to this section based on their morphology. The 31 specimens grouped into five distinct, well-supported clades corresponding to five species: A. glabriusculus already known from Pakistan and India, A. robustulus first recorded from Pakistan and briefly described here but already known from Bénin, Malaysia, China, and Thailand, and three possibly endemic new species described in detail A. badiosquamulosus sp. nov., A. dunensis sp. nov., and A. violaceopunctatus sp. nov. The sixth species currently known in Pakistan, including A. latiumbonatus also found in Thailand, were included in a multigene tree based on ITS, LSU, and Tef-1α sequence data. They all belong to a large pantropical paraphyletic group while most temperate species belong to a distinct clade, which includes about half of the species of the section. The current study aims to propose three novel species of genus Agaricus based on comprehensive morphological as well as molecular phylogenetic evidences from Pakistan.

Matched MeSH terms: DNA, Fungal/genetics
Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple

Ismail SI, Batzer JC, Harrington TC, Crous PW, Lavrov DV, Li H, et al.

Mycologia, 2016 Mar-Apr;108(2):292-302.
PMID: 26740537 DOI: 10.3852/15-036

Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi.

Matched MeSH terms: DNA, Fungal/genetics
Durianella, a new gasteroid genus of boletes from Malaysia

Desjardin DE, Wilson AW, Binder M

Mycologia, 2009 2 11;100(6):956-61.
PMID: 19202849

Hydnangium echinulatum, described originally from a single specimen collected in Malaysia, has been recollected, and based on morphological and molecular characters is recognized as representing a new gasteroid genus of boletes with affinities to the Boletineae, herein named Durianella. Diagnostic features include an epigeous, ovoid, pyramidal-warted, durian fruit-like basidiome with gelatinized glebal locules and a columella that turns indigo blue upon exposure, and subglobose basidiospores with long, curved, thin-walled and collapsible spines. A redescription, phylogenetic analysis and comparison with allied taxa are presented.

Matched MeSH terms: DNA, Fungal/genetics
Novel black yeast-like species in chaetothyriales with ant-associated life styles

Quan Y, Ahmed SA, Menezes da Silva N, Al-Hatmi AMS, Mayer VE, Deng S, et al.

Fungal Biol, 2021 04;125(4):276-284.
PMID: 33766306 DOI: 10.1016/j.funbio.2020.11.006

Among ancestral fungi in Chaetothyriales, several groups have a life style in association with tropical ants, either in domatia or in carton-nests. In the present study, two strains collected from ant carton in Thailand and Malaysia were found to represent hitherto undescribed species. Morphological, physiological, phylogenetic data and basic genome information are provided for their classification. Because of the relatively large phylogenetic distances with known species confirmed by overall genome data, large subunit (LSU) and Internal Transcribed Spacer (ITS) ribosomal DNA sequences were sufficient for taxonomic circumscription of the species. The analyzed strains clustered with high statistical support as a clade in the family Trichomeriaceae. Morphologically they were rather similar, lacking sporulation in vitro. In conclusion, Incumbomyces delicatus and Incumbomyces lentus were described as new species based on morphological, physiological and phylogenetic analysis.

Matched MeSH terms: DNA, Fungal/genetics
Fulltext Characterization of Fusarium species section Liseola by restriction analysis of the IGS region

Heng MH, Baharuddin S, Latiffah Z

Genet. Mol. Res., 2012;11(1):383-92.
PMID: 22370941 DOI: 10.4238/2012.February.16.4

Fusarium species section Liseola namely F. fujikuroi, F. proliferatum, F. andiyazi, F. verticillioides, and F. sacchari are well-known plant pathogens on rice, sugarcane and maize. In the present study, restriction analysis of the intergenic spacer regions (IGS) was used to characterize the five Fusarium species isolated from rice, sugarcane and maize collected from various locations in Peninsular Malaysia. From the analysis, and based on restriction patterns generated by the six restriction enzymes, Bsu151, BsuRI, EcoRI, Hin6I, HinfI, and MspI, 53 haplotypes were recorded among 74 isolates. HinfI showed the most variable restriction patterns (with 11 patterns), while EcoRI showed only three patterns. Although a high level of variation was observed, it was possible to characterize closely related species and isolates from different species. UPGMA cluster analysis showed that the isolates of Fusarium from the same species were grouped together regardless of the hosts. We conclude that restriction analysis of the IGS regions can be used to characterize Fusarium species section Liseola and to discriminate closely related species as well as to clarify their taxonomic position.

Matched MeSH terms: DNA, Fungal/genetics
Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species

Avin FA, Bhassu S, Shin TY, Sabaratnam V

Mol Biol Rep, 2012 Jul;39(7):7355-64.
PMID: 22327649 DOI: 10.1007/s11033-012-1567-2

Morphological identification of edible mushrooms can sometimes prove troublesome, because phenotypic variation in fungi can be affected by substrate and environmental factors. One of the most important problems for mushroom breeders is the lack of a systematic consensus tool to distinguish different species, which are sometimes morphologically identical. Basidiomycetes as one of the largest groups of edible mushrooms have become more important in recent times for their medicinal and nutritional properties. Partial rDNA sequences, including the Internal Transcribed Spacer I-5.8SrDNA-Internal Transcribed Spacer II, were used in this study for molecular identification and assessment of phylogenetic relationships between selected edible species of the Basidiomycetes. Phylogenetic trees showed five distinct clades; each clade belonging to a separate family group. The first clade included all the species belonging to the Pleurotaceae (Pleurotus spp.) family; similarly, the second, third, fourth, and fifth clades consist of species from the Agaricaceae (Agaricus sp.), Lyophllaceae (Hypsigygus sp.), Marasmiaceae (Lentinula edodes sp.) and Physalacriaceae (Flammulina velutipes sp.) families, respectively. Moreover, different species of each family were clearly placed in a distinct sub-cluster and a total of 13 species were taken for analysis. Species differentiation was re-confirmed by AMOVA analysis (among the populations: 99.67%; within: 0.33%), nucleotide divergence, haplotyping and P value. Polymorphism occurred throughout the ITS regions due to insertion-deletion and point mutations, and can be clearly differentiated within the families as well as genera. Moreover, this study proves that the sequence of the ITS region is a superior molecular DNA barcode for taxonomic identification of Basidiomycetes.

Matched MeSH terms: DNA, Fungal/genetics*
Fulltext Spongiforma squarepantsii, a new species of gasteroid bolete from Borneo

Desjardin DE, Peay KG, Bruns TD

Mycologia, 2011 Sep-Oct;103(5):1119-23.
PMID: 21558499 DOI: 10.3852/10-433

A gasteroid bolete collected recently in Sarawak on the island of Borneo is described as the new species Spongiforma squarepantsii. A comprehensive description, illustrations, phylogenetic placement and a comparison with a closely allied species are provided.

Matched MeSH terms: DNA, Fungal/genetics
Detection of 10 medically important Candida species by seminested polymerase chain reaction

Than LT, Chong PP, Ng KP, Seow HF

Diagn Microbiol Infect Dis, 2012 Feb;72(2):196-8.
PMID: 22154674 DOI: 10.1016/j.diagmicrobio.2011.10.008

A seminested PCR detecting ten medically important Candida species were achieved. Analytical sensitivity and specificity were not compromised.

Matched MeSH terms: DNA, Fungal/genetics
An alternative Candida spp. cell wall disruption method using a basic sorbitol lysis buffer and glass beads

Lim CS, Tung CH, Rosli R, Chong PP

J Microbiol Methods, 2008 Dec;75(3):576-8.
PMID: 18727938 DOI: 10.1016/j.mimet.2008.07.026

This report describes a modified, cost-effective method of cell wall disruption for the yeast Candida spp., which employs the use of glass beads in a simple sorbitol lysis buffer. This method can be used in conjunction with a commercial RNA or genomic DNA isolation method to obtain high-quality RNA or DNA.

Matched MeSH terms: DNA, Fungal/genetics
Polyancora globosa gen. sp. nov., an aeroaquatic fungus from Malaysian peat swamp forests

Voglmayr H, Yule CM

Mycol. Res., 2006 Oct;110(Pt 10):1242-52.
PMID: 17018253

During an investigation of submerged leaves and twigs sampled from tropical peat swamp forests located in Peninsular Malaysia, an anamorphic fungus not attributable to a described genus was detected and isolated in pure culture. Conidial ontogeny was thoroughly studied and illustrated using both light and SEM, which revealed a unique conidial morphology. Analysis of partial nuLSU rDNA and ITS data revealed a phylogenetic position within the Xylariales (Ascomycota), but family affiliation remained unclear.

Matched MeSH terms: DNA, Fungal/genetics
Isolation and characterisation of a partial peptide synthetase gene from Trichoderma asperellum

Chutrakul C, Peberdy JF

FEMS Microbiol Lett, 2005 Nov 15;252(2):257-65.
PMID: 16214297

Many species of Trichoderma have attracted interest as agents for the biological control of soil borne fungal pathogens of a range of crop plants. Research on the biochemical mechanisms associated with this application has focused on the ability of these fungi to produce enzymes which lyse fungal cell walls, and antifungal antibiotics. An important group of the latter are the non-ribosomal peptides called peptaibols. In this study Trichoderma asperellum, a strain used in biological control in Malaysia, was found to produce the peptaibol, trichotoxin. This type of peptide molecule is synthesised by a peptide synthetase (PES) enzyme template encoded by a peptide synthetase (pes) gene. Using nucleotide sequences amplified from adenylation (A-) domains as probes, to hybridise against a lambda FIXII genomic library from T. asperellum, 25 clones were recovered. These were subsequently identified as representative of four groups based on their encoding properties for specific amino acid incorporation modules in a PES. This was based on analysis of their amino acid sequences which showed up to 86% identity to other PESs including TEX 1.

Matched MeSH terms: DNA, Fungal/genetics
Molecular subtyping of clinical isolates of Candida albicans and identification of Candida dubliniensis Malaysia

Tay ST, Chai HC, Na SL, Ng KP

Mycopathologia, 2005 Apr;159(3):325-9.
PMID: 15883714

The genotypes of 221 recent isolates of Candida albicans from various clinical specimens of 213 patients admitted to the University Malaya Medical Centre, Malaysia was determined based on the amplification of a transposable intron region in the 25 S rRNA gene. The analyses of 178 C. albicans isolated from nonsterile clinical specimens showed that they could be classified into three genotypes: genotype A (138 isolates), genotype B (38 isolates) and genotype C (2 isolates). The genotyping of 43 clinical isolates from sterile specimens showed that they belonged to genotype A (29 isolates), genotype B (10 isolates), genotype C (2 isolates) and genotype D (2 isolates). The overall distribution of C. albicans genotypes in sterile and nonsterile specimens appeared similar, with genotype A being the most predominant type. This study reported the identification of C. dubliniensis (genotype D) in 2 HIV-negative patients with systemic candidiasis, which were missed by the routine mycological procedure. The study demonstrated the genetic diversity of clinical isolates of C. albicans in Malaysia.

Matched MeSH terms: DNA, Fungal/genetics
Three new species of Physalacria from China, with a key to the Asian taxa

Qin J, Yang ZL

Mycologia, 2016 Jan-Feb;108(1):215-26.
PMID: 26553778 DOI: 10.3852/15-166

Three new and one previously described species of Physalacria (Physalacriaceae, Agaricales) are reported from China. Specimens of two additional species described from Malaysia and North America were studied for comparison. Placements of these species were corroborated based on morphological observations and molecular evidence from partial sequences of the nuc rDNA internal transcribed spacer regions (ITS) and the 28S D1-D3 region, and genes for translation elongation factor 1-α (tef1α) and the second largest subunit of RNA polymerase II (rpb2). These new species of Physalacria distributed in subtropical China were found on rotten wood of broadleaf trees or bamboo and possess stipitate-capitate basidiomata with four-spored basidia, clamp connections and smooth, inamyloid basidiospores. To facilitate studies of the genus in Asia, a key is provided for all Physalacria species reported from this region.

Matched MeSH terms: DNA, Fungal/genetics
Morphological and molecular characterization of yellow oyster mushroom, Pleurotus citrinopileatus, hybrids obtained by interspecies mating

Rosnina AG, Tan YS, Abdullah N, Vikineswary S

World J Microbiol Biotechnol, 2016 Feb;32(2):18.
PMID: 26745978 DOI: 10.1007/s11274-015-1959-2

Pleurotus citrinopileatus (yellow oyster mushroom) has an attractive shape and yellow colour but the fragile texture complicates packaging, and its strong aroma is unappealing to consumers. This study aimed to improve the characteristics and yield of P. citrinopileatus by interspecies mating between monokaryotic cultures of P. citrinopileatus and P. pulmonarius. Ten monokaryon cultures of the parental lines were crossed in all combinations to obtain hybrids. Eleven compatible mating pairs were obtained and cultivated to observe their sporophore morphology and yield. The selected hybrid, i.e. P1xC9, was beige in colour while hybrid P3xC8 was yellow in colour. Their sporophores had less offensive aroma, improved texture and higher yield. The DNA sequences of these hybrids were found to be in the same clade as the P. citrinopileatus parent with a bootstrap value of 99%. High bootstrap values indicate high genetic homology between hybrids and the P. citrinopileatus parent. The biological efficiencies of these hybrids P1xC9 (70.97%) and P3xC8 (52.14%) were also higher than the P. citrinopileatus parent (35.63%). Interspecies hybrids obtained by this mating technique can lead to better strains of mushrooms for genetic improvement of the Pleurotus species.

Matched MeSH terms: DNA, Fungal/genetics
Fulltext Issues in identifying germ tube positive yeasts by conventional methods

Yazdanpanah A, Khaithir TM

J Clin Lab Anal, 2014 Jan;28(1):1-9.
PMID: 24375729 DOI: 10.1002/jcla.21635

Candida speciation is vital for epidemiology and management of candidiasis. Nonmolecular conventional methods often fail to identify closely related germ tube positive yeasts from clinical specimens. The present study was conducted to identify these yeasts and to highlight issues in conventional versus molecular methods of identification. A total of 98 germ tube positive yeasts from high vaginal swabs were studied over a 12-month period. Isolates were examined with various methods including growth at 42 °C and 45 °C on Sabouraud dextrose agar (SDA), color development on CHROMagar Candida medium, chlamydospore production on corn meal agar at 25 °C, carbohydrate assimilation using ID 32C system, and polymerase chain reaction using a single pair of primers targeting the hyphal wall protein 1 (Hwp1) gene. Of all the isolates studied, 97 were molecularly confirmed as C. albicans and one isolate was identified as C. dubliniensis. No C. africana was detected in this study. The molecular method used in our study was an accurate and useful tool for discriminating C. albicans, C. dubliniensis, and C. africana. The conventional methods, however, were less accurate and riddled with many issues that will be discussed in further details.

Matched MeSH terms: DNA, Fungal/genetics
Fulltext Morphological and phylogenetic analysis of Fusarium solani species complex in Malaysia

Chehri K, Salleh B, Zakaria L

Microb Ecol, 2015 Apr;69(3):457-71.
PMID: 25238930 DOI: 10.1007/s00248-014-0494-2

Members of Fusarium solani species complex (FSSC) have been known as plant, animal, and human pathogens. Nevertheless, the taxonomic status of such an important group of fungi is still very confusing and many new species as well as lineages have been elucidated recently. Unfortunately, most of the new taxa came from temperate and subtropical regions. Therefore, the objectives of the present study were to identify strains of FSSC recovered from different sources in Malaysia. In the present study, 55 strains belonging to the FSSC were examined and phylogenetically analyzed on the basis of internal transcribed spacer (ITS) regions and partial translation elongation factor-1 (TEF-1α) sequences. Based on morphological features, a total of 55 strains were selected for molecular studies. Based on morphological features, the strains were classified into four described Fusarium species, namely Fusarium keratoplasticum, Fusarium falciforme, FSSC 5, and Fusarium cf. ensiforme, and one unknown phylogenetic species was introduced. Although the data obtained from morphological and molecular studies sufficiently supported each other, the phylogenetic trees based on ITS and TEF-1α dataset clearly distinguished closely related species and distinctly separated all morphological taxa. All members of FSSC in this research were reported for the first time for Malaysian mycoflora.

Matched MeSH terms: DNA, Fungal/genetics
Identification of Botryosphaeriaceae associated with stem-end rot of mango (Mangifera indica L.) in Malaysia

Li L, Mohd MH, Mohamed Nor NMI, Subramaniam S, Latiffah Z

J Appl Microbiol, 2021 Apr;130(4):1273-1284.
PMID: 32813902 DOI: 10.1111/jam.14828

AIMS: To identify Botryosphaeriaceae fungal species that are associated with stem-end rot of mango, and to study their pathogenicity on mango fruit.
METHODS AND RESULTS: Based on the sequences of internal transcribed spacer (ITS), TEF1-α and β-tubulin, as well as on the phylogenetic analysis of combined sequences, four species of Lasiodiplodia (L. theobromae,L. pseudotheobromae, L. iranensis, L. mahajangana) and two species of Neofusicoccum (N. ribis, N. parvum) were identified. Pseudofusicoccum violaceum, Neoscytalidium dimidiatum and three species of Botryosphaeria (B. scharifii, B. dothidea, B. ramosa) were identified based on sequences of ITS and TEF1-α. Pathogenicity test of selected isolates were tested on Chok Anan, Waterlily and Falan mango cultivars. Generally, all species were observed to be pathogenic on the three tested mango cultivars on wounded fruits, except for N. ribis and N. parvum, which were pathogenic on both wounded and unwounded fruits. However, N. ribis was only pathogenic on cultivar Falan, whereas B. ramosa were pathogenic on cultivars Waterlily and Falan.
CONCLUSIONS: Eleven species of Botryosphaeriaceae were associated with mango stem-end rot in Malaysia. To the best of our knowledge, four species, namely L. mahajangana, B. ramosa, N. ribis and P. violaceum are the first recorded Botryosphaeriaceae fungi associated with stem end rot of mango.
SIGNIFICANCE AND IMPACT OF THE STUDY: The identification of Botryosphaeriaceae fungi is important to establish suitable control measures and quarantine requirements. Many species have a wide host range, which means that there is a possibility of cross infection from other infected plants.

Matched MeSH terms: DNA, Fungal/genetics
Evidence for a general-purpose genotype in Candida albicans, highly prevalent in multiple geographical regions, patient types and types of infection

Schmid J, Herd S, Hunter PR, Cannon RD, Yasin MSM, Samad S, et al.

Microbiology (Reading), 1999 Sep;145 ( Pt 9):2405-2413.
PMID: 10517593 DOI: 10.1099/00221287-145-9-2405

Epidemiological studies, using the probe Ca3, have shown that in a given patient population a single cluster of genetically related Candida albicans isolates usually predominates. The authors have investigated whether these local clusters are part of a single group, geographically widespread and highly prevalent as an aetiological agent of various types of candidiasis. An unrooted neighbour-joining tree of 266 infection-causing C. albicans isolates (each from a different individual) from 12 geographical regions in 6 countries was created, based on genetic distances generated by Ca3 fingerprinting. Thirty-seven per cent of all isolates formed a single genetically homogeneous cluster (cluster A). The remainder of isolates were genetically diverse. Using the maximum branch length within cluster A as a cut-off, they could be divided into 37 groups, whose prevalence ranged between 0.3% and 9%. Strains from cluster A were highly prevalent in all but one geographical region, with a mean prevalence across all regions of 41%. When isolates were separated into groups based on patient characteristics or type of infection, strains from cluster A had a prevalence exceeding 27% in each group, and their mean prevalence was 43% across all patient characteristics. These data provide evidence that cluster A constitutes a general-purpose genotype, which is geographically widespread and acts as a predominant aetiological agent of all forms of candidiasis in all categories of patients surveyed.

Matched MeSH terms: DNA, Fungal/genetics
Notes on Amanita section Caesareae from Malaysia

Tang LP, Lee SS, Zeng NK, Cai Q, Zhang P, Yang ZL

Mycologia, 2017 12 04;109(4):557-567.
PMID: 29200380 DOI: 10.1080/00275514.2017.1394789

Some Amanita specimens collected from Malaysia are critically investigated by morphological examination and molecular analysis of two gene fragments, the nuc rDNA partial 28S (28S) gene and the internal transcriber spacer (ITS1-5.8S-ITS2 = ITS) regions. Six phylogenetic species of Amanita section Caesareae are recognized among the studied collections. One of them is described as new, A. malayensis. Four of the phylogenetic species correspond with existing morphology-based taxa: A. aporema, A. javanica, A. princeps, and A. similis. The remaining species is not described because of the paucity of material. Detailed descriptions and the distribution of these southeastern Asian species are provided, along with a key to the species of section Caesareae from Malaysia.

Matched MeSH terms: DNA, Fungal/genetics
Fulltext Diversity of fungal pathogens associated with loquat and development of novel virulence scales

Fahim Abbas M, Batool S, Khaliq S, Mubeen S, Azziz-Ud-Din, Ullah N, et al.

PLoS One, 2021;16(10):e0257951.
PMID: 34648523 DOI: 10.1371/journal.pone.0257951

Loquat [Eriobotrya japonica (Thunb.) Lindl.] is an important fruit crop in Pakistan; however, a constant decline in its production is noted due biotic and abiotic stresses, particularly disease infestation. Fungal pathogens are the major disease-causing agents; therefore, their identification is necessary for devising management options. This study explored Taxila, Wah-Cantt, Tret, Chatar, Murree, Kalar-Kahar, Choa-Saidan-Shah and Khan-Pur districts in the Punjab and Khyber Paktoon Khawa (KPK) provinces of Pakistan to explore the diversity of fungal pathogens associated with loquat. The samples were collected from these districts and their microscopic characterizations were accomplished for reliable identification. Alternaria alternata, Curvularia lunata, Lasiodiplodia theobromae, Aspergilus flavis, Botrytis cinerea, Chaetomium globosum, Pestalotiopsis mangiferae and Phomopsis sp. were the fungal pathogens infesting loquat in the study area. The isolates of A. alternata and C. lunata were isolated from leaf spots and fruit rot, while the isolates of L. theobromae were associated with twig dieback. The remaining pathogens were allied with fruit rot. The nucleotide evidence of internal transcribed spacer (ITS) regions (ITS1, 5.8S, and ITS2) were computed from all the pathogens and submitted in the database of National Center for Biotechnology Information (NCBI). For multigene analysis, beta-tubulin (BT) gene and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) regions were explored for A. alternata and C. lunata isolates, respectively. The virulence scales of leaf spots, fruit rot, and twig dieback diseases of loquat were developed for the first time through this study. It is the first comprehensive study with morpho-molecular identification, and newly developed virulence scales of the fungal pathogens associated with loquat, which improves the understanding of these destructive diseases.

Matched MeSH terms: DNA, Fungal/genetics

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