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Boeremia was established to accommodate phoma-resembling fungi. Its species occur in terrestrial ecosystems as endophytes, saprobes and pathogens, except one species reported from a marine ecosystem. Boeremia species are characterized by hyaline, thin-walled, and aseptate (occasionally 1(–2)-septate) conidia that are variable in shape, and hyaline, straight or slightly curved, thick-walled, and 1-septate ascospores that are usually constricted at the septum. In the past, host associations were used to delimit Boeremia species. However, since Boeremia taxa have overlapping morphological characters and are cryptic, it renders taxonomic identification arduous. Therefore, the use of other approaches including multi-gene phylogenetic analyses are imperative. Recommended DNA markers for species delineation are the internal transcribed spacer (ITS, nuclear rDNA consisting of ITS1-5.8S-ITS2) and large subunit (28S, D1–D2 domains of nuclear 28S rDNA) loci, and the genes for actin (ACT1), beta-tubulin (TBB1), RNA polymerase 2 (RPB2) and translation elongation factor 1α (TEF1). Here, we applied morphological and molecular phylogenetic analyses to establish a new taxon (B. albae), and a new host and geographical record for B. maritima associated with leaf spots of Morus alba (Moraceae) in northern Thailand. By providing sequence data for three additional gene regions, our phylogenetic analyses impart a stable phylogenetic placement of the ex-type strain of B. maritima , as illustrated. This is the first study that reports Boeremia species from M. alba , and B. maritima from a terrestrial habitat. • Boeremia taxa are cryptic, and morphologically similar to Phoma. • Boeremia species occur as endophytes, saprobes and pathogens. • Boeremia albae sp. nov. and a new host and location for B. maritima were identified through morphology and phylogeny. • Three additional gene sequences support the classification of B. maritima , previously unreported in a terrestrial habitat. • Including the new taxon, there are 26 species of Boeremia and 14 varieties of Boeremia exigua. [ABSTRACT FROM AUTHOR]

Background: The family Lauraceae is subdivided into six main lineages: Caryodaphnopsideae, Cassytheae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae. However, phylogenetic relationships among these lineages have been debatable due to incongruence between trees constructed using nuclear ribosomal DNA (nrDNA) sequences and chloroplast (cp) genomes. As with cp DNA, the mitochondrial (mt) DNA of most flowering plants is maternally inherited, so the phylogenetic relationships recovered with mt genomes are expected to be consistent with that from cp genomes, rather than nrDNA sequences. Results: The mitogenome of Machilus yunnanensis, with a length of 735,392 bp, has a very different genome size and gene linear order from previously published magnoliid mitogenomes. Phylogenomic reconstructions based on 41 mt genes from 92 Lauraceae mitogenomes resulted in highly supported relationships: sisterhood of the Laureae and a group containing Neocinnamomeae and Caryodaphnopsideae, with Cassytheae being the next sister group, followed by Cryptocaryeae. However, we found significant incongruence among the mitochondrial, chloroplast, and nuclear phylogenies, especially for the species within the Caryodaphnopsideae and Neocinnamomeae lineages. Time-calibrated phylogenetic analyses showed that the split between Caryodaphnopsideae and Neocinnamomeae dated to the later Eocene, around 38.5 Ma, Laureae originated in the Late Cretaceous, around 84.9 Ma, Cassytheae originated in the mid-Cretaceous around 102 Ma, and Cryptocaryeae originated in the Early Cretaceous around 116 Ma. From the Late Cretaceous to the Paleocene, net diversification rates significantly increased across extant clades of major lineages, and both speciation rates and net diversification rates continued steady growth towards the present. Conclusions: The topology obtained here for the first time shows that mt genes can be used to support relationships among lineages of Lauraceae. Our results highlight that both Caryodaphnopsideae and Neocinnamomeae lineages are younger than previously thought, likely first diversifying in the Eocene, and species in the other extant lineages of Lauraceae dates in a long-time span from the Early Cretaceous to the Eocene, and the climate of a period of about 90 million years was relatively warm, while the extant species of Lauraceae then continuously diversified with global cooling from the Eocene to the present day. [ABSTRACT FROM AUTHOR]

Asterostroma roseoalbum sp. nov. was found in Yunnan Province, China, is described here as a new species based on its morphology and phylogeny. Asterostroma roseoalbum is characterised by its felted-membranous to pellicular, fimbriate basidiomata with a smooth hymenophore and a dimitic hyphal system bearing generative hyphae with simple-septate and echinulate, subglobose to globose basidiospores measuring as 8–9.5 × 7–9 µm. Phylogenetic analyses of the new species were based on the internal transcribed spacer (ITS) and large subunit (nrLSU) of ribosomal DNA (rDNA) sequences. The phylogenetic analysis indicated that the new species belongs to the genus Asterostroma, and is closely related to two species A. macrosporum and A. muscicola. A full description, illustrations and phylogenetic analysis results of the new species are provided. Furthermore, a key to the genus Asterostroma in China is provided. [ABSTRACT FROM AUTHOR]

ABSTRACT Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long‐read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full‐length rDNA operons fished from publicly available genome assemblies. Full‐length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non‐haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full‐length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full‐length rDNA operons to the scientific community. [ABSTRACT FROM AUTHOR]

The bovine lungworm, Dictyocaulus viviparus (Bloch, 1782), is highly pathogenic and disease outbreaks can be difficult to predict and manage. Rapid and accurate diagnosis is vital, but without a sensitive diagnostic test this remains challenging in clinical practice. High performance molecular detection tools are therefore required to improve the diagnosis of this parasite and promote the implementation of strategic control measures. Loop-mediated isothermal amplification (LAMP), a rapid DNA assay, offers potential for field-based detection. Here we report a novel LAMP assay (DviLAMP), that was designed to target the D. viviparus internal transcribed spacer 2 (ITS2) ribosomal DNA region. Firstly, genomic DNA was extracted from a single D. viviparus L1 larva to amplify and clone the ITS2 into the recombinant plasmid (DviITS2). The DviLAMP successfully detected the target, with results shown by gel electrophoresis and real-time analysis, in addition to point-of-care amenable end-point detection: colorimetry and lateral flow dipstick (LFD). Analytical sensitivity can detect 0.5 ng DviITS2 following 45 min of incubation at 64°C, increasing to just 1 pg following 90 min of incubation. Using the same primers, other nematodes of cattle, Ostertagia ostertagi and Cooperia oncophora, were also detectable both by gel electrophoresis and real-time. However, when FITC and biotin tagged primers were incorporated to adapt the DviLAMP to LFD end-point detection, the LFD showed specific detection of D. viviparus. Further development of DviLAMP as a point-of-care test could significantly improve the sensitivity of lungworm diagnosis in the field. [ABSTRACT FROM AUTHOR]

The genus Albatrellus is an important group of stipitate terrestrial fungi in the order Russulales. Some species in the genus form ectomycorrhizae, mostly with trees of Pinaceae; some are well-known edible mushrooms. However, its diversity and biogeography are unclear. Taxonomic and phylogenetic studies on Albatrellus were carried out by morphological examination, which included detailed observations of the fruiting body, spore shape and size, and other key features, together with potential hosts. These observations were then compared and analysed using multi-locus molecular phylogenetic analyses, including the internal transcribed spacer regions (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), the translation elongation factor 1-α gene (tef1), the largest subunit of RNA polymerase II (rpb1), the second largest subunit of RNA polymerase II (rpb2), the small subunit mitochondrial rRNA gene (mtSSU), and the small subunit of the nuclear ribosomal RNA gene (nucSSU). The results demonstrated that the species of Albatrellus formed eight clades. Nine new species are described and illustrated, and two new combinations are proposed. A total of 38 species are accepted in Albatrellus worldwide. Of those species, 26, 7, and 8 species are distributed in Asia, Europe, and North America, respectively. The divergence time indicated that the maximum crown age of Albatrellus was approximately 70.5 million years ago, and East Asia and North America are the likely ancestral areas. Dispersal and differentiation to other continents occurred during the late Paleocene and Miocene. Three kinds of dispersal routes are proposed: East Asia and Europe, East Asia and North America, and Europe and North America. [ABSTRACT FROM AUTHOR]

This paper reports the South American rust fungi Puccinia modiolae and P. platyspora (Pucciniales/Uredinales) as new alien species of the European rust funga. Puccinia modiolae is presently known from Switzerland and Germany, P. platyspora from Switzerland, Germany, and France. The records of P. platyspora are the first ones from outside South America. The specimens were identified by teliospore characters and sequences of the nuclear ribosomal DNA (internal transcribed spacer 2 and domains D1–D2 of the nuclear ribosomal large subunit) and the mitochondrial CO3 (cytochrome c oxidase III) gene. Puccinia modiolae and P. platyspora have been recorded so far in Europe on members of the genera Alcea, predominantly on Alcea rosea, Althaea, and Malva of the Malvaceae, subfam. Malvoideae. Alcea rosea is host of both species and shared also with the common mallow rust, P. malvacearum, allowing for mixed infections. The plant is commonly grown as an ornamental and may play a major role for the spread of the alien Malvaceae rust fungi. It was observed for the first time that P. platyspora can produce spermogonia and aecidium-type aecia, suggesting phenotypic plasticity regarding the formation of spore states. The observed spermogonia mainly remained closed and did not liberate spermatia. They produced telio- and aeciospores besides spermatia in their cavity and eventually converted entirely into telia or, rarely, into aecidium-like sori. Small clusters of aeciospores and peridial cells were commonly found hidden in the telial plectenchyma, and well-developed aecidium-type aecia provided with a peridium developed rarely in the center of mature telia. Spermogonia belonging to group V type 4 were found in P. malvacearum, which is generally supposed to lack spermogonia. Some spermogonia produced only spermatia in their cavity; others formed spermatia and teliospores, and some eventually converted into telia. [ABSTRACT FROM AUTHOR]

Background: Hyperactive RNA Polymerase I (Pol I) transcription is canonical in cancer, associated with malignant proliferation, poor prognosis, epithelial-mesenchymal transition, and chemotherapy resistance. Despite its significance, the molecular mechanisms underlying Pol I hyperactivity remain unclear. This study aims to elucidate the role of long noncoding RNAs (lncRNAs) in regulating Pol I transcription in lung adenocarcinoma (LUAD). Methods: Bioinformatics analyses were applied to identify lncRNAs interacting with Pol I transcriptional machinery. Fluorescence in situ hybridization was employed to examine the nucleolar localization of candidate lncRNA in LUAD cells. RNA immunoprecipitation assay validated the interaction between candidate lncRNA and Pol I components. Chromatin isolation by RNA purification and Chromatin Immunoprecipitation (ChIP) were utilized to confirm the interactions of candidate lncRNA with Pol I transcriptional machinery and the rDNA core promoter. Functional analyses, including lncRNA knock-in and knockdown, inhibition of Pol I transcription, quantitative PCR, cell proliferation, clonogenicity, apoptosis, cell cycle, wound-healing, and invasion assays, were performed to determine the effect of candidate lncRNA on Pol I transcription and associated malignant phenotypes in LUAD cells. ChIP assays and luminometry were used to investigate the transcriptional regulation of the candidate lncRNA. Results: We demonstrate that oncogenic LINC01116 scaffolds essential Pol I transcription factors TAF1A and TAF1D, to the ribosomal DNA promoter, and upregulate Pol I transcription. Crucially, LINC01116-driven Pol I transcription activation is essential for its oncogenic activities. Inhibition of Pol I transcription abrogated LINC01116-induced oncogenic phenotypes, including increased proliferation, cell cycle progression, clonogenicity, reduced apoptosis, increased migration and invasion, and drug sensitivity. Conversely, LINC01116 knockdown reversed these effects. Additionally, we show that LINC01116 upregulation in LUAD is driven by the oncogene c-Myc, a known Pol I transcription activator, indicating a functional regulatory feedback loop within the c-Myc-LINC01116-Pol I transcription axis. Conclusion: Collectively, our findings reveal, for the first time, that LINC01116 enhances Pol I transcription by scaffolding essential transcription factors to the ribosomal DNA promoter, thereby driving oncogenic activities in LUAD. We propose the c-Myc-LINC01116-Pol I axis as a critical oncogenic pathway and a potential therapeutic target for modulating Pol I transcription in LUAD. [ABSTRACT FROM AUTHOR]

There is a high demand for natural agrochemicals to control postharvest phytopathogens in fruit. In this study, the Colletotrichum magnum strain was isolated from Maradol papaya fruits showing symptoms of anthracnose, identified based on its morphological characteristics and confirmed by an analysis of its 5.8S ribosomal DNA sequence. The antifungal activity of aqueous and ethanol extracts from Acacia pennatula, Acalypha gaumeri, Bonellia flammea, Calea urticifolia and Croton chichenensis was evaluated against Colletotrichum magnum by agar dilution bioassay at a concentration of 1 mg mL−1 and recording mycelial growth inhibition (MGI), sporulation inhibition (SI) and spore germination inhibition (SGI) were recorded. The extracts that caused MGI of C. magnum by more than 30% were re-evaluated. It was concluded that the aqueous and ethanol extracts from B. flammea stem bark were the most effective in the MGI (91.53–94.49%), SI (99.32–99.65%), and SGI (91.65–100%) of C. magnum at a 3% (w/v) concentration. A serial dilution of the aqueous extract of B. flammea demonstrated that 2.35% and 3% (w/v) were highly effective against C. magnum in vitro, and both concentrations were randomly applied to postharvest Maradol papaya fruit by dip. The results found that both concentrations caused an anthracnose disease severity of 0.92–0.97% in papaya fruits, which was lower than the commercial fungicide Tecto 60®. The aqueous extract from B. flammea stem bark represents a promising opportunity for developing a natural biopesticide to effectively control anthracnose in papaya fruits induced by C. magnum. [ABSTRACT FROM AUTHOR]

Two new species of Dulcicalothrix, D. adhikaryi sp. nov. and D. iyengarii sp. nov., were discovered in India and are characterized and described in accordance with the rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). As a result of phylogenetic analysis, Calothrix elsteri is reassigned to Brunnivagina gen. nov. During comparison with all Dulcicalothrix for which sequence data were available, we observed that the genus has six ribosomal operons in three orthologous types. Each of the three orthologs could be identified based upon indels occurring in the D1–D1′ helix sequence in the ITS rRNA region between the 16S and 23S rRNA genes, and in these three types, there were operons containing ITS rRNA regions with and without tRNA genes. Examination of complete genomes in Dulcicalothrix revealed that, at least in the three strains for which complete genomes are available, there are five ribosomal operons, two with tRNA genes and three with no tRNA genes in the ITS rRNA region. Internal transcribed spacer rRNA regions have been consistently used to differentiate species, both on the basis of secondary structure and percent dissimilarity. Our findings call into question the use of ITS rRNA regions to differentiate species in the absence of efforts to obtain multiple operons of the ITS rRNA region through cloning or targeted PCR amplicons. The ITS rRNA region data for Dulcicalothrix is woefully incomplete, but we provide herein a means for dealing with incomplete data using the polyphasic approach to analyze diverse molecular character sets. Caution is urged in using ITS rRNA data, but a way forward through the complexity is also proposed. [ABSTRACT FROM AUTHOR]

Barathronus is a genus of blind cusk eels comprising 11 valid species. In this paper, we report the second specimen ever documented of Barathronus roulei (Bythitidae) obtained from the Porcupine Bank by R.V. Vizconde de Eza using a bottom trawl at a depth of 1349 m. Morphological description and illustrations, including a radiograph, are provided. In addition, three new sequences corresponding to three different genes, cytochrome c oxidase subunit I (COI)‐DNA barcoding, 16S ribosomal RNA (16S), and recombination activating protein 1 (RAG1), have been added to the molecular repositories, representing the first sequences for the species. [ABSTRACT FROM AUTHOR]

Rhabditis maupasi is re-described and reviewed based on morphological, morphometric, and molecular (D2-D3 expansion segment of the rDNA 28S) analysis collected from northwest Iran. The species is characterised by having a 1.1-1.9 mm long body, lateral fields with three incisures, the lip region offset by a depression, 12-15 μm wide, with six globular lips, the stoma rhabditoid, 14-20 μm long, with distinct cheilo-, gymno- and stegostom; cheilostom slightly cuticularised, gymno-promesostegostom a short tube with well-cuticularised walls, metastegostom with glottoid apparatus bearing small teeth, stomatal or pharyngeal collar covering 40-60% of stoma; pharynx well developed, the pharyngeal corpus consisting of a more or less cylindrical procorpus and swollen metacorpus (median bulb), basal bulb ovoid to pyriform, with grinder and narrow haustrulum, excretory pore at basal bulb level; vulva a transverse slit with protruding lips, the female tail conical-elongated (65-75 μm, c = 16-26, c′ = 2.0-2.5), the male tail conoid, ventrally arcuate (29-34 μm, c = 22-41, c′ = 0.7-1.0); spicules free, with pointed end and dagger-shaped, 61-72 μm long, bursa pseudopeloderan, and with eight pairs of genital papillae plus the phasmid, and gubernaculum 34-36 μm long. Furthermore, its relationship with four closely related species of the genus is discussed. A molecular phylogenetic study using a partial sequence of large subunit ribosomal DNA fragments revealed that R. maupasi forms a clade with R. terricola, recorded previously from Iran. [ABSTRACT FROM AUTHOR]

The genus Didymocarpus Wall. is a core group of the subfamily Didymocarpoideae in Gesneriaceae with a complex taxonomic history. It has long been controversial to delimit Didymocarpus and its allies. We conducted phylogenetic reconstructions with high‐density sampling of Didymocarpus and related genera by using four nuclear ribosomal DNAs (external transcribed spacer [ETS], internal transcribed spacer [ITS], 18S, 26S) and five chloroplast DNAs (atpB‐rbcL, rpl16, rps16, trnH‐psbA, and trnL‐F). The results indicated that neither Didymocarpus nor Allocheilos are monophyletic. Based on molecular phylogenetic and morphological analyses, we delimitated the range of the Didymocarpus sensu stricto (s. str.) with two‐section division, and established a new genus Palmatiboea for species originally placed in Didymocarpus. This genus is remarkably distinguished from Didymocarpus s. str. not only in molecular phylogeny and morphology but also in its specific geographic distribution, in that it is found only in Southeast China. In addition, we proposed a new monotypic genus Hequnia for Allocheilos guangxiensis that is completely isolated in phylogeny, consistent with a range of remarkably distinctive morphological characteristics. Our results clarify the systematics of Didymocarpus and the delimitation between it and related genera with establishment of two new genera. [ABSTRACT FROM AUTHOR]

China has a complex and diverse forest ecological environment, which breeds abundant forest macrofungi, including some edible, medicinal, and poisonous species. During the investigations of macrofungi in the Saihanba National Nature Reserve, North China, we collected abundant specimens of Agaricales and Polyporales within the Agaricomycetes. Based on the morphological characters and molecular evidence of DNA sequences including the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nLSU), the small subunit of mitochondrial rRNA gene (mtSSU), the small subunit of nuclear ribosomal RNA gene (nuSSU), the largest subunit of RNA polymerase II (RPB1), the second largest subunit of RNA polymerase II gene (RPB2), the β-tubulin gene (TUB), and the translation elongation factor 1-α gene (TEF1), this study identifies ten species of Agaricales and Polyporales new to science, viz. Cyanosporus subpopuli, Gelatinofungus betulina, Lycoperdon pseudoperlatum, Macrocystidia hebeiensis, Mycena subbrunnea, M. subpura, M. variispora, M. violocea-ardesiaca, Picipes griseus, and Pleuroflammula hebeiensis. Detailed morphological descriptions, fruiting bodies, and microscopic structure diagrams of these ten novel species are provided. [ABSTRACT FROM AUTHOR]

Apple is an economically important fruit crop in northern Shaanxi Province in China. In recent years, a new type of apple black spot disease, "bagged apple black spot disease," has occurred in the main apple production area of Yan'an City, Shaanxi Province, during the apple ripening season. It seriously affects the appearance quality and commercial value of apples. In this study, 120 isolates recovered from symptomatic apples were identified based on morphological characteristics, pathogenicity, and multilocus sequence analyses of the internal transcribed spacer of ribosomal DNA (rDNA-ITS), translation elongation factor 1-α (EF1-α), RNA polymerase II subunit B (RPB2), endopolygalacturonase (endo- PG), and anonymous region OPA1-3. Alternaria alternata was the most abundant species (64%), followed by Fusarium acuminatum (36%). Pathogenicity assays were conducted by inoculating them individually and together on detached apples (Venus Golden and Fuji varieties). The results showed that the two fungal species could infect apples individually and together. Co-infection enhanced the disease severity. F. acuminatum led to increased severity and speed of disease development compared to A. alternata. This is the first report of Fusarium and Alternaria co-infection causing apple black spot disease worldwide, and the first report of F. acuminatum affecting apples. The optimal growth of A. alternata occurred at 25--30°C and pH 7; the optimal growth of F. acuminatum occurred at 25°C and pH 7. The results of this study can provide a theoretical basis for exploring the occurrence and epidemiology of apple black spot disease and strategies for its control. [ABSTRACT FROM AUTHOR]

Volvox sect. Volvox is a group of green algae with unique morphological features (thick cytoplasmic bridges between somatic cells and spiny zygote walls) and a worldwide distribution. Despite research interest in the diversity of organisms in ancient lakes, Volvox sect. Volvox from ancient lakes worldwide has not been identified to the species level. Here, we established clonal cultures of two species of this group originating from Lake Biwa, an ancient lake in Japan, and performed identification based on morphological and molecular data. One was identified as Volvox kirkiorum based on the nuclear ribosomal DNA internal spacer region (ITS) sequence, bisexual (monoicous or monoecious) spheroids, and zygote morphology. The other showed genetic separation from related species based on the secondary structure of the ITS and results of phylogenetic analysis of a combined data set from the nuclear actin gene, ITS, and two plastid genes (large subunit of RuBisCO and photosystem II CP43 apoprotein gene); it represented a new phylogenetic lineage within Volvox sect. Volvox, suggesting possible endemism in Lake Biwa. This species produced bisexual spheroids with different zygote morphology and zygote number from other species with bisexual spheroids in Volvox sect. Volvox. Therefore, Volvox biwakoensis Nozaki et H. Yamaguchi sp. nov. is described herein. This is the first endemic species of the genus Volvox described from an ancient lake. [ABSTRACT FROM AUTHOR]

A newspecies of nematode, Molinostrongylus longmenensis n.sp., parasite of the genus Molinostrongylus, is described based on specimens recovered from the small intestine of Scotophilus kuhlii Leach, 1822 (Chiroptera: Vespertilionidae) in Longmen County, Guangdong Province, China. To date, 135 species of bat-parasitic nematodes have been reported worldwide. Overall, 13 species belonging to seven genera in three families have been described in China. The new species is characterized by the presence of three ventral and three dorsal longitudinal cuticular ridges perpendicular to the body surface, which appear posterior to the cephalic vesicle and extend to the caudal bursa in males and the posterior end in females. The female tail has two medium-sized subventral conical processes of equal length, as well as one large dorsal conical process, and one thin spine, lateral alae that extend to the position of the vulva, with a fin-like ending. In addition, the new species was also characterized using molecular approaches, such as sequencing and analyzing the internal transcribed spacer 1 (ITS-1) of the ribosomal DNA. [ABSTRACT FROM AUTHOR]

Urban dumpsites are excellent sources of microbes which can biodegrade numerous materials present in waste. This study focused on the assessment of the mycodegradation potential of LDPE (Low-Density Polyethylene) by ascomycetous microfungi from urban dumpsites in Sri Lanka. Out of the collection obtained from five localities in Sri Lanka, eight species of ascomycetes, viz. Talaromyces purpureogenus (GF85), T. beijingensis (GGF03), Penicillium citrinum (GF89), Purpureocillium lilacinum (GF99), Aspergillus flavus (GF94), Aspergillus sp. (GF82), A. terreus (MMF08), and Fusarium falciforme (GF77), demonstrated mycodegradation potential based on the primary screening. All the isolates were accurately identified based on morphology, Sanger sequencing, and phylogenetic analysis of nuclear internal transcribed spacer region with 5.8 s ribosomal DNA (ITS). Among the isolates, T. purpureogenus GF85 showed a 13–17% weight reduction of LDPE. The same fungus showed evidence of remarkable ability to cause biodeterioration of LDPE by Fourier-transform infrared spectroscopy (FTIR) and Scanning Electron Microscopy (SEM). This study highlights the significance of extensive sampling, morphological, molecular characterisation, and comparative analysis of fungi from unexplored habitats towards developing sustainable solutions for the polyethylene waste crisis. [ABSTRACT FROM AUTHOR]

Due to its nutritional value and health benefits, the date palm (Phoenix dactylifera L.) is an essential dietary food crop throughout Middle Eastern and African countries. Consumers are concerned about the possible microbial contamination of dates, especially since most dates arriving in local markets are unprocessed. The absence of processing increases the possibility of microbial contamination, which raises the probability of microbial contamination. This study aims to analyze and evaluate the variability of fungal and bacterial microbiota identified in the most popular date palm fruits in Saudi Arabia. The study assessed ten date variety fruits from the most popular date palm varieties for consumption in Saudi Arabia and analyzed the microbial count. Morphological and molecular characterization and comparison of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences identified 78 fungi, including 36 distinct species across 15 fungal genera. Alternaria, Fusarium, Curvilaria, Aspergillus, and Penicillium were the most frequent genera among the ten fruit cultivars studied, according to ITS-rDNA sequence analysis. Furthermore, 36 bacterial isolates were obtained from ten date varieties studied, each with a unique colony morphology. These isolates were identified based on sequence alignment and comparison of their 16S rDNA internal spacer regions to those available in public databases. The results showed that the bacterial isolates included 15 species from five bacterial genera. The results suggested that Bacillus, Stenotrophomonas, and Brucella were the prevailing genera among the ten tested fruit varieties. Some bacterial genera, such as Brucella, Achromobacter, and Stenotrophomonas, are well-known potential human pathogens. Chaetomium globosum was also recognized as air pollution causing adverse health effects such as allergies and as the causal agent of human fungal infections among the tested date varieties; the Rashodiah type exhibited the highest fungal contamination, whereas the Sagai variety displayed the lowest fungal contamination. Conversely, the Sukkari, Barhi, and Mejdool varieties were the most contaminated with bacteria among the ten tested varieties, while the Khalas variety showed the least bacterial contamination. To the best of the authors' knowledge, this study provides the initial comprehensive account of the molecular and morphological identification of all fungal and bacterial genera associated with date palm (P. dactylifera) fruits. [ABSTRACT FROM AUTHOR]

Global warming is a leading environmental stress that reduces plant productivity worldwide. Several beneficial microorganisms reduce stress; however, the mechanism by which plant–microbe interactions occur and reduce stress remains to be fully elucidated. The aim of the present study was to elucidate the mutualistic interaction between the plant growth-promoting rhizobacterial strain SH-19 and soybeans of the Pungsannamul variety. The results showed that SH-19 possessed several plant growth-promoting traits, such as the production of indole-3-acetic acid, siderophore, and exopolysaccharide, and had the capacity for phosphate solubilisation. The heat tolerance assay showed that SH-19 could withstand temperatures up to 45 °C. The strain SH-19 was identified as P. megaterium using the 16S ribosomal DNA gene sequence technique. Inoculation of soybeans with SH-19 improved seedling characteristics under high-temperature stress. This may be due to an increase in the endogenous salicylic acid level and a decrease in the abscisic acid level compared with the negative control group. The strain of SH-19 increased the activity of the endogenous antioxidant defense system, resulting in the upregulation of GSH (44.8%), SOD (23.1%), APX (11%), and CAT (52.6%). Furthermore, this study involved the transcription factors GmHSP, GmbZIP1, and GmNCED3. The findings showed upregulation of the two transcription factors GmbZIP1 (17%), GmNCED3 (15%) involved in ABA biosynthesis and induced stomatal regulation, similarly, a downregulation of the expression pattern of GmHSP by 25% was observed. Overall, the results of this study indicate that the strain SH-19 promotes plant growth, reduces high-temperature stress, and improves physiological parameters by regulating endogenous phytohormones, the antioxidant defense system, and genetic expression. The isolated strain (SH-19) could be commercialized as a biofertilizer. [ABSTRACT FROM AUTHOR]

The dinoflagellate genus Bysmatrum is an unusual member of the Peridiniales and cannot be attributed to any known family. Bysmatrum differs from typical peridinialean genera in that the second and third anterior intercalary plates are separated and both antapical plates are asymmetrical. Currently, Bysmatrum encompasses six epibenthic or tide-pool species, but information on their genetic diversity and biogeography remains limited. In the present study, we obtained five strains of Bysmatrum from the South China Sea by isolating single cells and three strains from Ingril, a French Mediterranean lagoon by incubating sediments. Strains from Ingril Lagoon displayed the plate formula Po, cp, X, 4′, 3a, 7′′, 6C, 4S, 5′′′, 2′′′′. They also exhibited an elongated nucleus in the hypocone and a type B eyespot. Smooth and spherical cysts were produced in culture. Small and/or partially large subunit ribosomal DNA sequences were obtained for all eight strains. Molecular phylogeny was inferred using these concatenated sequences through maximum likelihood and Bayesian inference methods. Bysmatrum granulosum and B. subsalsum were identified from Thailand and China for the first time, each of them comprising of two ribotypes. Bysmatrum ingrilense sp. nov. was monophyletic and closest to B. subsalsum ribotype B. Pinnatoxin and related toxins were examined in two strains of Bysmatrum ingrilense by LC-MS/MS, but none were detected. Our results highlight that the diversity of Bysmatrum might be underestimated. [ABSTRACT FROM AUTHOR]

For this molecular genetic research, helminthological samples were collected from the lungs of 17 samples of Pelophylax terentievi (Mezhzherin, 1992) distributed in Kashkadarya and Surkhondarya regions in the spring and summer of 2024. The difference between the nucleotides of the R. engelbrechti_uz (PQ219671) sample belonging to the Rhabdias genus collected from the southern regions of our republic and the R. engelbrechti (MG428406) sample obtained from the NCBI database was 0.4%. Nucleotide sequence obtained as a result of molecular-genetic study of engelbrechti belonging to Rhabdias genus was placed in the National Center for Biotechnology Information. This species was recorded for the first time to the best of our knowledge in the territory of the Republic of Uzbekistan. [ABSTRACT FROM AUTHOR]

This study provides a comprehensive molecular phylogenetic analysis of Uroteuthis squid from the Indo-Pacific region. The main aim was to increase sample coverage from northern and eastern Australian waters to resolve the identity and distribution of Uroteuthis species taken by local fisheries. Two mitochondrial regions, cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA), were sequenced from 220 new specimens and analysed with a further 51 sequences from GenBank to create a combined phylogeny for the genus. Three nuclear regions, 18S ribosomal DNA (18S rDNA), 28S ribosomal DNA (28S rDNA) and rhodopsin, were also sequenced from representatives of each species. Based on the mitochondrial phylogeny plus distance and tree-based delimitation models, a COI species barcode gap of 4–5% is proposed for discriminating Uroteuthis species. Applying this gap partitioned many described species into species complexes; for example, U. duvaucelii, U. noctiluca and U. edulis resolved into 10 species. Although more conserved, mitochondrial 16S rRNA sequences differentiated all new species clades, whereas none of the nuclear markers resolved the closest species. Results confirm that neither U. chinensis nor U. edulis occurs in Australian waters. Five undescribed species are identified from northern and eastern Australia, of which four are consistent with earlier allozyme studies (and two align with existing DNA sequences). One is a new southeastern, deeper shelf species differentiated in this study, along with a sixth undescribed species from Indonesian waters. Results of the molecular analysis are now being used to inform complementary morphometric analyses for new species descriptions, and genetic stock structure assessments of these important fisheries resources. [ABSTRACT FROM AUTHOR]

Calliostoma Swainson, 1840, as currently conceived, is the most species-rich genus of the order Trochida, with over 350 recognized species worldwide. The shell variability in these vetigastropods is extremely high, resulting in conflicting taxonomic attributions at both the genus and species levels. In the Mediterranean Sea, the remarkable morphological diversity of the Calliostoma top shells has led to the description of dozens of different taxa, of which nine are currently accepted. This taxonomic framework was tested using an iterative taxonomic approach. Species delimitation (using assemble species by automatic partitioning, clade monophyly and Kimura-2-parameter distances) and phylogenetic analyses (maximum likelihood and Bayesian inference) were carried out on 247 specimens from the Mediterranean and neighbouring Atlantic, including eight Mediterranean species and the Azorean C. lividum , spanning a large part of the morphological diversity and geographic distribution of the genus in the area. The molecular dataset comprised one nuclear marker, internal transcribed spacer 2 (ITS 2), and two mitochondrial markers (cytochrome c oxidase subunit 1 and 16S ribosomal RNA). Results indicate that the number of species is overestimated, as only C. conulus, C. granulatum, C. zizyphinum and C. laugieri are supported by molecular data among the assessed species. It is suggested that the morphological characters commonly used to diagnose species are variable within a single taxon, as three nominal taxa, allegedly endemic to the Mediterranean Sea, are here shown to be a single genetic species (C. laugieri). An ITS 2 2D folding structure is also reported as potentially distinctive for calliostomatids, compared to known Vetigastropoda. Our study indicates that to address the taxonomy of calliostomatid top shells, an integrative approach including molecular data is highly advisable to support species delimitation and especially new species description. [ABSTRACT FROM AUTHOR]

We present descriptions of two newly discovered species of Myxobolus (Myxobolidae) that infect Mugil curema: Myxobolus mundauensis n. sp. found in gills and Myxobolus patriciae n. sp. found in intestines. These descriptions are based on the morphology of myxospores, histological analysis, and sequencing of the small subunit ribosomal DNA (ssrDNA). The myxospores of both species differ in the width and length of their spore bodies, and their ssrDNA sequences showed a 10.6% difference. These findings support the identification of these parasites as distinct and previously unknown species. Phylogenetic analysis revealed a subclade consisting of species that parasitize Mugiliformes, with Myxobolus mundauensis n. sp. being closely related to Myxobolus maceioensis, and Myxobolus patriciae n. sp. being closely related to Myxobolus curemae. Our analysis aligns with previous research suggesting a strong correlation between host orders and phylogenetic patterns within the Myxobolidae family. [ABSTRACT FROM AUTHOR]

In healthy conditions, blood was considered a sterile environment until the development of new analytical approaches that allowed for the detection of circulating bacterial ribosomal DNA. Currently, debate exists on the origin of the blood microbiota. According to advanced research using dark field microscopy, fluorescent in situ hybridization, flow cytometry, and electron microscopy, so-called microbiota have been detected in the blood. Conversely, others have reported no evidence of a common blood microbiota. Then, it was hypothesized that blood microbiota may derive from distant sites, e.g., the gut or external contamination of blood samples. Alteration of the blood microbiota's equilibrium may lead to dysbiosis and, in certain cases, disease. Cardiovascular, respiratory, hepatic, kidney, neoplastic, and immune diseases have been associated with the presence of Gram-positive and Gram-negative bacteria and/or their products in the blood. For instance, lipopolysaccharides (LPSs) and endotoxins may contribute to tissue damage, fueling chronic inflammation. Blood bacteria can interact with immune cells, especially with monocytes that engulf microorganisms and T lymphocytes via spontaneous binding to their membranes. Moreover, LPSs, extracellular vesicles, and outer membrane vesicles interact with red blood cells and immune cells, reaching distant organs. This review aims to describe the composition of blood microbiota in healthy individuals and those with disease conditions. Furthermore, special emphasis is placed on the interaction of blood microbiota with host cells to better understand disease mechanisms. [ABSTRACT FROM AUTHOR]

Ribosomal DNA (rDNA) copies exist across multiple chromosomes, and interindividual variation in copy number is speculated to influence the hypertrophic response to resistance training. Thus, we examined if rDNA copy number was associated with resistance training-induced skeletal muscle hypertrophy. Participants (n = 53 male, 21 ± 1 yr old; n = 29 female, 21 ± 2 yr old) performed 10–12 wk of full-body resistance training. Hypertrophy outcomes were determined, as was relative rDNA copy number from preintervention vastus lateralis (VL) biopsies. Pre- and postintervention VL biopsy total RNA was assayed in all participants, and mRNA/rRNA markers of ribosome content and biogenesis were also assayed in the 29 female participants before training, 24 h following training bout 1, and in the basal state after 10 wk of training. Across all participants, no significant associations were evident between relative rDNA copy number and training-induced changes in whole body lean mass (r = −0.034, P = 0.764), vastus lateralis thickness (r = 0.093, P = 0.408), mean myofiber cross-sectional area (r = −0.128, P = 0.259), or changes in muscle RNA concentrations (r = 0.026, P = 0.818), and these trends were similar when examining each gender. However, all Pol-I regulon mRNAs as well as 45S pre-rRNA, 28S rRNA, and 18S rRNA increased 24 h following the first training bout in female participants. Follow-up studies using LHCN-M2 myotubes demonstrated that a reduction in relative rDNA copy number induced by bisphenol A did not significantly affect insulin-like-growth factor-induced myotube hypertrophy. These findings suggest that relative rDNA copy number is not associated with myofiber hypertrophy. NEW & NOTEWORTHY: We examined ribosomal DNA (rDNA) copy numbers in men and women who resistance trained for 10–12 wk and found no significant associations with skeletal muscle hypertrophy outcomes. These data, along with in vitro data in immortalized human myotubes whereby rDNA copy number was reduced, provide strong evidence that relative rDNA copy number is not associated with anabolism. [ABSTRACT FROM AUTHOR]

The genes encoding ribosomal RNA are highly conserved across life and in almost all eukaryotes are present in large tandem repeat arrays called the rDNA. rDNA repeat unit size is conserved across most eukaryotes but has expanded dramatically in mammals, principally through the expansion of the intergenic spacer region that separates adjacent rRNA coding regions. Here, we used long-read sequence data from representatives of the major amniote lineages to determine where in amniote evolution rDNA unit size increased. We find that amniote rDNA unit sizes fall into two narrow size classes: "normal" (∼11–20 kb) in all amniotes except monotreme, marsupial, and eutherian mammals, which have "large" (∼35–45 kb) sizes. We confirm that increases in intergenic spacer length explain much of this mammalian size increase. However, in stark contrast to the uniformity of mammalian rDNA unit size, mammalian intergenic spacers differ greatly in sequence. These results suggest a large increase in intergenic spacer size occurred in a mammalian ancestor and has been maintained despite substantial sequence changes over the course of mammalian evolution. This points to a previously unrecognized constraint on the length of the intergenic spacer, a region that was thought to be largely neutral. We finish by speculating on possible causes of this constraint. [ABSTRACT FROM AUTHOR]

Background: Changes in gastric microbiome are associated with gastric carcinogenesis. Studies on the association between gastric mucosa-associated gastric microbiome (MAM) and metachronous gastric cancer are limited. This study aimed to identify gastric MAM as a predictive factor for metachronous recurrence following endoscopic resection of gastric neoplasms. Method: Microbiome analyses were conducted for 81 patients in a prospective cohort to investigate surrogate markers to predict metachronous recurrence. Gastric MAM in non-cancerous corporal biopsy specimens was evaluated using Illumina MiSeq platform targeting 16S ribosomal DNA. Results: Over a median follow-up duration of 53.8 months, 16 metachronous gastric neoplasms developed. Baseline gastric MAM varied with Helicobacter pylori infection status, but was unaffected by initial pathologic diagnosis, presence of atrophic gastritis, intestinal metaplasia, or synchronous lesions. The group with metachronous recurrence did not exhibit distinct phylogenetic diversity compared with the group devoid of recurrence but showed significant difference in β-diversity. The study population could be classified into two distinct gastrotypes based on baseline gastric MAM: gastrotype 1, Helicobacter-abundant; gastrotype 2: Akkermansia-abundant. Patients in gastrotype 2 showed higher risk of metachronous recurrence than gastrotype (Cox proportional hazard analysis, adjusted hazard ratio [95% confidence interval]: 5.10 [1.09–23.79]). Conclusions: Gastric cancer patients can be classified into two distinct gastrotype groups by their MAM profiles, which were associated with different risk of metachronous recurrence. [ABSTRACT FROM AUTHOR]

A survey of plant parasitic nematodes was carried out in 650 garlic fields in Korea from 2020 to 2022. Migratory endoparasite nematodes (Ditylenchus sp.) were recovered from 6% of the garlic samples, with an average density of 494 individuals per garlic bulb. The morphological characteristics of males and females from the 2022 survey were very similar to D. destructor, but D. dipsaci was not found. The Korean population traits have a lateral field containing six incisures, and the posterior esophagus part overlaps the intestine dorsally. PCR and DNA sequencing were performed for the D2/D3 region of the ribosomal DNA 28S and the ITS region, and the phylogenetic analysis strongly supports the monophyly of D. destructor. This is the first report of D. destructor parasitizing garlic in the Republic of Korea. In Korea, due to changes in agricultural or environmental conditions, the most damaging potential PPNs changed from D. dipsaci to D. destructor in garlic cultivation. [ABSTRACT FROM AUTHOR]

Whether in the field of medical care, or in people's daily life and health protection, the importance of masks has been paid more and more attention. Acne, the most common complication after wearing masks, which is also called maskne, has been successfully introduced into the common language as a common topic of dermatologist consultations. This study aims to study the changes of microflora in maskne patients and healthy controls before and after wearing masks. In the summer of 2023, we collected a total of 50 samples from 15 maskne patients and 10 healthy controls before and after wearing surgical masks for a long time. 16 S ribosomal DNA sequencing and identification technology with V3-V4 variable region were adopted to explore the microbiome changes caused by mask wearing, analyze the changes in microbial diversity, and make interaction network. LDA effect size analysis was used to identify which bacteria showed significant changes in their relative abundance from phylum to genus. After wearing a mask, the microbiome of the maskne patients changed significantly more than that of the healthy controls, with both α diversity and β diversity lower than those of maskne patients before wearing masks and those of healthy controls after wearing masks. Co-occurrence network analysis showed that compared with other groups, the network of maskne patients after wearing masks for a long time had the lowest connectivity and complexity, but the highest clustering property, while the opposite was true for healthy controls. Many microbes that are potentially beneficial to the skin decreased significantly after wearing a mask. There was almost no difference in healthy controls before and after wearing a mask. [ABSTRACT FROM AUTHOR]

Prunus discoidea is a unique cherry blossom germplasm resource native to China. It is widely distributed across the provinces of Anhui, Zhejiang, Jiangxi, Jiangsu, and Henan, with significant variation. We employed phylogeographic analysis to reveal the evolutionary history of P. discoidea to better understand its genetic diversity and structure. This study provides more accurate molecular insights for the effective conservation and utilization of this germplasm resource. We conducted a phylogeographic analysis of 348 individual plants from 13 natural populations using three fragments (rpoB, rps16, and trnD–E) of chloroplast DNA (cpDNA) and one fragment (ITS) of ribosomal DNA. The results revealed that P. discoidea demonstrates a significant level of genetic diversity (Hd = 0.782; Rd = 0.478). Gene flow among populations was limited, and the variation within populations was the main source of genetic diversity in P. discoidea (among populations: 34.26%, within populations: 65.74%). Regarding genetic differences among populations, Nst (0.401) showed greater differences than Gst (0.308; p < 0.05), demonstrating that there was a significant geographical structure of lineage. One lineage was the central region of Anhui and the western region of Hubei. The other lineage was the Jiangsu region and the Zhejiang region. P. discoidea diverged from Prunus campanulata approximately 1.5 million years ago, during the Pleistocene epoch. This study provides a scientific theoretical basis for the conservation and utilization of germplasm resources of P. discoidea. [ABSTRACT FROM AUTHOR]

Photodynamic therapy (PDT) is a promising cancer treatment. This study investigated the antitumor effects and mechanisms of a novel photosensitizer meso-5-[-diethylene triamine pentaacetic acid-aminophenyl]-10,15,20-triphenyl-porphyrin (DTP) mediated PDT (DTP-PDT). Cell viability, reactive oxygen species (ROS), and apoptosis were measured with a Cell Counting Kit-8 assay, DCFH-DA fluorescent probe, and Hoechst staining, respectively. Cell apoptosis- and autophagy-related proteins were examined using western blotting. RNA sequencing was used to screen differentially expressed mRNAs (DERs), and bioinformatic analysis was performed to identify the major biological events after DTP-PDT. Our results show that DTP-PDT inhibited cell growth and induced ROS generation in MCF-7 and SGC7901 cells. The ROS scavenger N-acetyl-L-cysteine (NAC) and the P38 MAPK inhibitor SB203580 alleviated DTP-PDT-induced cytotoxicity. DTP-PDT induced cell apoptosis together with upregulated Bax and downregulated Bcl-2, which could also be inhibited by NAC or SB203580. The level of LC3B-II, a marker of autophagy, was increased by DTP-PDT. A total of 3496 DERs were obtained after DTP-PDT. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that DERs included those involved in cytosolic ribosomes, the nuclear lumen, protein binding, cell cycle, protein targeting to the endoplasmic reticulum, and ribosomal DNA replication. Disease Ontology and Reactome enrichment analyses indicated that DERs were associated with a variety of cancers and cell cycle checkpoints. Protein-protein interaction results demonstrated that cdk1 and rps27a ranked in the top 10 interacting genes. Therefore, DTP-PDT could inhibit cell growth and induce cell apoptosis and autophagy, partly through ROS and the P38 MAPK signaling pathway. Genes associated with the cell cycle, ribosomes, DNA replication, and protein binding may be the key changes in DTP-PDT-mediated cytotoxicity. [ABSTRACT FROM AUTHOR]

Purpose: Crenosoma vulpis (Dujardin,1845) is a lungworm which has spread worldwide in canines and is associated with upper respiratory infections. In a majority of cases, the infections are accompanied with chronic cough. Diagnosis of lungworms is often underdiagnosed and can be misinterpreted as other respiratory diseases. Methods: The Small Animal Clinic of the University Veterinary Hospital admitted an 11-month-old dog presented with persistent cough associated with difficulty in breathing and even asphyxia. Based on clinical symptoms, the patient underwent radiological and bronchoscopic examination. Bronchoscopy revealed the presence of lungworms obturating the branches of the tracheobronchial tree. Larvae were collected by bronchoscopic lavage and subjected to parasitological and molecular examination. Results: Microscopic detection and morphological identification of the worms removed during the bronchoscopy confirmed the presence of female adult worms. The subsequent molecular characterisation of the mitochondrial (cytochrome c oxidase subunit I gene (cox1) and 12S ribosomal DNA (rDNA)), nuclear (18S rDNA) genes, as well as the analysis of the second internal transcribed spacer (ITS-2) region of the ribosomal DNA, confirmed the Crenosoma vulpis species. Faecal samples were processed using the Baermann method, which confirmed the presence of the larval stage 1 of C. vulpis. The therapy with fenbendazole at a dose of 50 mg/kg of live weight once daily for the period of 7 days was initiated for the patient. Conclusion: This paper presents the first molecularly confirmed clinical case of a Crenosoma vulpis infection in an 11-month-old female dog of the Miniature Schnauzer breed in Slovakia. [ABSTRACT FROM AUTHOR]

Multicopy sequences evolve adaptations for increasing their copy number within nuclei. The activities of multicopy sequences under constraints imposed by cellular and organismal selection result in a rich intranuclear ecology in germline cells. Mitochondrial and ribosomal DNA are managed as domestic herds subject to selective breeding by the genes of the single-copy genome. Transposable elements lead a peripatetic existence in which they must continually move to new sites to keep ahead of inactivating mutations at old sites and undergo exponential outbreaks when the production of new copies exceeds the rate of inactivation of old copies. Centromeres become populated by repeats that do little harm. Organisms with late sequestration of germ cells tend to evolve more "junk" in their genomes than organisms with early sequestration of germ cells. [ABSTRACT FROM AUTHOR]

Background: Blastocystis, a widely distributed zoonotic protozoan infecting both humans and numerous animals, remains poorly understood with its potential medical and veterinary significance. This study examined the molecular occurrence and genetic variation of Blastocystis in children and calves in Bangladesh to explore cross-species transmission and disease burden. Methods: In total, 998 DNA samples were investigated, comprising 299 stool DNA from children and 699 fecal DNA from calves, using polymerase chain reaction and sequencing of the small subunit ribosomal RNA (SSU rRNA) gene. Results: This study detected Blastocystis in 5.35% of the children and 14.74% of the calves. While slight variations in occurrence rates were observed across different study variables, none were statistically significant. The occurrence was highest among children under 5 years and calves aged 1–3 months. Regarding breed, the Holstein Friesian cross and the Jersey cross exhibited higher rates of infection. Conversely, occurrences were lower among children and calves in Gazipur district. The remaining parameters displayed nearly equivalent percentages of Blastocystis. The subtypes identified in children included ST1, ST3, and ST4, with ST1 comprising 50% of them. ST3 and ST4 were also found in calves, alongside ST10 (55.34%) being the most prevalent. Other subtypes found in calves were ST14, ST21, and ST24–ST26. Conclusions: This study found that Blastocystis is more common in calves than in children in Bangladesh, with genetic diversity of nine subtypes. The common occurrence of identical variants of two subtypes in both populations suggests potential zoonotic transmission, highlighting the necessity for further molecular investigations and comprehensive measures within the One Health framework to mitigate public health risks. [ABSTRACT FROM AUTHOR]

Protein synthesis in response to neuronal activity, known as activity-dependent translation, is critical for synaptic plasticity and memory formation. However, the signaling cascades that couple neuronal activity to the translational events remain elusive. In this study, we identified the role of calmodulin (CaM), a conserved Ca2+-binding protein, in ribosomal RNA (rRNA) biogenesis in neurons. We found the CaM-regulated rRNA synthesis is Ca2+-dependent and necessary for nascent protein synthesis and axon growth in hippocampal neurons. Mechanistically, CaM interacts with nucleolar DEAD (Asp–Glu–Ala–Asp) box RNA helicase (DDX21) in a Ca2+-dependent manner to regulate nascent rRNA transcription within nucleoli. We further found CaM alters the conformation of DDX21 to liberate the DDX21- sequestered RPA194, the catalytic subunit of RNA polymerase I, to facilitate transcription of ribosomal DNA. Using high-throughput screening, we identified the small molecules batefenterol and indacaterol that attenuate the CaM-DDX21 interaction and suppress nascent rRNA synthesis and axon growth in hippocampal neurons. These results unveiled the previously unrecognized role of CaM as a messenger to link the activity-induced Ca2+ influx to the nucleolar events essential for protein synthesis. We thus identified the ability of CaM to transmit information to the nucleoli of neurons in response to stimulation. [ABSTRACT FROM AUTHOR]

Background: Microbial community dynamics have been involved in numerous diseases, including cancer. The diversity of intertumoral microbiota in human papillomavirus independent endocervical adenocarcinoma (HPVI ECA) is not well-characterized. Objective: Our objective is to delineate the intratumoral microbiota profile in HPVI ECA and investigate its potential influence on oncogenesis. Methods: We analyzed 45 HPVI ECA cases, comprising 36 gastric-type ECA (GEA) and 9 clear cell carcinomas (CCC). We compared the microbial composition within cancerous and adjacent noncancerous tissue samples using 5R-16S ribosomal DNA sequencing. Further, we investigated the correlation between specific microbes and clinical-pathological metrics as well as patient outcomes. Results: Our findings demonstrate notable differences in the microbial spectra between cancerous and adjacent noncancerous tissues. Amongst HPVI ECA subtypes, GEAs exhibit more microbial variations compared to CCCs. Using the Random Forest algorithm, we identified two distinct microbial signatures that could act as predictive biomarkers for HPVI ECA and differentiate between GEA and CCC. Varied microbial abundances was related to clinical characteristics of HPVI ECA patients. In addition, high levels of Micrococcus and low levels of unknown genus75 from the Comamonadaceae family were associated with poorer outcomes in HPVI ECA patients. Similarly, an abundance of Microbacterium correlated with reduced overall survival (OS), and a high presence of Streptococcaceae family microbes was linked to reduced recurrence-free survival (RFS) in GEA patients. Intriguingly, a high abundance of Micrococcus was also associated with a worse OS in GEA patients. Conclusion: The study reveals distinct microbial signatures in HPVI ECA, which have potential as biomarkers for disease prognosis. The correlation between these tumor-associated microbiota features and clinicopathological characteristics underscores the possibility of microbiome-based interventions. Our research provides a foundation for more in-depth studies into the cervical microbiome's role in HPVI ECA. [ABSTRACT FROM AUTHOR]

Background: Leishmaniosis caused by Leishmania infantum, L. major and L. tropica is endemic in Morocco. Growing evidence of both human and canine Leishmania infections in urban centres has been reported. Since many forms of the disease are zoonotic, veterinarians play an important role in leishmaniosis control by intervening at the parasite host level. This study aimed to bring together One Health principles to connect canine and feline leishmaniosis epidemiology within urban centres of Morocco (Rabat and Fez) and assess the level of awareness of Moroccan veterinarians about facing this threat. Methods: A molecular survey was conducted for Leishmania DNA detection in canine (n = 155) and feline (n = 32) whole-blood samples. Three conventional polymerase chain reaction (PCR) protocols were implemented. The first PCR aimed at identifying infected animals by targeting Leishmania spp. kinetoplast minicircle DNA (kDNA). The second and third PCR targeted the Leishmania internal transcribed spacer region (ITS-1) and the Leishmania small subunit ribosomal RNA (SSUrRNA) gene, respectively, aiming at identification of the infecting species after Sanger sequencing-positive amplicons. Total immunoglobulin G (IgG) against Leishmania spp. was evaluated in 125 dogs by enzyme-linked immunosorbent assays (ELISA) using an in-house protocol, including three Leishmania-specific antigens (SPLA, rKDDR and LicTXNPx). Sera from 25 cats were screened for total IgG to Leishmania spp. by an indirect immunofluorescence antibody test (IFAT). An online questionnaire was presented to Moroccan veterinarians addressing their knowledge and practices towards animal leishmaniosis. Results: Overall, 19.4% of the dogs tested positive for Leishmania kDNA and ITS-1 and sequencing revealed infection with L. infantum among PCR-positive dogs. These animals presented a wide range of ELISA seropositivity results (16.7%, 34.9% and 51.6%) according to the tested antigens (rKDDR, SPLA and LicTXNPx, respectively). Use of kDNA-PCR revealed 12.5% cats positive to Leishmania spp. otherwise found to be seronegative by IFAT. Conclusions: A considerable prevalence of infection was identified in dogs from urban centres of Morocco. Additionally, this is the first report of feline infection with Leishmania spp. in this country and in urban settings. Moroccan veterinarians are aware that animal leishmaniosis is endemic in Morocco, representing a public health threat, and are knowledgeable about canine leishmaniosis diagnosis and treatment. [ABSTRACT FROM AUTHOR]

Chlorosplenium is a small genus comprising five species of inoperculate discomycetes in the order Helotiales (Leotiomycetes) often recognizable by their bright yellowish-green colors and gregarious growth on wood. In this study, we describe five new species—C. aotearoa, C. australiense, C. cusucoense, C. epimorsicum, and C. hawaiiense—based on a combination of recent fieldwork and examination of previously collected fungarium specimens. We use an integrative taxonomic approach to support the distinction of new species, incorporating morphology and DNA sequence data with biogeography. Macro- and micromorphological features of apothecia for all species and culture characteristics for four of the five new species are documented. A multilocus phylogeny based on nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, partial large subunit nuc ribosomal DNA (28S nuc rDNA), and A–B regions of the largest subunit of RNA polymerase II (RPB1) gene is presented. Additionally, we report Chlorosplenium chlora from Europe for the first time and expand our knowledge of the diversity and distributions of species in this genus in America, Australia, and New Zealand. [ABSTRACT FROM AUTHOR]

Banana (Musa spp.) is one of the most economically important horticultural crops. There are many types of banana, with differing ploidy (usually diploid, triploid, or tetraploid) and genome types (most containing the A or/and B genome). Currently, observation and genome type detection are commonly used to identify banana germplasm resources. However, observation is tedious, while genome type detection cannot distinguish categories below genome types. It is, therefore, urgent to establish a simple and effective method for identifying banana germplasm resources. This study sequenced and analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 62 banana germplasm resources and found that the sequencing peaks, especially the 20 bp region near the 420-bp position (referred to as the 420-bp region), exhibited relatively recognizable and repeatable polymorphism characteristics. Using the 420-bp region as a marker, we were able to quickly distinguish bananas belonging to different genome type groups or different subgroups in the same genome type group. Moreover, it appeared that Sanger sequencing of ITS could be used to identify hybrid banana offspring. In general, ITS sequencing simplifies the classification of banana germplasm resources and has potential application in several areas of Musa improvement. [ABSTRACT FROM AUTHOR]

Gregarine apicomplexans are ubiquitous endosymbionts of invertebrate hosts. Despite their ecological and evolutionary importance, inferences about the phylogenetic relationships of major gregarine groups, such as the Lecudinidae and Urosporidae, have been hindered by vague taxonomic definitions and limited molecular and morphological data. In this study, we investigated five gregarine species collected from four families of polychaete hosts (Nereididae, Oenonidae, Hesionidae, and Phyllodocidae) using light microscopy (LM) and scanning electron microscopy (SEM). We also generated small subunit ribosomal DNA sequences from these species and conducted molecular phylogenetic analyses to elucidate the evolutionary relationships within the Lecudinoidea. Our results include new molecular and morphological data for two previously described species (Lecudina cf. platynereidis and Lecudina cf. arabellae), the discovery of a new species of Lecudina (L. oxydromus n. sp.), and the discovery of two novel species, namely Amplectina cordis n. gen. et. n. sp. and Sphinctocystis inclina n. sp. These two species exhibited unique shapes and movements, resembling those of urosporids but with a phylogenetic affinity to lecudinids, blurring the border between lecudinids and urosporids. Our study emphasizes the need for further investigations into this highly diverse group, which has achieved great success across multiple animal phyla with diverse shapes and movements. [ABSTRACT FROM AUTHOR]

Monogeneans are highly host‐specific parasites infecting marine and freshwater fish. However, little information is available about the parasitic taxa within Heteraxinidae. An integrative study was performed to understand the taxonomic status of an unconfirmed heteraxinid marine species parasitizing the gill region of Acanthopagrus bifasciatus (Sparidae) from the Arabian Gulf (Saudi Arabia). Based on the morphological study, this parasite has all the generic features of the genus Kannaphallus (Heteraxinidae, Mazocraeidea). Distinct criteria that discriminated this species from other taxa of the same genus are the presence of genital spines (26–29), a short sclerotized duct in the male copulatory organ, the number of testes (mean 40, range 30–50), and clamps in the haptoral structure (45–50 in a long row and 19–22 in a short row). DNA of parasite species reported in the present study was amplified and sequenced for the nuclear large subunit of the ribosomal RNA (28S rRNA) gene and the mitochondrial cytochrome c oxidase subunit I (COI) gene. Results indicate that sequences obtained from both genes are unique and different from related sequences from the genus Kannaphallus. Morphological as well as molecular data indicate that our specimens are from a new species, and the name Kannaphallus acanthopagrusi n. sp. is suggested. This is the first report of a heteraxinid parasitizing marine sparid fish from Saudi Arabia, with unique morphological and molecular features. [ABSTRACT FROM AUTHOR]

Introduction: Trichoderma species establish symbiotic relationships with plants through both parasitic and mutualistic mechanisms. While some Trichoderma species act as plant pathogenic fungi, others utilize various strategies to protect and enhance plant growth. Methods: Phylogenetic positions of new species of Trichoderma were determined through multi-gene analysis relying on the internal transcribed spacer (ITS) regions of the ribosomal DNA, the translation elongation factor 1-α (tef1-α) gene, and the RNA polymerase II (rpb2) gene. Additionally, pathogenicity experiments were conducted, and the aggressiveness of each isolate was evaluated based on the area of the cross-section of the infected site. Results: In this study, 13 Trichoderma species, including 9 known species and 4 new species, namely, T. delicatum, T. robustum, T. perfasciculatum, and T. subulatum were isolated from the diseased tubers of Gastrodia elata in Yunnan, China. Among the known species, T. hamatum had the highest frequency. T. delicatum belonged to the Koningii clade. T. robustum and T. perfasciculatum were assigned to the Virens clade. T. subulatum emerged as a new member of the Spirale clade. Pathogenicity experiments were conducted on the new species T. robustum, T. delicatum, and T. perfasciculatum, as well as the known species T. hamatum, T. atroviride, and T. harzianum. The infective abilities of different Trichoderma species on G. elata varied, indicating that Trichoderma was a pathogenic fungus causing black rot disease in G. elata. Discussion: This study provided the morphological characteristics of new species and discussed the morphological differences with phylogenetically proximate species, laying the foundation for research aimed at preventing and managing diseases that affect G. elata. [ABSTRACT FROM AUTHOR]

Protoperidinium claudicans is a planktonic, heterotrophic, bioluminescent dinoflagellate species commonly found in neritic waters. It has long been considered to display phenotypic variation in its second anterior intercalary plate, which could vary between quadra, penta and hexa. The equivalent spinose, cordate cyst goes under the name of Votadinium spinosum. Here we perform incubation experiments with cysts from France, Canada, China and Japan, which demonstrate that P. claudicans forms a species complex, with at least two ribotypes with a penta configuration (P. claudicans) and one with a quadra configuration (P. carriae sp. nov.). A fossil-based cyst, V. multispinosum sp. nov., is described as the equivalent of P. carriae. Molecular phylogenetics using large subunit ribosomal DNA supports these observations. The cyst–theca relationships for Votadinium psilodora and another, undescribed, cordate, spineless Votadinium species are also reported from China. Macromolecular analyses of the cyst wall of V. multispinosum reveal it is comprised of a protein-rich carbohydrate compound. We show that this compound is not uncommon in dinoflagellate and ciliate cysts and that it is unlikely to preserve very well upon sedimentation and burial. [ABSTRACT FROM AUTHOR]

Phyllachora (Phyllachoraceae, Phyllachorales) species are parasitic fungi with a wide global distribution, causing tar spots on plants. In this study, we describe three newly discovered species: Phyllachora chongzhouensis, Phyllachora neidongensis, and Phyllachora huiliensis from Poaceae in China. These species were characterized using morphological traits and multi-locus phylogeny based on the internal transcribed spacer region (ITS) with the intervening 5.8S rRNA gene, the large subunit of the rRNA gene (LSU), and the 18S ribosomal RNA gene (SSU). Three known species of P. chloridis, P. graminis, and P. miscanthi have also been redescribed, because, in reviewing the original references of P. chloridis, P. graminis, and P. miscanthi, these were found to be relatively old and in Chinese or abbreviated. In addition, the illustrations were simple. In molecular identification, the ITS sequence is short, while the ITS, LSU, and SSU are incomplete. Therefore, this study provides new important references for the redescription of three known species and provides further evidence for the identification of new taxa. [ABSTRACT FROM AUTHOR]

Simple Summary: The class Insecta constitutes the largest group of terrestrial animals, with more than a million described species. As in all other animals, insect genomes contain clusters of specific genes, which are essential for producing and assembling ribosomes. These clusters harbor two types of repetitive DNA, i.e., 45S and 5S ribosomal DNA (rDNA). Currently, 45S and 5S rDNA clusters have been studied in about 1000 and 100 insect species, respectively. Although the number of species with known 45S rDNA clusters constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Currently, clusters of 45S and 5S ribosomal DNA (rDNA) have been studied in about 1000 and 100 species of the class Insecta, respectively. Although the number of insect species with known 45S rDNA clusters (also referred to as nucleolus-organizing regions, or NORs) constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and molecular mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Chromosome structure (i.e., monocentric vs. holokinetic chromosomes), excessive numbers of rRNA gene copies per cluster, interactions with transposable elements, pseudogenization, and meiotic recombination are perhaps the most important among them. [ABSTRACT FROM AUTHOR]

In June 2020, branch canker and brown spot of leaves on walnut were observed in Qingyang, China. A total of five strains were isolated from symptomatic samples and verified for pathogenicity based on Koch's Postulates, which showed that strains Hz4–1, Hz5–2, and Hy3–1 were the causative agents, and preliminarily identified them as members of the genus Nothophoma based on morphological characteristics. Subsequently, multi-locus phylogenetic analysis of the partial sequences of internal transcribed spacer (ITS), nuclear large ribosomal subunit (LSU), partial β-tubulin (TUB2), and RNA polymerase II second largest subunit (RPB2) showed that the three strains were clustered into two groups on the phylogenetic tree: strain Hz4–1 and Hz5–2 and Nothophoma quercina (CBS 6633.92) clustered into one branch with 84% support, while Hy3–1 and Nothophoma spiraeae (CFCC 53 929) clustered within a well-supported clade with a bootstrap value of 99%. As a result, combining morphological characteristics and multi-locus systematic analysis, the strains Hz4–1 and Hz5–2 were identified as N. quercina, and Hy3–1 was identified as N. spiraeae, which is the first report of N. spiraeae causing walnut disease in China. [ABSTRACT FROM AUTHOR]

Summary: The population of the genus Paramerlinius was discovered from potato rhizosphere in a government potato seed farm, located in Tiksen, Munsiari, Pithoragarh, Uttarakhand, India. It is here described as Paramerlinius shamimi n. sp. based on morphological, morphometric and molecular data. The new species is characterised by having a body length of 841.8-1208.8 μ m, continuous head bearing 7-8 annuli, a prominent stylet (28.4-32.3 μ m) with well-developed posteriorly sloping basal knobs, six lateral incisures at the mid-body, a well-developed median bulb, a secretory-excretory (S-E) pore (123.5-160.7 μ m) almost at the level of basal bulb, hemizonid covering 2-3 annuli that are located 3-4 annuli above the S-E pore, phasmids located in the front half of the tail, tail subcylindrical, having a hemispherical smooth terminus (62.7-94.1 μ m) with 38-48 tail annuli, males common, spicule arcuate (27.4-31.4 μ m), gubernaculum curved ventrally (8.8-9.8 μ m) and peloderan bursa. Molecular characterisation of the population was performed by sequencing nuclear ribosomal DNA (rRNA) genes, viz. ITS-1, 18S (partial) and D2-D3 region of 28S rRNA. Maximum likelihood and Bayesian phylogenetic analyses of P. shamimi n.sp. using the D2-D3 region show it forms a distinct clade with other unidentified Paramerlinius spp. and P. neohexagrammus and, using 18S rRNA, groups it in the same clade as P. hexagrammus. A tabular key for 13 species including P. shami1mi n.sp. under the genus Paramerlinius is given. [ABSTRACT FROM AUTHOR]

ITS sections, which are situated inside the ribosomal DNA operon, are recognized for their high levels of diversity and slow rate of evolution, which makes them important for plant phylogenetic studies. The objective of this work is to use the internal transcribed spacer (ITS) regions of 18 alfalfa (Medicago sativa) genotypes/varieties to determine their genetic relationships and to verify possible genetic markers for variety identification and classification. This has been done by validating the secondary structures of the ITS regions and observing the effects of the relationships among the lowest energy state, the total number of possible secondary structure hairpins, and (GC) content. The results indicated that the length of the ITS sequences varied between 426 and 629 nucleotides and that the G + C content of the ITS region varied between 46.6 and 50%. In this study, the analysis of molecular variance (AMOVA) was used to validate the effectiveness of configuration analysis and revealed that fluctuations in the data accounted for a substantial amount of the observed total variance. Moreover, 94 percent of the genotypes analyzed exhibited a significant degree of variety. This shows that a large fraction of the observed variation is likely attributable to genetic variables. Population four, comprising Bilensoy80, Emily, Quin, Vendor, and Felicia, had the highest degree of heterozygosity at 68.8%, whereas population two, including Gozlu1, Prosementi, Nimet and Local (Van), had the lowest level at 37.5%. The original Shannon's approach as an unbiased estimator employed in population genetics research validated the differences among alfalfa genotypes with the AMOVA analysis results of this study. Individual differences were found to be 59%, whereas population differences were found to be 41%. There have been a few ITS studies on Medicago sativa that have utilized ITS as a phylogenetic marker to estimate connections and define new taxonomic categories (e.g., tribes). However, our research also includes an analysis of the secondary structure of these sequences and the results of this study imply that ITS sequence and secondary structure data can be utilized to understand the intraspecific genetic makeup of different alfalfa varieties. [ABSTRACT FROM AUTHOR]