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Background: We report two cases of fungal endophthalmitis induced by Candida species identified based on internal transcribed spacer 1 (ITS1) sequencing. Case presentation: In two cases, endophthalmitis was suspected, and the patients underwent pars plana vitrectomy. Case 1 was a 64-year-old woman with a history of cataract surgery 10 days prior. She had a history of anal primary melanoma, which metastasized throughout the body and subsequently relapsed. Vitreous culture and ITS-1 deep sequencing revealed the presence of the rare fungus, Candida dubliniensis. Case 2 was a 54-year-old man with a history of liver cancer and kidney failure. Culture methods and ITS1 deep sequencing both revealed the presence of Candida albicans. Both patients exhibited good visual prognoses after treatment with topical and systemic antibiotics. Conclusions: We present two cases of fungal endophthalmitis caused by two Candida species identified by both the culture method and ITS1 deep sequencing. The fungal pathogen was identified by ITS deep sequencing three days after sample submission; the culture method yielded results after 1 week. These findings support the applicability of ITS1 sequencing for timely pathogen identification for cases of fungal endophthalmitis and provide detailed taxonomic information at the species level. [ABSTRACT FROM AUTHOR]

Abstract Background We report two cases of fungal endophthalmitis induced by Candida species identified based on internal transcribed spacer 1 (ITS1) sequencing. Case presentation In two cases, endophthalmitis was suspected, and the patients underwent pars plana vitrectomy. Case 1 was a 64-year-old woman with a history of cataract surgery 10 days prior. She had a history of anal primary melanoma, which metastasized throughout the body and subsequently relapsed. Vitreous culture and ITS-1 deep sequencing revealed the presence of the rare fungus, Candida dubliniensis. Case 2 was a 54-year-old man with a history of liver cancer and kidney failure. Culture methods and ITS1 deep sequencing both revealed the presence of Candida albicans. Both patients exhibited good visual prognoses after treatment with topical and systemic antibiotics. Conclusions We present two cases of fungal endophthalmitis caused by two Candida species identified by both the culture method and ITS1 deep sequencing. The fungal pathogen was identified by ITS deep sequencing three days after sample submission; the culture method yielded results after 1 week. These findings support the applicability of ITS1 sequencing for timely pathogen identification for cases of fungal endophthalmitis and provide detailed taxonomic information at the species level.

The affinities of the Ocotea species from Cuba are examined based on sequences of the nuclear ITS region and the chloroplast psbA‐trnH spacer, supplemented by SEM studies on stomatal morphology. The species with bisexual flowers, all of them endemic either to the Greater Antilles or Cuba only, form (at least) two phylogenetically distinct groups. Ocotea bucheri, O. libanensis, O. moaensis, O. reticularis, and an undescribed species, all of them endemics of Eastern Cuba, form the sister group to the genus Damburneya. The remaining species form two clades nested in the Praelicaria clade. It remains uncertain if these two clades are sister to each other or not. The two widespread dioecious species show the expected affinities to conspecific material from other parts of the Neotropics. [ABSTRACT FROM AUTHOR]

Lyophyllum consists of rare edible and medicinal mushrooms. Considering this group's economic and ecological significance, understanding its biodiversity could be strategically important. Our analysis involved an extensive examination of publicly available ITS sequences from NCBI-GenBank and fungal amplicon sequencing data obtained from NCBI-SRA. At a 98% sequence similarity level, we deliminated 88 Lyophyllum OTUs, 49 of which were not categorized as 'known species'. The diversity of Lyophyllum is predominantly concentrated in the Northern Hemisphere and tends to display endemic distribution, and Europe is particularly notable for its high diversity of Lyophyllum. Given the escalating volume of data produced by amplicon sequencing, employing the amplicon dataset can facilitate an accurate survey of species diversity in Lyophyllum taxonomy. By using data from amplicon datasets, the fieldwork time and research funding for taxonomists can be saved, thereby significantly advancing the progress of the entire field of biodiversity research. [ABSTRACT FROM AUTHOR]

Summary: Between 1959 and 1988, three populations of purple-flowered terrestrial orchids attributable to Dactylorhiza subgenus Dactylorhiza were discovered in Canada. The populations at Timmins, Ontario, and St John's, Newfoundland were strongly marked on both flowers and leaves, in contrast with the anthocyanin-deficient population at Tilt Cove, Newfoundland. All three populations have since experienced a wide range of taxonomic assignments; debates are also ongoing regarding their origin and most appropriate conservation status. Here, we address these questions by combining detailed in situ morphometric analyses based on 52 characters with allozyme profiles and data from nrITS, 15 plastid microsatellites and seven nuclear microsatellites. The allozyme data alone are sufficient to both confirm allopolyploidy and categorically refute past assignments of these populations to D. incarnata, D. maculata, D. fuchsii, D. majalis or D. purpurella. Several morphometric characters, nuclear microsatellites and nrITS all reliably distinguish each of the three study populations, whereas the two sampled subpopulations from St John's proved near-identical morphologically. In contrast, morphological variation within each of the three populations is strikingly low, particularly in characters other than those influenced by plant vigour. Similarly, compared with 14 European populations, the three Canadian populations proved genetically impoverished (two were near-invariant) and likely experienced recent, extreme genetic bottlenecks during establishment. The three populations differ substantially, both morphologically and molecularly, therefore probably representing independent immigration events. Although clearly attributable to D. praetermissa, all three populations deviate significantly in morphology and DNA data from comparable populations sampled across Europe, preventing identification of their precise geographic origins. Any attempt to determine their mode or origin — through natural long-distance transport, or accidental or deliberate introduction by humans – is challenged to explain why three lineages of a single European Marsh-orchid species, each in different ways atypical of that species, arrived independently in North America whereas no other European dactylorchid species has become established there. [ABSTRACT FROM AUTHOR]

As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi‐marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior‐supported primers for immediate applications. The ITS2 was the best‐performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications. [ABSTRACT FROM AUTHOR]

The humid climatic condition of the Koraput district of the eastern ghat of Odisha, India favors the growth of a diverse range of microbial and fungal strains, which not only lay scathing consequences on the environment but also prove to be beneficial in many industrial and biotechnological sectors. Hence, proper exploration of their roles and impacts is the necessity for an hour. With this goal, the present study reports on the identification and molecular characterization of the fungal strain collected from Koraput district of the eastern ghat of Odisha. The fungal strain was cultured, isolated, and identified using Internal transcribed spacer (ITS) 18S rRNA-specific primers. The estimation of fungal biomass was carried out by taking the dry weight of fungal mycelia after 48, 72, 96, and 120 hours of inoculation, which showed an increase in biomass (in w/w) exponentially. The fungal isolate (CAR02) was identified as Rhizopus delemar with GenBank accession number OQ683833. The SDS PAGE protein analysis showed more intensified and concentrated multiple fungal protein bands ranging from 13 to 97 kDa. ELISA (Enzyme- Linked Immunosorbent Assay) was used to estimate the antigenicity of the isolated R. delemar proteins from soil samples of Koraput. The proteins of Pythium species with an absorbance value of 1.5 shared 50-60% of similar antigenic sequences with the R. delemar proteins. Hence, the findings of our investigation suggests that the obtained antigenic sequences could further be used to isolate its epitopic specific regions that are responsible for the rot infections, against which antibodies could be developed. Further study is required to explore the rot causing fungal diversity in the soil of eastern ghats which will be helpful in designing novel disease diagnostic strategies in agriculture sectors. Furthermore, this identified fungus can also be used to synthesize various enzymes that will aid in the production of commercially significant by-products. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum L.) ranks as the second most important vegetable crop globally, but its production and quality are known to be largely affected by many pest and diseases. One of the major hindrances to tomato production is the fungal disease caused by Alternaria spp. In the current study we isolated, visually examined and characterized the fungal pathogen both morphologically and at the molecular level were carried by employing standard techniques for tissue isolation, microscopic observations and PCR methods. Under the microscope, morphological features like dark brown to blackish mycelium with prominent septations and muriform conidia with horizontal and transverse septations were observed. To delve deeper into their genetic makeup, the molecular characterization of pathogens was done by amplification, sequencing of Internal Transcribed Spacer (ITS1/ITS4) and phylogenetic analysis. This allowed us to gain insights into the genetic identity of these pathogens. Furthermore, phylogenetic analysis shed light on the evolutionary relationships within the group of fungi we studied. This comprehensive approach provides a deeper understanding of Alternaria spp. in the context of tomato cultivation and offers valuable knowledge for disease management and sustainable tomato production. [ABSTRACT FROM AUTHOR]

(1) The fungal genus Simplicillium (Cordycipitaceae: Hypocreales) has an extensive distribution and a broad spectrum of hosts and substrates. The species Simplicillium lanosoniveum is a mycoparasite with potential for biological control of coffee leaf rust, Hemileia vastatrix. Morphologically, Simplicillium closely resembles mycoparasitic and entomopathogenic Lecanicillium fungi, often resulting in misidentification. A fungal isolate was obtained from leaf-rust-infested coffee plants from Cienfuegos Province, Cuba. (2) Combined analyses of morphology and molecular markers (ITS, LSU, EF-1alpha) were used for fungal identification. (3) In the NJ, ML, and BI phylogenies which were reconstructed, the isolate LBSim-01 was located in the Simplicillium lanosoniveum clade. This species-level identification was supported by morphological features. (4) The isolate LBSim-01 was assigned to the species Simplicillium lanosoniveum. This is the first description of a Simplicillium fungus associated with coffee leaf rust in Cuba. The presented results hold implications for the biological control of this economically relevant plant disease. [ABSTRACT FROM AUTHOR]

Lyophyllum consists of rare edible and medicinal mushrooms. Considering this group’s economic and ecological significance, understanding its biodiversity could be strategically important. Our analysis involved an extensive examination of publicly available ITS sequences from NCBI-GenBank and fungal amplicon sequencing data obtained from NCBI-SRA. At a 98% sequence similarity level, we deliminated 88 Lyophyllum OTUs, 49 of which were not categorized as ‘known species’. The diversity of Lyophyllum is predominantly concentrated in the Northern Hemisphere and tends to display endemic distribution, and Europe is particularly notable for its high diversity of Lyophyllum. Given the escalating volume of data produced by amplicon sequencing, employing the amplicon dataset can facilitate an accurate survey of species diversity in Lyophyllum taxonomy. By using data from amplicon datasets, the fieldwork time and research funding for taxonomists can be saved, thereby significantly advancing the progress of the entire field of biodiversity research.

Abstract Background Fritillariae Cirrhosae Bulbus is an antitussive and expectorant Chinese medicinal material derived from the dried bulbs of six Fritillaria species. In the 2015 edition of the Chinese Pharmacopoeia, the polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) is the officially listed method for their authenfication. Specifically, the ~ 300-bp ITS1 amplicon of only Fritillariae Cirrhosae Bulbus but not other Fritillaria species can be cleaved into two smaller fragments with restriction enzyme SmaI. Considering repeated reported cases of incomplete digestion of ITS1 amplicon, this study aims to investigate the possibility of heterogeneous ITS1 sequences contained in the Fritillariae Cirrhosae Bulbus. Methods In this study, ITS1 amplicons of Fritillaria Cirrhosae Bulbus and four other Fritillaria species were sequenced on Illumina platform. We utilised high-throughout amplicon sequencing to determine ITS1 haplotypes and their frequencies in Fritillaria genomes. Results Our results showed that all six botanical sources of Fritillariae Cirrhosae Bulbus indeed possess ITS1 haplotypes with no SmaI restriction site, and the average percentages of ITS1 reads containing SmaI restriction site ranged from 63.60% to 91.81%. Conclusion Our findings suggest that the incomplete digestion in PCR–RFLP analysis of Fritillariae Cirrhosae Bulbus is caused by the presence of ITS1 haplotypes without SmaI restriction site due to intragenomic heterogeneity.

Aspergillus species are among the most significant producers of aflatoxins, which can contaminate a wide range of agricultural and food products at any stage of production. The aim of this research was to utilize molecular methods to determine and characterize the variability between isolates of standard Aspergillus species. Genomic DNA was isolated from the mycelium of all tested Aspergillus isolates. PCR amplifications were performed using gene-specific primers. The PCR method successfully amplified the ITS1-5.8S rDNA-ITS2 region and portions of the b-tubulin and calmodulin genes of all tested Aspergillus isolates. PCR products obtained after amplification with primer pairs (ITS1/ITS4 and Bt2a/Bt2b), followed by digestion with restriction enzymes HhaI, MwoI, and AlwI in RFLP analysis, facilitated the identification of variability among the studied Aspergillus species. The results of PCR-RFLP analysis on the tested isolates were consistent with those previously obtained through morphological examinations, indicating the effectiveness of this molecular method for identification and determination of variability among important Aspergillus species. The presented molecular method based on PCR-RFLP analysis, due to its advantages such as reproducibility, speed, and high sensitivity, represents a valuable tool for monitoring and controlling contamination by Aspergillus species in the food supply chain. The method described in this study can be successfully used for rapid identification and determination of variability between isolates of Aspergillus species, contributing to improved food safety control and public health.

(1) The fungal genus Simplicillium (Cordycipitaceae: Hypocreales) has an extensive distribution and a broad spectrum of hosts and substrates. The species Simplicillium lanosoniveum is a mycoparasite with potential for biological control of coffee leaf rust, Hemileia vastatrix. Morphologically, Simplicillium closely resembles mycoparasitic and entomopathogenic Lecanicillium fungi, often resulting in misidentification. A fungal isolate was obtained from leaf-rust-infested coffee plants from Cienfuegos Province, Cuba. (2) Combined analyses of morphology and molecular markers (ITS, LSU, EF-1alpha) were used for fungal identification. (3) In the NJ, ML, and BI phylogenies which were reconstructed, the isolate LBSim-01 was located in the Simplicillium lanosoniveum clade. This species-level identification was supported by morphological features. (4) The isolate LBSim-01 was assigned to the species Simplicillium lanosoniveum. This is the first description of a Simplicillium fungus associated with coffee leaf rust in Cuba. The presented results hold implications for the biological control of this economically relevant plant disease.

AbstractWood-decaying fungi are essential decomposers in forest ecosystems. They decompose wood substrates by producing various lignocellulolytic enzymes, which have significant industrial and medical applications. A survey was conducted at the Juwangsan National Park from 2018 to 2019 to determine the diversity of macrofungi in Korea. Five previously unrecorded wood-decaying polyporoid and corticioid fungi were identified among the collected specimens: Eichleriella sinensis, Hymenochaete anomala, Hyphoderma subsetigerum, Lyomyces orientalis, and Pseudowrightoporia crassihypha. These species were identified based on morphological, molecular, and phylogenetic analyses of the internal transcribed spacer (ITS) and nuclear large subunit rDNA (nLSU) region. In this study, we provide detailed macro- and micro-morphological figures with phylogenetic trees to support the discovery of five new species in Korea.

Background: Fritillariae Cirrhosae Bulbus is an antitussive and expectorant Chinese medicinal material derived from the dried bulbs of six Fritillaria species. In the 2015 edition of the Chinese Pharmacopoeia, the polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) is the officially listed method for their authenfication. Specifically, the ~ 300-bp ITS1 amplicon of only Fritillariae Cirrhosae Bulbus but not other Fritillaria species can be cleaved into two smaller fragments with restriction enzyme SmaI. Considering repeated reported cases of incomplete digestion of ITS1 amplicon, this study aims to investigate the possibility of heterogeneous ITS1 sequences contained in the Fritillariae Cirrhosae Bulbus. Methods: In this study, ITS1 amplicons of Fritillaria Cirrhosae Bulbus and four other Fritillaria species were sequenced on Illumina platform. We utilised high-throughout amplicon sequencing to determine ITS1 haplotypes and their frequencies in Fritillaria genomes. Results: Our results showed that all six botanical sources of Fritillariae Cirrhosae Bulbus indeed possess ITS1 haplotypes with no SmaI restriction site, and the average percentages of ITS1 reads containing SmaI restriction site ranged from 63.60% to 91.81%. Conclusion: Our findings suggest that the incomplete digestion in PCR–RFLP analysis of Fritillariae Cirrhosae Bulbus is caused by the presence of ITS1 haplotypes without SmaI restriction site due to intragenomic heterogeneity. [ABSTRACT FROM AUTHOR]

Wood-decaying fungi are essential decomposers in forest ecosystems. They decompose wood substrates by producing various lignocellulolytic enzymes, which have significant industrial and medical applications. A survey was conducted at the Juwangsan National Park from 2018 to 2019 to determine the diversity of macrofungi in Korea. Five previously unrecorded wood-decaying polyporoid and corticioid fungi were identified among the collected specimens: Eichleriella sinensis, Hymenochaete anomala, Hyphoderma subsetigerum, Lyomyces orientalis, and Pseudowrightoporia crassihypha. These species were identified based on morphological, molecular, and phylogenetic analyses of the internal transcribed spacer (ITS) and nuclear large subunit rDNA (nLSU) region. In this study, we provide detailed macro- and micro-morphological figures with phylogenetic trees to support the discovery of five new species in Korea. [ABSTRACT FROM AUTHOR]

Angelica (Apiaceae) is a large complex genus with high morphological diversity. The many taxonomic treatments explain the controversy regarding the number of European species, which range from four to ten. Molecular methods have unraveled the complicated Asian and American taxonomies; however, no comprehensive molecular study has been conducted on the European taxa. We aim to determine the number of different European Angelica s.l. taxa and their relationship within the Selineae tribe by conducting Maximum Likelihood (ML) and Bayesian Inference (BI) analyses based on the nuclear Internal Transcribed Spacer (ITS) and haplotype networks by Templeton Crandall and Sing and neighbour-net analyses based on the plastid trnL. Three separate Iberian species (A. angelicastrum, A. razulii and A. pyrenaea) form the new Iberian Angelica clade, which is sister to the Archangelica clade. Although morphologically different, A. pachycarpa cannot be differentiated from A. angelicastrum by molecular methods, casting new doubts on the existing taxonomies. Molecular evidences suggest that A. heterocarpa should be considered an estuary forma of A. sylvestris. The east and west A. sylvestris subclades support the subspecies A. sylvestris subsp. elatior and A. sylvestris subsp. villosa (including A. heterocarpa). Our evidences support the classification of A. palustris as Ostericum palustre. [ABSTRACT FROM AUTHOR]

The harmful algal bloom (HAB) species Pseudo-nitzschia multiseries is widely distributed worldwide and is known to produce the neurotoxin domoic acid, which harms marine wildlife and humans. Early detection and preventative measures are more critical than late management. However, the major challenge related to early detection is the accurate and sensitive detection of microalgae present in low abundance. Therefore, developing a sensitive and specific method that can rapidly detect P. multiseries is critical for expediting the monitoring and prediction of HABs. In this study, a novel assay method, recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD), is first developed for the detection of P. multiseries. To obtain the best test results, several important factors that affected the amplification effect were optimized. The internal transcribed spacer sequence of the nuclear ribosomal DNA from P. multiseries was selected as the target region. The results showed that the optimal amplification temperature and time for the recombinase polymerase amplification (RPA) of P. multiseries were 37 °C and 15 min. The RPA products could be visualized directly using the lateral flow dipstick after only 3 min. The RPA-LFD assay sensitivity for detection of recombinant plasmid DNA (1.9 × 100 pg/μL) was 100 times more sensitive than that of RPA, and the RPA-LFD assay sensitivity for detection of genomic DNA (2.0 × 102 pg/μL) was 10 times more sensitive than that of RPA. Its feasibility in the detection of environmental samples was also verified. In conclusion, these results indicated that the RPA-LFD detection of P. multiseries that was established in this study has high efficiency, sensitivity, specificity, and practicability. Management measures made based on information gained from early detection methods may be able to prevent certain blooms. The use of a highly sensitive approach for early warning detection of P. multiseries is essential to alleviate the harmful impacts of HABs on the environment, aquaculture, and human health. [ABSTRACT FROM AUTHOR]

Ganoderma is a genus of biomedical fungus that is used in the development of numerous health products throughout the world. The Lower Volta River Basin of Ghana is an undulating land surface covered by extensive vegetation and water bodies and is rich in polypore mushrooms resembling various members of the Ganoderma genus. Despite the extensive biopharmaceutical benefits of Ganoderma spp., the isolates from the Lower Volta River Basin have not been properly characterized, thus limiting their use in the development of biotechnological products. In this study, Ganoderma spp. collected from the Lower Volta River Basin were genetically analyzed using the nuclear ribosomal sequences, the internal transcribed spacer 2 (ITS 2), the complete internal transcribed spacer (ITS), and the nuclear large subunit (nLSU). Blastn search and sequence analysis revealed that the sample we coded as Ganoderma LVRB-2 belongs to G. mbrekobenum, whereas Ganoderma LVRB-1, Ganoderma LVRB-14, and Ganoderma LVRB-16 belong to the species G. enigmaticum. Our analysis further demonstrates that Ganoderma LVRB-17 belongs to the species G. resinaceum. Thus, the five samples collected in the present study were positioned in three different distinct groups, namely G. mbrekobenum, G. enigmaticum, and G. resinaceum. The current data may serve as reference points for future studies. [ABSTRACT FROM AUTHOR]

Copyright of Mesopotamian Journal of Marine Science is the property of Republic of Iraq Ministry of Higher Education & Scientific Research (MOHESR) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This study developed a PCR‐based mating‐type analysis of 30 intraspecific Beauveria bassiana isolates after ITS phylogenetic analysis. Out of 30 isolates, only 11 B. bassiana isolates, viz., Bb4, Bb5, Bb11, Bb18, Bb19, Bb20, Bb23, Bb25, Bb27, Bb28, and Bb29, exhibited amplification of the mating‐type loci and were thought to be heterothallic. All of these isolates, with the exception of Bb20, had MAT1 mating‐type amplification. All these 11 isolates were clustered together with the MAT1‐ and MAT2‐specific reference strains of B. bassiana in the maximum likelihood phylogenetic analysis of mating‐type genes (IFO 31953 and IFO 31676, respectively). Although the PCR products obtained by the mating‐type assay were short, the phylogenetic trees of the mating‐type genes gave better resolution than that of the ITS region. Understanding the mating type of fungi can clarify the biological species concept and the identification of sex‐related genes in fungi without the presence of teleomorphs. So, combining phylogenetic, developmental, and mating research on each teleomorph specimen has the potential to clarify the systematics of Beauveria species. [ABSTRACT FROM AUTHOR]

This report provides the first record of Prosthogonimus cuneatus infection in Indian peafowl. Chickens, turkeys, geese, ducks, and other pet birds are recognized as direct hosts of Prosthogonimus species; however, P. cuneatus has not been reported to infect peafowl globally. Here, we identify the trematode present in the bursa of the peafowl by both morphological and molecular methods, in addition to the changes in the bursal tissue induced by the parasite, using histopathology. After a necropsy examination, the trematodes were found in the bursa of Fabricius in three peafowl. Morphological and molecular approaches based on taxonomic characteristics and the sequencing of the trematode-specific internal transcribed spacer (ITS) gene, respectively, were employed for trematode identification. The consensus sequences were compared to P. cuneatus reference sequences from GenBank. In order to assess the pathology caused by the parasite, a histological study of the bursa was also performed. Trematodes were confirmed as P. cuneatus based on morphology and DNA sequencing. Further, histopathological evaluation revealed mild lymphoid depletion of the bursal follicles in both the cortex and medulla with associated thinning of the bursal follicular lining epithelium. Indian peafowl can act as a natural host of P. cuneatus. This study provides a detailed pathological and molecular analysis of P. cuneatus affecting Indian peafowl. [ABSTRACT FROM AUTHOR]

Shorea robusta Gaertn. (sal) forests are rapidly decreasing across India owing to the low survival rate and establishment of their seedlings. Because of this, the present study identified ectomycorrhizal (ECM) associates of S. robusta and the role they play in increasing the growth and efficiency of nutrient uptake by the mycorrhizal roots of this plant. During the field survey we identified, collected, cultured and systematically investigated three dominant ECM associates of S. robusta: Russula kanadii Dutta & Acharya, R. cyanoxantha (Schaeff.) Fr. and Lactarius shiwalikensis Kumar and Atri, organically connected to the host plant roots. Pure cultures of each of these mycorrhizal fungal associates were grown using tissue culture techniques. We prepared spawn via purified mycelium using boiled wheat grains for mass inoculation and used the prepared inoculums for inoculating the germinating sal seeds for establishing the mycorrhizal association. To evaluate the effects of mycorrhizal colonization on various growth parameters, we observed the inoculated and control plants every three months for one year. The growth parameters in the sal seedlings grown in ECM‐inoculated soil exhibited significantly higher values over the un‐inoculated control soil owing to the increased uptake of both macro‐ and micronutrients. The overall results indicate that S. robusta seedlings inoculated with ECM fungal partners exhibited better establishment and enhanced growth and development, essential for the regeneration and survival of this plant. This technique will accelerate and assure successful reforestation programs and contribute toward appropriate functioning of sal forest ecosystems. [ABSTRACT FROM AUTHOR]

Copyright of Die Dermatologie is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The mangosteen (Garcinia mangostana L.) germplasm still has limitations in fruit quality, drought tolerance and susceptibility to pests or diseases. This study investigated the genetic diversity and relationships of mangosteen with its wild relatives (Garcinia spp.) based on leaf morphology and the internal transcribed spacer (ITS) region, including its secondary structure.Based on leaf morphology, the mangosteen and its wild relatives generally showed a low genetic diversity. However, the leaf texture and pubescence had a high genetic diversity (0.71 and 0.77, respectively). Furthermore, based on the ITS markers, the genetic diversity of Garcinia at the interspecies level was much higher than that at the intraspecies one (0.043 and 0.005, respectively). The unweighted pair group method with the arithmetic average (UPGMA) revealed that mangosteen is grouped into four main clusters, with ‘Manggis Banjar’ and ‘Palembang’ in the same cluster. Similarly, the ITS positioned Garcinia into several clades, with ‘Manggis Banjar’, ‘Kandangan’ and ‘Palembang’ grouped into a similar clade. The biochemical reconstruction showed that Garcinia has unique ITS secondary structures, i.e., ring and four-helix models. Even though the cultivated mangosteen and its wild relatives had low diversity based on leaf morphology, the ITS markers showed a high genetic diversity. Furthermore, the reconstruction of the ITS secondary structure has supported this germplasm’s phylogenetic tree.

Intestinal microsporidiosis is most often caused by Enterocytozoon bieneusi, and to a lesser extent by species of the genus Encephalitozoon. Until now, Encephalitozoon hellem was not clearly known to induce disease restricted to the intestine, or rarely in HIV subjects or in tropical countries. We report here 11 cases of delineated intestinal microsporidioses due to E. hellem diagnosed in France in non-HIV patients. Briefly, all patients were immunocompromised. They all suffered from diarrhoea, associated in nearly 50% of cases with weight loss. Concerning treatment, 5/11 patients had a discontinuation or a decrease of their immunosuppressive therapy, and 4/11 received albendazole. All patients recovered. Five different genotypes were identified based on the rRNA ITS sequence.

Fungi play key roles in forest soils and provide benefits to trees via mycorrhizal symbioses. After severe disturbance, forest regrowth can be impeded because of changes in fungal communities. In 2013–2014, soil fungi in forest floor and mineral soil were examined by Roche 454 pyrosequencing in undisturbed, harvested, and burned jack pine stands in a forested area near Fort Chipewyan, Alberta. These fungal communities were compared with jack pine, white spruce, and larch stands in Gateway Hill, a nearby certified reclaimed area. In 2014, a more detailed sampling of forestry and reclamation jack pine sites examined fungi in soil fractions using two high-throughput sequencing platforms and a sporocarp survey. The significances of compositional and functional differences in fungal communities between the forested and reclamation sites were assessed using permutation tests of partially constrained ordinations, accounting for confounding factors by variance partitioning. Taxa associated with the forestry area were primarily ectomycorrhizal. Fungal richness and diversity were greater in soils from the reclamation sites and included significantly more pathogenic taxa and taxa with unknown functional properties. Fungal community dissimilarities may have been artefacts of historical legacies or, alternatively, may have resulted from contrasting niche differentiation between forestry and reclamation sites. [ABSTRACT FROM AUTHOR]

Trichoderma longibrachiatum rarely reported can cause disease in plants. The present study investigates the pathogenicity of T. longibrachiatum isolate UPMT14 on the red leaf lettuce (Lactuca sativa L.) plants grown in sterile soil under a controlled growth room environment. The fungal isolate was initially characterized morphologically as Trichoderma sp. and was then further characterized by (ITS) region sequencing and BLAST comparison identified as T. longibrachiatum. To observe the response of Trichoderma isolate UPMT14 when imposed on lettuce plants. The injection was made and repeated five times, and then the lettuce growth followed for 36 days. On day 36, the present study found that the red leaf lettuce plants expressed foliar symptoms that began as chlorotic, reduced plant height, reduced leaf length and diameter, wilt, and dried up before it collapsed at day 45 compared to untreated control lettuce plants. Microscopic observation on lettuce roots showed that the Trichoderma spores invading the root system by mass sporulation and spatial competition possibly impaired plant water uptake and eventually caused plant wilting. Therefore, this study indicates that T. longibrachiatum is among the causal agents of wilt disease in the lettuce plant. [ABSTRACT FROM AUTHOR]

Phyllodistomum is the large digenean group of fish parasites, with 25 species described so far in the Indian subcontinent. Here, we redescribed two adult species of Phyllodistomum (P. srivastava Rai 1964 and P. parorchium Jaiswal 1957) collected from freshwater fish Heteropneustes fossilis Bloch, 1974 and Glossogobius giuris Ham, 1822, respectively, and an unknown Phyllodistomum metacercaria from shrimp (Macrobrachium dayanum Henderson, 1893). These parasites were genetically characterized using 28S and first and second internal transcribed spacers (ITS1 and ITS2) regions of the nuclear ribosomal DNA and CoxI region of the mitochondrial (mt) DNA to establish the link between metacercaria and adult. Morphologically, both the unknown metacercaria in shrimp and adult Phyllodistomum srivastava in fish, resembled in terms of crenulated margin of hind body, arrangement of diagonal testes, bipartite seminal vesicle, and compact paired vitelline masses. The two adult parasite species, P. srivastava from P. parorchium, were different in terms of shape and size of the body, ratio of suckers, the absence of crenulated margin of hind body, a single chambered seminal vesicle, and deeply lobed paired vitelline masses, in the former species. Comparison of the 28S, ITS, and mtCoxI sequence data suggested P. srivastava and Phyllodistomum metacercaria belong to the same species, and supported the distinction between P. srivastava and P. parorchium. Exploring the potential impact of Phyllodistomum infection on host behaviour and health would be prospective areas for future research. [ABSTRACT FROM AUTHOR]

Genome or genomic dominance (GD) is a phenomenon observed in hybrids when one parental genome becomes dominant over the other. It is manifested by the replacement of chromatin of the submissive genome by that of the dominant genome and by biased gene expression. Nucleolar dominance (ND) - the functional expression of only one parental set of ribosomal genes in hybrids - is another example of an intragenomic competitive process which, however, concerns ribosomal DNA only. Although GD and ND are relatively well understood, the nature and extent of their potential interdependence is mostly unknown. Here, we ask whether hybrids showing GD also exhibit ND and, if so, whether the dominant genome is the same. To test this, we used hybrids between Festuca and Lolium grasses (Festulolium), and between two Festuca species in which GD has been observed (with Lolium as the dominant genome in Festulolium and F. pratensis in interspecific Festuca hybrids). Using amplicon sequencing of ITS1 and ITS2 of the 45S ribosomal DNA (rDNA) cluster and molecular cytogenetics, we studied the organization and expression of rDNA in leaf tissue in five hybrid combinations, four generations and 31 genotypes [F. pratensis × L. multiflorum (F1, F2, F3, BC1), L. multiflorum × F. pratensis (F1), L. multiflorum × F. glaucescens (F2), L. perenne × F. pratensis (F1), F. glaucescens × F. pratensis (F1)]. We have found that instant ND occurs in Festulolium, where expression of Lolium-type rDNA reached nearly 100% in all F1 hybrids and was maintained through subsequent generations. Therefore, ND and GD in Festulolium are manifested by the same dominant genome (Lolium). We also confirmed the concordance between GD and ND in an interspecific cross between two Festuca species. [ABSTRACT FROM AUTHOR]

Further knowledge of the interactions between rhizospheric fungi and medicinal plants is needed to promote the manufacture of crude medications, as it has recently been clear how these fungi have a significant impact on the quality and quantity of crude pharmaceuticals through a specific fungus-host interaction. The present study was aimed to find out the diversities of fungi in the rhizospheric soil of medicinal plants particularly (Gingiber officinale, Calotropis gigantea, Endographis paniculata, Vigna mungo, Chrysopogon giganoids and Tinospora cordifolia) collected from CIMAP CSIR situated in Indian city Lucknow and from nearby Paikramau agriculture field Lucknow, U.P., India. The DNA of the rhizospheric fungal isolates was amplified through PCR for species level identification using a specific internal transcribed spacer primer (ITS1/ITS4). This study revealed that five different type of fungi identified surrounding the Rhizospheric region of the selected aforementioned plants such as Rhizopus oryzae, Fusarium incarnatum, Penicillium expansum, Aspergillus ochraceous and Aspergillus flavus further validated by sequencing the PCR findings and comparing them to other relevant sequences in GenBank (NCBI). [ABSTRACT FROM AUTHOR]

Concurrent infections caused by multiple fungal pathogens in immunocompromised patients can pose diagnostic and treatment challenges. Here, we presented the first reported case in Taiwan of an AIDS patient who had concurrent infection with Cryptococcus neoformans meningitis and Talaromyces amestolkiae lymphadenopathy. The patient presented with an enlarged inguinal lymph node and was diagnosed with T. amestolkiae lymphadenitis. The species T. amestolkiae was identified using DNA sequencing, which had the capability of differentiating it from other Talaromyces species. The patient was discharged from the hospital following treatment with amphotericin B and subsequent administration of voriconazole. This case highlights the importance of maintaining a suspicion of co-infections and utilizing appropriate diagnostic tools, such as DNA sequencing, to identify possible pathogens. Further studies are needed to determine the optimal treatment for T. amestolkiae and other co-infecting fungal pathogens. [ABSTRACT FROM AUTHOR]

Gastrointestinal nematode parasites are of major concern for horses, where Strongylus vulgaris is considered the most pathogenic among the Strongylus species. Diagnosis of S. vulgaris infections can be determined with next generation sequencing techniques, which are inherently dependent on reference sequences. The best marker for parasitic nematodes is internal transcribed spacer 2 (ITS2) and we provide the first complete ITS2 sequences from five morphologically identified S. vulgaris and additional sequences from two S. edentatus. These sequences have high similarity to already published partial sequences and amplicon sequence variants (ASV) based on next generation sequencing (NGS). The ITS2 sequences from S. vulgaris matched available partial ITS2 sequences and the full ASVs, whereas the S. edentatus sequence matched another complete sequence. We also compare Sanger sequencing and NGS methods and conclude that the ITS2 variation is better represented with NGS methods. Based on this, we recommend that further sequencing of morphologically identified specimens of various species should be performed with NGS cover the intraspecific variation in the ITS2. [ABSTRACT FROM AUTHOR]

Phalaris arundinacea L. (reed canary grass) is a widely occurring grass throughout the Northern Hemisphere. In North America, it is thought to consist of introduced agricultural forms from Europe as well as native populations.During a survey of Phalaris arundinacea in western Canada, we discovered two distinct ribotypes in the sequences of the internal transcribed spacer (ITS) of the nuclear ribosomal DNA: one full length (ITS-long) and one with a seven base pair deletion (ITS-short). In addition, ITS-long plants have fixed heterozygosity indicating possible polyploidy. Phylogenetic analysis reveals that ITS-short is a unique ribotype that characterises an intraspecific clade. We designed an efficient PCR-based assay that allows sizing of a 238/245 base pair fragment in a capillary sequencer. This approach provides a novel marker that could be useful in future surveys of Phalaris arundinacea.

Genome or genomic dominance (GD) is a phenomenon observed in hybrids when one parental genome becomes dominant over the other. It is manifested by the replacement of chromatin of the submissive genome by that of the dominant genome and by biased gene expression. Nucleolar dominance (ND) – the functional expression of only one parental set of ribosomal genes in hybrids – is another example of an intragenomic competitive process which, however, concerns ribosomal DNA only. Although GD and ND are relatively well understood, the nature and extent of their potential interdependence is mostly unknown. Here, we ask whether hybrids showing GD also exhibit ND and, if so, whether the dominant genome is the same. To test this, we used hybrids between Festuca and Lolium grasses (Festulolium), and between two Festuca species in which GD has been observed (with Lolium as the dominant genome in Festulolium and F. pratensis in interspecific Festuca hybrids). Using amplicon sequencing of ITS1 and ITS2 of the 45S ribosomal DNA (rDNA) cluster and molecular cytogenetics, we studied the organization and expression of rDNA in leaf tissue in five hybrid combinations, four generations and 31 genotypes [F. pratensis × L. multiflorum (F1, F2, F3, BC1), L. multiflorum × F. pratensis (F1), L. multiflorum × F. glaucescens (F2), L. perenne × F. pratensis (F1), F. glaucescens × F. pratensis (F1)]. We have found that instant ND occurs in Festulolium, where expression of Lolium-type rDNA reached nearly 100% in all F1 hybrids and was maintained through subsequent generations. Therefore, ND and GD in Festulolium are manifested by the same dominant genome (Lolium). We also confirmed the concordance between GD and ND in an interspecific cross between two Festuca species.

Harmful algal blooms (HABs), mainly formed by dinoflagellates, have detrimental effects on marine ecosystems and public health. Therefore, detecting HABs is crucial for early warning and prevention of HABs as well as the mitigation of their adverse effects. Although various methods, such as light microscopy, electron microscopy, real-time PCR, andmicroarrays, have already been established for the detection of HABs, they are still cumbersome to be exploited in the field. Therefore, rapid nucleic detection methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP)-lateral flow dipstick (LFD) have been developed for monitoring bloom-forming algae. However, the CRISPR/Cas-based detection of HABs has yet to be applied to this field. In this study, we developed a method for detecting Karenia mikimotoi (K. mikimotoi), a typical ichthyotoxic dinoflagellate responsible for global blooms. Our method utilized Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) to target and cleave the internal transcribed spacer (ITS) of K.mikimotoi, guided by RNA. We leveraged the target-activated non-specific single-stranded deoxyribonuclease cleavage activity of LbCas12a to generate signals that can be detected using fluorescence-read machines or LFDs. By combining RPA and LbCas12a with reporters, we significantly enhanced the sensitivity, enabling the detection of ITS-harboring plasmids at concentrations as low as 9.8 aM and genomic DNA of K. mikimotoi at levels as low as 3.6 × 10-5 ng/µl. Moreover, we simplified the genomic DNA extraction method using cellulose filter paper (CFP) by directly eluting the DNA into RPA reactions, reducing the extraction time to <30 s. The entire process, from genomic DNA extraction to result reporting, takes less than an hour, enabling the identification of nearly a single cell. In conclusion, our method provided an easy, specific, and sensitive approach for detecting K. mikimotoi, offering the potential for efficient monitoring and management of K. mikimotoi blooms. [ABSTRACT FROM AUTHOR]

In this study, a new spherical cyst nematode belonging to the genus Globodera, herein described as Globodera vulgaris n. sp., was extracted from the roots and rhizosphere soil of potato and circumjacent weeds belonging to different families in three provinces in southwest China. The new species was characterized by 8 to 24 ridges between the anus and fenestra and an average Granek's ratio of 2.8 to 3.8 in cysts, a head with three to four annules, a dorsal knob anteriorly projected, ventral knobs round or anteriorly projected in second stage juveniles, a head with three to five annules, a short spicule with an average length of less than 30.0 pm, and a developed velum in males. Pathogenicity tests showed that G. vulgaris n. sp. infected potato but did not damage or affect the potato yield compared with the control, and it parasitized tomato with a low reproduction rate (RF < 1) while it did not parasitize tobacco (RF = 0). The new species was closely related to G. rostochiensis, based on molecular diagnostic marker sequences and constructed phylogenetic analysis, based on internal transcribed spacers of ribosomal DNA, large-subunit rDNA, and small-subunit rDNA. However, the new species exhibited differences from G. rostochiensis in terms of morphological characteristics, a wide host preference, lack of damage to hosts, and an egg-hatching rate induced by hatching factors. [ABSTRACT FROM AUTHOR]

Trichophyton interdigitale, an anthropophilic species, is one of the main causative agents of tinea unguium and tinea pedis. T. interdigitale and the zoophilic species T. mentagrophytes are morphologically and physiologically very similar. Isolates of the T. interdigitale/T. mentagrophytes complex from around the world have been classified into more than 10 internal transcribed spacer (ITS) genotypes. In this study, we isolated T. interdigitale from Japanese patients and investigated which ITS type was more common. The ITS regions of 29 clinical isolates of T. interdigitale and one clinical isolate of T. mentagrophytes were sequenced. The phylogenetic analysis of the ITS region sequences revealed that the 29 isolates of T. interdigitale belong to ITS type II of T. interdigitale. The one clinical isolate of T. mentagrophytes was in the same cluster with ITS type II* of T. mentagrophytes. One terbinafine-resistant strain of T. interdigitale also belonged to ITS type II of T. interdigitale. [ABSTRACT FROM AUTHOR]

Objective: The harnessing of medicinal plants for the treatment of infectious diseases has an environmental concern, and therefore environmentally friendly alternative sources like harnessing the potential of endophytes are of paramount importance. The present study aimed to evaluate chemical composition and antimicrobial activity of crude extracts of endophytic fungi isolated from C. bonariensis (L.) in Tanzania. Materials and Methods: Initially, endophytic fungi were isolated from C. bonariensis (L.) and characterized, followed by mass cultivation and the harvesting of crude extracts. Then crude extracts were tested against selected microorganisms: Two Gram-positive bacteria, Staphylococcus aureus and Bacillus subtilis; Two Gram-negative bacteria, Escherichia coli and Salmonella typhi, and a yeast Candida albicans. Gas Chromatography-Mass Spectrometry analyzed the chemical composition of crude extracts. Results: Five endophytic fungi (Talaromyces sp., Penicillium daleae, Neurospora crassa, Talaromyces radicus 1 and Talaromyces radicus 2) were isolated. Furthermore, crude extract of N. crassa had the highest antimicrobial activity with the range of MIC found to be 1.5 µg/mL > MIC > 0.78 µg/mL for all tested microorganisms except for S. aureus where the range of MIC was 40 µg/mL>MIC>20 µg/mL. On the other hand, the crude extract of Talaromyces radicus 1 had the lowest MIC range (100 mg/mL>MIC>50 mg/mL). The GC-MS results demonstrated variation in chemical composition with proved various biological properties. Conclusions: Ethyl acetate crude extracts of N. crassa demonstrated the highest antimicrobial activity, therefore warranting further exploration of the endophyte and their crude extracts for various medicinal and industrial applications. Further studies on the characterization of pure compounds, which may be responsible for the antimicrobial activity that was observed, are urgently needed. [ABSTRACT FROM AUTHOR]

Human infections by Trichophyton mentagrophytes occur mainly due to contact with diseased animals. In Iran, T. mentagrophytes genotype V is the most prevalent variant of the fungus. We aimed to determine the animal reservoir of T. mentagrophytes genotype V infection. The study was done on a total of 577 dermatophyte strains obtained from animals with signs of dermatophytosis and human patients. The list of extensively sampled animals included sheep, cows, cats and dogs. For human cases, epidemiological data were collected. All dermatophyte isolates from animals along with 70 human isolates morphologically similar to T. verrucosum and T. mentagrophytes genotype V were identified by rDNA internal transcribed spacer region restriction fragment length polymorphism analysis and DNA sequencing. A total of 334 animal dermatophyte strains were identified as Microsporum canis, T. mentagrophytes genotype V, T. verrucosum, Nannizzia gypsea, T. mentagrophytes genotype II*, T. mentagrophytes genotype VII, T. quinckeanum , and N. fulva. All clinical isolates identified as T. mentagrophytes genotype V originated from skin and scalp infections. Almost all veterinary isolates of T. mentagrophytes genotype V were cultured from sheep, but epidemiological data on animal-to-human transmission of T. mentagrophytes genotype V infection were limited and we found evidence in favor of interhuman transmission. In Iran, sheep maintain T. mentagrophytes genotype V population and therefore serve as animal reservoir of respective infections. The role of sheep as the source of human dermatophytosis due to T. mentagrophytes genotype V isolates is yet to be proven. [ABSTRACT FROM AUTHOR]

Cellulases are used in textile, pulp and paper, brewery and wine, sugars, and ethanol industries. Four fungal isolates obtained from organic municipal solid wastes (OMSW) were selected based on their cellulolytic activity on carboxymethyl cellulose (CMC) agar medium. Based on the internal transcribed spacer (ITS) sequence of the ribosomal DNA, the four cellulolytic isolates were identified as Aspergillus fumigatus AKAL1, Aspergillus oryzae AKAL4, Aspergillus flavus AKAL8, and Aspergillus flavus AKAL9. After 9 days of fermentation at 30°C and pH 6.5 under 110 rpm agitation, these isolates produced the maximum amount of cellulase. The cellulase showed optimum activity at temperature 35–40°C and pH 6.0–7.0 and was stable for 1 h at 25–45°C and pH 5.0–7.0. The Mg2+ and Zn2+ significantly increased but Hg2+, K+, and Ca2+ severely repressed the cellulase activity. Degradation of filter papers and bio‐stoning of denim was successfully done with the crude cellulase. An endo‐β‐1,4‐glucanase was isolated and characterized from Aspergillus isolates. Genome‐wide analysis revealed that the genomes of A. oryzae, A. fumigatus, and A. flavus, the pertinent species of the fungal isolates, had 23, 25, and 22 cellulase genes, respectively. Phylogenetic analysis revealed that the cellulases in these fungal species were divided into three major groups, and the isolated endo‐β‐1,4‐glucanase clustered to Group II. Ten different motifs are present in cellulases of the three species. Results herein provide a valuable resource for understanding cellulase genes in Aspergillus species and potential application of cellulase in textile and fermentable sugars production industries. [ABSTRACT FROM AUTHOR]