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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 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]

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]

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]

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]

The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence. [ABSTRACT FROM AUTHOR]

Sourdough is one of the oldest technologies employed by humans to leaven bread because of its ability to enhance the flavour and structure of bread using micro-organisms. However, there is a lack of comprehensive information in Botswana regarding the diversity of sourdough starters and the fermentative micro-organisms responsible for spontaneous fermentation. The present study aimed to explore the microbial species diversity of sourdoughs in Botswana and gain insight into the unique microbial communities involved in sourdough production. A total of nine samples were collected from different areas in Botswana. The microbial diversity in sourdoughs was characterized through the sequencing of amplicons of the 16S ribosomal DNA and internal transcribed spacer regions. In silico polymerase chain reaction–restriction fragment length polymorphism and phylogenetics were utilized to determine the genetic diversity among the isolates. The dominant yeast species identified were Saccharomyces cerevisiae, Wickerhamomyces anomamlus, Pichia kudriazverii and kazachstania humilis. Additionally, the presence of Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, Liquorilactobacillus nageli and Bacillus cereus was also detected. It is worth noting that two species of acetic acid bacteria (AAB), namely Acetobacter pasteurianus and A. indonesiensis, were isolated, though in low levels, but the finding is significant in sourdough fermentation. The low occurrence of AAB (acetic acid bacteria) species observed in this study could be an important finding, as these bacteria are considered understudied, yet they are known to contribute significantly to the final product. [ABSTRACT FROM AUTHOR]

Purpose: In threatened diversity hotspots, such as mountain cloud forests, microbiome studies have focused essentially on bacteria. Unlike prokaryotic microbiomes, the study of the microeukaryotes has largely been restricted to the visual identification of specific groups. Herein, microeukaryotic edaphic diversity from a pristine mountain cloud forest (MCF) of Mexico was analyzed via the metabarcoding of the ITS1 region of ribosomal DNA. Materials and methods: An exploratory triangular sampling was conducted in the mountain cloud forest located in El Relámpago Mount, Santiago Comaltepec, Oaxaca, Mexico. Each vertex was located adjacent to a dominant plant species in the ecosystem (Oreomunnea mexicana and Alsophila salvinii). After DNA extraction the ITS1 region (rDNA) was amplified. Microeukaryotic sequences were filtered by computational subtraction against the ITS2 Database. Next, alpha and beta diversity indexes were calculated, and the relationship between abiotic variables and diversity patterns were inferred by means of a Canonical Correspondence Analysis. Results: Overall, 138 inferred sequence variants were identified, including 87 protists, 35 animals (microfauna), and 16 algae. Within the animals, the nematodes were the dominant group, chlorophytes dominated algae, and in Protista, no dominance patterns were observed given the high diversity and equitability of this group. Soil available carbon, carbon degrading enzymes and the pH play a key role in modeling the community structure. Remarkably, high beta diversity levels were obtained, evidencing a strong spatial heterogeneity at the small scale. Conclusions: The ITS metabarcoding proved to be a useful tool to conduct multi-taxa diversity assessments for microeukaryotes, allowing the identification of alpha and beta diversity patterns and overcoming limitations of sampling and the direct observation of individuals. The results presented in this work evidenced high microeukaryotic diversity levels in the soil of MCF and encourage future studies aiming to explore the taxonomic diversity of individual taxa. [ABSTRACT FROM AUTHOR]

Numerous phosphorus (P)‐acquisition and ‐utilisation strategies have evolved in plants growing in severely P‐impoverished environments. Although these strategies have been well characterised for certain taxa, like Proteaceae, P‐poor habitats are characterised by a high biodiversity, and we know little about how species in other families cope with P scarcity. We compared the P‐acquisition and leaf P‐allocation strategies of Fabaceae and Myrtaceae with those of Proteaceae growing in the same severely P‐impoverished habitat. Myrtaceae and Fabaceae exhibited multiple P‐acquisition strategies: P‐mining by carboxylates or phosphatases, P uptake facilitated by carboxylate‐releasing neighbours, and dependence on the elevated soil P availability after fire. Surprisingly, not all species showed high photosynthetic P‐use efficiency (PPUE). Highly P‐efficient species showed positive correlations between PPUE and the proportion of metabolite P (enzyme substrates), and negative correlations between PPUE and phospholipids (cellular membranes) and nucleic acid P (mostly ribosomal RNA), while we found no correlations in less P‐efficient species. Overall, we found that Myrtaceae and Fabaceae used a wider range of strategies than Proteaceae to cope with P scarcity, at both the rhizosphere and leaf level. This knowledge is pivotal to better understand the mechanisms underlying plant survival in severely nutrient‐impoverished biodiverse ecosystems. [ABSTRACT FROM AUTHOR]

AbstractGolovinomyces (Erysiphaceae, Ascomycota) is an obligate plant pathogenic group causing powdery mildew on diverse angiosperm plants, including economically significant crops. Despite advancements in the taxonomy and phylogeny of Golovinomyces species using ribosomal DNA markers (ITS and LSU), several taxonomic issues remain unresolved. Previously, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, which exhibits higher nucleotide variation, has been proposed as an additional marker for powdery mildew species. In this study, we designed a new primer set (GoGPD-F and GoGPD-R) to improve the PCR success and efficiency of the GAPDH gene across various Golovinomyces species and dried herbarium specimens. The primers were successful in amplifying and sequencing the GAPDH gene in sixteen Golovinomyces species, including six species not previously registered in GenBank and two undescribed species. This development is a significant contribution to future research on the identification, taxonomy, and phylogeny of Golovinomyces species, offering a more robust tool for resolving existing taxonomic issues. [ABSTRACT FROM AUTHOR]

The Doradidae fishes constitute one of the most diverse groups of Neotropical freshwater environments. Acanthodoradinae is the oldest lineage and the sister group to all other thorny catfishes, and it includes only the genus Acanthodoras. The diversity of Acanthodoras remains underestimated, and the use of complementary approaches, including genetic studies, is an important step to better characterize this diversity and the relationships among the species within the genus. Therefore, we conducted a comprehensive analysis using conventional cytogenetic techniques and physical mapping of three multigene families (18S and 5S ribosomal DNA [rDNA], U2 small nuclear DNA [snDNA]) and four microsatellite motifs, namely (AC)n, (AT)n, (GA)n, and (GATA)n, in two sympatric species from the Negro River: Acanthodoras cataphractus and Acanthodoras cf. polygrammus. We found significant differences in constitutive heterochromatin (CH) content, distribution of the microsatellite (AT)n, and the number of 5S rDNA and U2 snDNA sites. These differences may result from chromosome rearrangements and repetitive DNA dispersal mechanisms. Furthermore, the characterization of the diploid number (2n) of these Acanthodoras species enables us to propose 2n = 58 chromosomes as the plesiomorphic 2n state in Doradidae based on ancestral state reconstruction. Acanthodoradinae is the oldest lineage of the thorny catfishes, and knowledge about its cytogenetic patterns is crucial for disentangling the karyotype evolution of the whole group. Thus, this study contributes to the understanding of the mechanisms behind chromosome diversification of Doradidae and highlights the importance of Acanthodoradinae in the evolutionary history of thorny catfishes. [ABSTRACT FROM AUTHOR]

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

Introduction: Clostridioides difficile infection (CDI) is the most common cause of antibiotic-associated diarrhoea. Fidaxomicin and fecal microbiota transplantation (FMT) are effective, but expensive therapies to treat recurrent CDI (reCDI). Our objective was to develop a prediction model for reCDI based on the gut microbiota composition and clinical characteristics, to identify patients who could benefit from early treatment with fidaxomicin or FMT. Methods: Multicentre, prospective, observational study in adult patients diagnosed with a primary episode of CDI. Fecal samples and clinical data were collected prior to, and after 5 days of CDI treatment. Follow-up duration was 8 weeks. Microbiota composition was analysed by IS-pro, a bacterial profiling technique based on phylum- and species-specific differences in the 16–23 S interspace regions of ribosomal DNA. Bayesian additive regression trees (BART) and adaptive group-regularized logistic ridge regression (AGRR) were used to construct prediction models for reCDI. Results: 209 patients were included, of which 25% developed reCDI. Variables related to microbiota composition provided better prediction of reCDI and were preferentially selected over clinical factors in joint prediction models. Bacteroidetes abundance and diversity after start of CDI treatment, and the increase in Proteobacteria diversity relative to baseline, were the most robust predictors of reCDI. The sensitivity and specificity of a BART model including these factors were 95% and 78%, but these dropped to 67% and 62% in out-of-sample prediction. Conclusion: Early microbiota response to CDI treatment is a better predictor of reCDI than clinical prognostic factors, but not yet sufficient enough to predict reCDI in daily practice. [ABSTRACT FROM AUTHOR]

Nucleolar morphology is a well-established indicator of ribosome biogenesis activity that has served as the foundation of many screens investigating ribosome production. Missing from this field of study is a broad-scale investigation of the regulation of ribosomal DNA morphology, despite the essential role of rRNA gene transcription in modulating ribosome output. We hypothesized that the morphology of rDNA arrays reflects ribosome biogenesis activity. We established GapR-GFP, a prokaryotic DNA-binding protein that recognizes transcriptionally-induced overtwisted DNA, as a live visual fluorescent marker for quantitative analysis of rDNA organization in Schizosaccharomyces pombe. We found that the morphology—which we refer to as spatial organization—of the rDNA arrays is dynamic throughout the cell cycle, under glucose starvation, RNA pol I inhibition, and TOR activation. Screening the haploid S. pombe Bioneer deletion collection for spatial organization phenotypes revealed large ribosomal protein (RPL) gene deletions that alter rDNA organization. Further work revealed RPL gene deletion mutants with altered rDNA organization also demonstrate resistance to the TOR inhibitor Torin1. A genetic analysis of signaling pathways essential for this resistance phenotype implicated many factors including a conserved MAPK, Pmk1, previously linked to extracellular stress responses. We propose RPL gene deletion triggers altered rDNA morphology due to compensatory changes in ribosome biogenesis via multiple signaling pathways, and we further suggest compensatory responses may contribute to human diseases such as ribosomopathies. Altogether, GapR-GFP is a powerful tool for live visual reporting on rDNA morphology under myriad conditions. Author summary: Cells devote significant energy and resources to produce ribosomes, large protein complexes that carry out protein synthesis. To ensure that ribosome production matches cellular needs, activation of ribosome assembly is regulated by many inputs. One key regulatory target is transcription of the tandemly repeated rRNA genes in the ribosomal DNA arrays. A broad understanding of how cells regulate the organization of the rDNA under different cellular conditions and transcriptional states has been difficult to assess with current tools and model systems. We present a new imaging reporter, a fluorescently tagged DNA-binding protein called GapR, that highlights rDNA spatial organization in fission yeast, a model system that shares similar regulatory networks with mammals. Using GapR, we found that the 3D organization of the rDNA arrays changes with the cell cycle, glucose starvation, RNA pol I inhibition, and TOR signaling. We surveyed hundreds of yeast mutants to identify factors that regulate rDNA spatial organization, discovering that the deletion of ribosome protein genes causes rDNA array expansion. Further experiments indicated that ribosome protein insufficiency activates conserved regulatory signaling pathways as part of a compensatory response. Our work presents the first broad investigation for regulators of rDNA spatial organization in any organism. Importantly, we identify a compensatory response to compromised ribosome biogenesis that could be conserved in mammals. [ABSTRACT FROM AUTHOR]

Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P. megaterium, shedding light on potential applications in agriculture and industry. [ABSTRACT FROM AUTHOR]

The major loci for the large primary ribosomal RNA (rRNA) genes (35S rRNAs) exist as hundreds to thousands of tandem repeats in all organisms and dozens to hundreds in Drosophila. The highly repetitive nature of the ribosomal DNA (rDNA) makes it intrinsically unstable, and many conditions arise from the reduction in or magnification of copy number, but the conditions under which it does so remain unknown. By targeted DNA damage to the rDNA of the Y chromosome, we created and investigated a series of rDNA alleles. We found that complete loss of rDNA leads to lethality after the completion of embryogenesis, blocking larval molting and metamorphosis. We find that the resident retrotransposons— R1 and R2 —are regulated by active rDNA such that reduction in copy number derepresses these elements. Their expression is highest during the early first instar, when loss of rDNA is lethal. Regulation of R1 and R2 may be related to their structural arrangement within the rDNA , as we find they are clustered in the flanks of the nucleolus organizing region (NOR ; the cytological appearance of the rDNA). We assessed the complex nucleolar dominance relationship between X - and Y -linked rDNA using a histone H3.3–GFP reporter construct and incorporation at the NOR and found that dominance is controlled by rDNA copy number as at high multiplicity the Y -linked array is dominant, but at low multiplicity the X -linked array becomes derepressed. Finally, we found that multiple conditions that disrupt nucleolar dominance lead to increased rDNA magnification, suggesting that the phenomena of dominance and magnification are related, and a single mechanism may underlie and unify these two longstanding observations in Drosophila. [ABSTRACT FROM AUTHOR]

Dynamics of nuclear bodies (NBs) in composition and function impact local and global chromatin status and organization, resulting in an altered gene expression profile in response to different cellular states and stresses. NBs serve as 'assemblers' and 'hubs' to modulate chromatin organization and gene expression. Recent advances in spatial multiomics have unveiled the intricate interplay between chromatin and NBs, highlighting the complexity of their interactions and functions. Nuclear bodies (NBs) are biomolecular condensates that participate in various cellular processes and respond to cellular stimuli in the nucleus. The assembly and function of these protein- and RNA-rich bodies, such as nucleoli, nuclear speckles, and promyelocytic leukemia (PML) NBs, contribute to the spatial organization of the nucleus, regulating chromatin activities locally and globally. Recent technological advancements, including spatial multiomics approaches, have revealed novel roles of nucleoli in modulating ribosomal DNA (rDNA) and adjacent non-rDNA chromatin activity, nuclear speckles in scaffolding active genome architecture, and PML NBs in maintaining genome stability during stress conditions. In this review, we summarize emerging functions of these important NBs in the spatial organization of the genome, aided by recently developed spatial multiomics approaches toward this direction. [ABSTRACT FROM AUTHOR]

Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells.We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus. [ABSTRACT FROM AUTHOR]

This study characterizes the chromosomal organization of DNA repetitive sequences and the karyotypic evolution in four representatives of the solitary wasp genus Trypoxylon using conventional and molecular cytogenetic techniques. Our findings present the first cytogenetic data for Trypoxylon rogenhoferi (2n = 30) and Trypoxylon albonigrum (2n = 32), while the karyotypes of Trypoxylon nitidum (2n = 30) and Trypoxylon lactitarse (2n = 30) were similar to those previously described. Fluorochrome staining and microsatellite distribution data revealed differences in the constitutive heterochromatin composition among species. Trypoxylon nitidum and T. albonigrum exhibited one major rDNA cluster, potentially representing an ancestral pattern for aculeate Hymenoptera, while T. rogenhoferi and T. lactitarse showed two pericentromeric rRNA gene sites, suggesting amplification events in their ancestral clade. The (TCAGG)n motif hybridized in the terminal regions of the chromosomes in all four Trypoxylon species, which may suggest that this sequence represents DNA telomeric repeat. Notably, the presence of this repetitive sequence in the centromeric regions of certain chromosome pairs in two species supports the hypothesis of chromosomal fusions or inversions in the ancestral karyotype of Trypoxylon. The study expands the chromosomal mapping data of repetitive sequences in wasps and offers insights into the dynamic evolutionary landscape of karyotypes in these insects. [ABSTRACT FROM AUTHOR]

Agaricus is a genus with more than 500 species. Most of the new species reported since 2000 are tropical or subtropical. The study area, the Malakand region, located in the north of Pakistan, has a subtropical climate. In this study, nine species, including three new species, of Agaricus subgenus Pseudochitonia, are reported from this region. Description of the new species are based on morphological characteristics and phylogenetic analyses using three DNA regions: nuc ribosomal DNA internal transcribed spacers (ITS), fragments of the large subunit of nuc ribosomal DNA (28S), and the translation elongation factor 1-alpha gene (TEF1). One new species, Agaricus lanosus, with wooly squamules on its cap, forms a lineage within Agaricus sect. Bivelares and cannot be classified with certainty in one of the two subsections (Cupressorum and Hortenses) of this section. Agaricus rhizoideus with rhizoid-like structure at the base of the stipe forms a basal clade in Agaricus sect. Hondenses. Specimens of the third new species, Agaricus malakandensis, form a species-level clade within Agaricus sect. Catenulati and exhibits the morphological characteristics of this section. Due to their similar ITS sequences, two previously unnamed specimens from Thailand (A. sp. LD2012162 and CA799) are considered conspecific with A. malakandensis. [ABSTRACT FROM AUTHOR]

Mexico ranks second in the world for Persian lime (Citrus latifolia) exports, making it the principal citrus exporter within the national citrus industry, exporting over 600,000 tons per year. However, diseases are the main factor reducing production, resulting in significant economic losses. Among these diseases, fungal diseases like dieback, caused by species of Lasiodiplodia, are an emerging issue in Persian lime. Symptoms include gummosis, twig and branch dieback, cankers, the necrosis of bark and wood, fruit mummification, and tree decline. The aim of this study was to investigate the occurrence and pathogenicity of the fungal species associated with twig and branch dieback, cankers, and decline of Persian lime trees in southern Mexico, and to elucidate the current status of the Lasiodiplodia species causing the disease in Mexico. During June, July, and August of 2023, a total of the 9229 Persian lime trees were inspected across 230 hectares of Persian lime orchards in southern Mexico, and symptoms of the disease were detected in 48.78% of the trees. Branches from 30 of these Persian lime trees were collected. Fungal isolates were obtained, resulting in a collection of 40 strains. The isolates were characterized molecularly and phylogenetically through the partial regions of four loci: the internal transcribed spacer region (ITS), the β-tubulin gene (tub2), the translation elongation factor 1-alpha gene (tef1-α), and the DNA-directed RNA polymerase II second largest subunit (rpb2). Additionally, pathogenicity was assessed, successfully completing Koch's postulates on both detached Persian lime branches and certified 18-month-old Persian lime plants. Through multilocus molecular phylogenetic identification, pathogenicity, and virulence tests, five species were identified as causal agents: L. iraniensis, L. lignicola, L. mexicanensis, L. pseudotheobromae, and L. theobromae. This study demonstrates that in southern Mexico, at least five species of the genus Lasiodiplodia are responsible for dieback in Persian lime. Additionally, this is the first report of L. lignicola and L. mexicanensis as causal agents of the disease in citrus, indicating novel host interactions between species of Lasiodiplodia and C. latifolia. [ABSTRACT FROM AUTHOR]

Pestalotioid fungi are associated with a wide variety of plants around the world as pathogens, endophytes, and saprobes. In this study, diseased leaves and branches of plants were collected from Guizhou and Sichuan in China. Here, the fungal isolates were identified based on a phylogenetic analysis of the internal transcribed spacer region (ITS), the translation elongation factor 1-alpha (tef1-α) and the beta-tubulin (tub2) of ribosomal DNA, and the morphological characteristics. Ten Neopestalotiopsis isolates and two Pestalotiopsis isolates were obtained, and these isolates were further confirmed as four novel species (N. acericola, N. cercidicola, N. phoenicis, and P. guiyangensis) and one known species, N. concentrica. [ABSTRACT FROM AUTHOR]

Covering: 1997 to July 2023 The adenylation reaction has been a subject of scientific intrigue since it was first recognized as essential to many biological processes, including the homeostasis and pathogenicity of some bacteria and the activation of amino acids for protein synthesis in mammals. Several foundational studies on adenylation (A) domains have facilitated an improved understanding of their molecular structures and biochemical properties, in particular work on nonribosomal peptide synthetases (NRPSs). In NRPS pathways, A domains activate their respective acyl substrates for incorporation into a growing peptidyl chain, and many nonribosomal peptides are bioactive. From a natural product drug discovery perspective, improving existing bioinformatics platforms to predict unique NRPS products more accurately from genomic data is desirable. Here, we summarize characterization efforts of A domains primarily from NRPS pathways from July 1997 up to July 2023, covering protein structure elucidation, in vitro assay development, and in silico tools for improved predictions. [ABSTRACT FROM AUTHOR]

Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes. [ABSTRACT FROM AUTHOR]

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site. [ABSTRACT FROM AUTHOR]

Fusarium root rot is usually classified as an extremely destructive soilborne disease. From 2020 to 2021, Fusarium root rot was observed in production areas and seriously affected the yield and quality of Scutellaria baicalensis in Shanxi Province, China. Based on morphological characteristics and combined analysis of the internal transcribed spacer region of ribosomal DNA and translation elongation factor 1 -alpha sequences. 68 Fusarium isolates obtained in this work were identified as E oxysporum (52.94%), F. acuminatum (20.59%), F. solani (16.17%). F. proliferatum (5.88%), F. incarnation (2.94%), and F. brachygibbosum (1.47%). In the pathogenicity tests, all Fusarium isolates could infect S. baicalensis roots, presenting different pathogenic ability. Among these isolates, F. oxysporum was found to have the highest virulence on S. baicalensis roots, followed by F. acuminatum, F. solani, F. proliferatum. F. brachygibbosum, and F. incarnation. According to fungicide sensitivity tests, Fusarium isolates were more sensitive to fludioxonil and difenoconazole, followed by carbendazim, thiophanate-methyl, and hymexazol. In brief, this is the first report of Fusarium species (F. oxysporum, F. acuminatum, F. solani, F. proliferatum, F. incamarum, and F. brachygibbosum) as causal agents of root rot of S', baicalensis in Shanxi Province, China. The fungicide sensitivity results will be helpful for formulating management strategies of baicalensis root rot. [ABSTRACT FROM AUTHOR]

Background: Dual RNA sequencing is a powerful tool that enables a comprehensive understanding of the molecular dynamics underlying plant-microbe interactions. RNA sequencing (RNA-seq) poses technical hurdles in the transcriptional analysis of plant-bacterial interactions, especially in bacterial transcriptomics, owing to the presence of abundant ribosomal RNA (rRNA), which potentially limits the coverage of essential transcripts. Therefore, to achieve cost-effective and comprehensive sequencing of the bacterial transcriptome, it is imperative to devise efficient methods for eliminating rRNA and enhancing the proportion of bacterial mRNA. In this study, we modified a strand-specific dual RNA-seq method with the goal of enriching the proportion of bacterial mRNA in the bacteria-infected plant samples. The enriched method involved the sequential separation of plant mRNA by poly A selection and rRNA removal for bacterial mRNA enrichment followed by strand specific RNA-seq library preparation steps. We assessed the efficiency of the enriched method in comparison to the conventional method by employing various plant-bacterial interactions, including both host and non-host resistance interactions with pathogenic bacteria, as well as an interaction with a beneficial rhizosphere associated bacteria using pepper and tomato plants respectively. Results: In all cases of plant-bacterial interactions examined, an increase in mapping efficiency was observed with the enriched method although it produced a lower read count. Especially in the compatible interaction with Xanthmonas campestris pv. Vesicatoria race 3 (Xcv3), the enriched method enhanced the mapping ratio of Xcv3-infected pepper samples to its own genome (15.09%; 1.45-fold increase) and the CDS (8.92%; 1.49-fold increase). The enriched method consistently displayed a greater number of differentially expressed genes (DEGs) than the conventional RNA-seq method at all fold change threshold levels investigated, notably during the early stages of Xcv3 infection in peppers. The Gene Ontology (GO) enrichment analysis revealed that the DEGs were predominantly enriched in proteolysis, kinase, serine type endopeptidase and heme binding activities. Conclusion: The enriched method demonstrated in this study will serve as a suitable alternative to the existing RNA-seq method to enrich bacterial mRNA and provide novel insights into the intricate transcriptomic alterations within the plant-bacterial interplay. [ABSTRACT FROM AUTHOR]

In the present study, we report for the first time the presence of Vitrina pellucida and Arion silvaticus as invasive species in Isla Grande of Tierra del Fuego, Argentina. Additionally, our research confirmed the presence in the same region of Deroceras reticulatum a previously reported invasive species from continental Patagonia. Taxonomic identification was achieved through morphological and molecular analyses (ribosomal 5.8S-ITS2-28S region and 16S rRNAgene). The finding of V. pellucida constitutes the first record of Vitrinidae for South America. This species is already naturalized in southern Tierra del Fuego and invaded natural areas of the National Park but still with small populations. In the case of Arion silvaticus , we observed a comparable situation, as this species has not only been collected from urban areas but also from within the forests of the protected area. These exotic species of land snails are exclusively cold-adapted Pulmonates. Their feeding types and diets range from herbivores on fresh plant material to omnivorous, occasionally on dead animals. The native micro snail species, coexisting in the same habitats, due to their minimal dispersal capacity and probable dependence on particular microhabitats, are particularly vulnerable not only to anthropogenic disturbances but also to the impacts and activities of these exotic species. Given the tourist impact in the region, the introduction of V. pellucida and Arion silvaticus in Tierra del Fuego has most likely occurred through accidental transport in soil by tourists arriving on the island. Another possible pathway of introduction is plant transportation. [ABSTRACT FROM AUTHOR]

The demand for common hazel (Corylus avellana) fruit increases constantly. Powdery mildew (PM) on hazels in Hungary and throughout Europe was previously caused mainly by Phyllactinia guttata. However, less than a decade ago, another fungus of Asian origin, Erysiphe corylacearum, appeared on hazels in Europe, including Hungary. Our investigation aimed to develop a species-specific PCR (ssPCR) to aid the identification of P. guttata and E. corylacearum, and to assess the presence of the latter, non-native fungus in Hungary. For this study, 59 samples were collected from Hungary between 2021 and 2023. The chasmothecial morphology of the PM fungi was observed, and the internal transcribed spacer (ITS) of ribosomal DNA was sequenced in representative samples. Morphological analysis distinguished two types of chasmothecia. Parts of the chasmothecia, typical of P. guttata, were flattened and spherical with bristle-like appendages, while other chasmothecia, characteristic of E. corylacearum, were distinctly smaller, bearing appendages with branched apices. Sequence data also verified the presence of P. guttata and E. corylacearum in our samples. The developed ssPCR revealed that E. corylacearum was present in more than three-quarters of the samples, more than a quarter of the samples contained both fungi and about one-fifth carried solely P. guttata. The alien fungus E. corylacearum was found in all but one of the sampled regions and was found on C. avellana and also on C. colurna. Erysiphe corylacearum spreads rapidly and can be considered an invasive pathogen. Its practical importance lies in its ability to infect hazelnuts, potentially causing economic losses. Our ssPCR ensures accurate and quick identification of the fungus, which is essential for effective plant protection. [ABSTRACT FROM AUTHOR]

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While genotoxic chemotherapeutic agents are among the most effective tools to combat cancer, they are often associated with severe adverse effects caused by indiscriminate DNA damage in non-tumor tissue as well as increased risk of secondary carcinogenesis. This study builds on our previous work demonstrating that the RNA Polymerase I (Pol I) transcription inhibitor CX-5461 elicits a non-canonical DNA damage response and our discovery of a critical role for Topoisomerase 2α (Top2α) in the initiation of Pol I-dependent transcription. Here, we identify Top2α as a mediator of CX-5461 response in the murine Eµ-Myc B lymphoma model whereby sensitivity to CX-5461 is dependent on cellular Top2α expression/activity. Most strikingly, and in contrast to canonical Top2α poisons, we found that the Top2α-dependent DNA damage induced by CX-5461 is preferentially localized at the ribosomal DNA (rDNA) promoter region, thereby highlighting CX-5461 as a loci-specific DNA damaging agent. This mechanism underpins the efficacy of CX-5461 against certain types of cancer and can be used to develop effective non-genotoxic anticancer drugs. [ABSTRACT FROM AUTHOR]

In the conducted research, a murine model for ulcerative colitis (UC) was established utilizing dextran sodium sulfate (DSS) to investigate the therapeutic potential of dandelion root polysaccharide extracts on this disease. This study employed an analysis of gut microbiota composition and serum metabolomics to understand the biochemical effects of these polysaccharides. Sequencing of the 16S ribosomal DNA component indicated an increased presence of Bacteroides in the DSS-treated model group, contrasting with a significant enhancement in Faecalibaculum populations in mice treated with dandelion root polysaccharides (DPs). This shift suggests a pivotal role of DPs in elevating fecal N-butyric acid levels—a crucial factor in the maintenance of gut microbiota equilibrium. Through metabolomic profiling of serum, this research identified distinct metabolic changes across the control, DSS model, and DP treatment groups, highlighting four major differential metabolites: (2S)-2-amino-3-[[(2R)-2-butanoyloxy-3-propanoyloxypropoxy]-hydroxyphosphoryl]oxypropanoic acid; (1R,8S,9S)-3,4-dihydroxy-8-methoxy-11,11-dimethyl-5-propan-2-yl-16-oxatetracyclo [7.5.2.01,10.02,7]hexadeca-2,4,6-trien-15-one; Aspartylasparagine; and Nap-Phe-OH. These metabolites are implicated in mitigating oxidative stress, suggesting that DPs facilitate a protective mechanism for the intestinal lining through various biochemical pathways. Additionally, a notable correlation was established between the altered gut microbiota and the serum metabolomic profiles, underscoring the intricate interplay between these two biological systems in the context of UC. This study's outcomes illustrate that UC induces significant alterations in both gut microbiota and metabolic signatures, whereas dandelion root polysaccharides exhibit a profound ameliorative effect on these disruptions. This investigation underscores the therapeutic promise of dandelion root polysaccharides in the management of UC by modulating gut microbiota and metabolic pathways. [ABSTRACT FROM AUTHOR]

Background: Fenofibrate is a compound with diverse biological properties that can be utilized to lower blood lipids. Understanding the impact of the gut microbiota in hyperlipidemia is vital for controlling systemic inflammation and improving serum lipid control. Nevertheless, the specific effects of fenofibrate on the phenotype and gene expression of resident gut bacteria, as well as its influence on the transformation of microbial metabolism into functional networks, remain unclear. In this study, our aimed to examine the gene and metabolic pathways of the gut microbiota in a hamster fed a high-fat diet (HFD) and administered fenofibrate. Results: In this study, we conducted metagenomic analyses on samples from HFD hamsters treated with fenofibrate. The results indicated that fenofibrate treatments significantly reduce the serum lipid levels in hyperlipidemia hamsters. And the group treated with fenofibrate exhibited higher levels of beneficial bacterial species associated with health, including Bacteroides ovatus, Bifidobacterium animalis, Bacteroides intestinalis, Allobaculum stercoricanis, Lactobacillus reuteri, and Bacteroides acidifaciens, in comparison to the HFD group. Additionally, analysis of metabolic pathways demonstrated that dietary fenofibrate significantly enhanced the biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, and pyrimidine metabolism, while reducing glyoxylate and dicarboxylate metabolism, tyrosine metabolism, tryptophan metabolism, and nonribosomal peptide structures. Furthermore, these metabolic pathway changes were associated with relative alterations in the abundance of genes from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, namely K01667, K11358, K13953, K04072, K06131, K00655, K04567, K02864, K06409, K05366, K01867, K21071, and K13292. Moreover, significant changes were observed in related to carbohydrate and antibiotic resistance, such as glycosyltransferase family 51 (GT51) as well as adeC, carA, and MexT. Conclusions: Dietary fenofibrate exerted significant effects on intestinal flora and genes related to lipid, energy, and amino acid metabolism, ultimately promoting a healthier colonic environment for the host. And these findings contribute to a better understanding of the mechanism of action of fenofibrate and provide a valuable foundation for future experimental and clinical studies, aiming to explore its practical applications. [ABSTRACT FROM AUTHOR]

Background: Malaria transmission in Tanzania is driven by mosquitoes of the Anopheles gambiae complex and Anopheles funestus group. The latter includes An. funestus s.s., an anthropophilic vector, which is now strongly resistant to public health insecticides, and several sibling species, which remain largely understudied despite their potential as secondary vectors. This paper provides the initial results of a cross-country study of the species composition, distribution and malaria transmission potential of members of the Anopheles funestus group in Tanzania. Methods: Mosquitoes were collected inside homes in 12 regions across Tanzania between 2018 and 2022 using Centres for Disease Control and Prevention (CDC) light traps and Prokopack aspirators. Polymerase chain reaction (PCR) assays targeting the noncoding internal transcribed spacer 2 (ITS2) and 18S ribosomal DNA (18S rDNA) were used to identify sibling species in the An. funestus group and presence of Plasmodium infections, respectively. Where DNA fragments failed to amplify during PCR, we sequenced the ITS2 region to identify any polymorphisms. Results: The following sibling species of the An. funestus group were found across Tanzania: An. funestus s.s. (50.3%), An. parensis (11.4%), An. rivulorum (1.1%), An. leesoni (0.3%). Sequencing of the ITS2 region in the nonamplified samples showed that polymorphisms at the priming sites of standard species-specific primers obstructed PCR amplification, although the ITS2 sequences closely matched those of An. funestus s.s., barring these polymorphisms. Of the 914 samples tested for Plasmodium infections, 11 An. funestus s.s. (1.2%), and 2 An. parensis (0.2%) individuals were confirmed positive for P. falciparum. The highest malaria transmission intensities [entomological inoculation rate (EIR)] contributed by the Funestus group were in the north-western region [108.3 infectious bites/person/year (ib/p/y)] and the south-eastern region (72.2 ib/p/y). Conclusions: Whereas An. funestus s.s. is the dominant malaria vector in the Funestus group in Tanzania, this survey confirms the occurrence of Plasmodium-infected An. parensis, an observation previously made in at least two other occasions in the country. The findings indicate the need to better understand the ecology and vectorial capacity of this and other secondary malaria vectors in the region to improve malaria control. [ABSTRACT FROM AUTHOR]