Ribosomal RNA Research Articles

Taxonomy of the cestodes Avitellina sudanea and A. centripunctata (Cyclophyllidea, Thysanosomatidae) parasitic in sheep and goats in India based on morphological and molecular evidence.

This study presents morphological, molecular and phylogenetic analyses of two species of the genus Avitellina, A. sudanea and A. centripunctata parasitic in sheep and goats and sampled in the region of the City of Chandigarh, North India. Three molecular markers were used: mitochondrial cytochrome c oxidase subunit 1 (cox1), nuclear small subunit ribosomal RNA (SSU rDNA) and internal transcribed spacer 1-5.8S rRNA (ITS1-5.8S rDNA) genes. Morphological analysis revealed differences in key structures, including paruterine organ shape and testis arrangement. Molecular analysis revealed that A. sudanea showed no exact match but significant similarity with other species: A. lahorea and A. centripunctata, exhibiting 91.39% and 85.89-86.52% (SSU rDNA), 96.27 and 94.31% (cox1), 94.19 and 94.41% (ITS1-5.8S rDNA) sequence similarity, respectively. The Maximum Likelihood phylogenetic trees based on DNA sequences of SSU rRNA, cox1 and ITS1 placed these species in a separate clade, which was distinct from anoplocephalids (sensu stricto) and supported the thysanosomatids as a distinct taxon at the family level. The evolutionary divergence based on base substitution rates confirmed substantial interspecific genetic distinctions, with high divergence values of 0.12 (cox1), 0.25 (SSU rDNA) and 0.11 (ITS1-5.8S rDNA) between A. sudanea and A. centripunctata. This study provides the first molecular characterization of A. sudanea, confirming its genetic distinctiveness and taxonomic status as a valid species. Our findings highlight the necessity for more molecular studies on Avitellina tapeworms using robust genetic tools to ensure accurate taxonomic delineation within the genus.

First Report of Pink Snow Mold Caused by Microdochium majus on Wheat in Xinjiang Uygur Autonomous Region, China.

Pink snow mold (PSM) is a destructive disease that primarily occurs in cold, humid regions with persistent snow cover. The main pathogens, Microdochium nivale and M. majus, can infect a wide range of graminaceous crops under snow cover (Ponomareva et al., 2021). In Xinjiang, PSM has caused significant damage to wheat in years with heavy snowfall. In March 2023, a detailed survey was conducted in Nilek County, Yili Prefecture, Xinjiang Uygur Autonomous Region, to investigate prevalent diseases impacting winter wheat (Triticum aestivum L.) following snow melt. Widespread infection was observed on seedlings in wheat fields, with dead leaves near the soil surface covered in a typical dusky-pink mold and the upper leaves displaying watery spots. Over 50% of the wheat exhibited these symptoms in approximately 10 hectares of the field. To identify the pathogen, 12 symptomatic leaf segments approximately 0.5 cm in length were collected, surface disinfected, placed on potato dextrose agar (PDA), and incubated at 20°C for 5 days. All symptomatic tissues yielded fungal colonies that exhibited vigorous growth, and pink to orange fluffy mycelium. After 1 week, orange-red conidial mounds appeared at the edges of the PDA. The conidia measured 2.52-6.41 × 9.23-21.27 μm (av = 4.05 × 14.79 μm; n = 60), with 1-6 septa. These morphological characteristics were consistent with previous reports and all 12 isolates were identified as M. majus (Glynn et al., 2005; Hernández-Restrepo et al., 2015). Molecular confirmation was performed using four primer pairs targeting the 28S ribosomal RNA (LSU) gene (Hernández-Restrepo et al., 2015), internal transcribed spacer (ITS) (White et al., 1990), RNA polymerase II second largest subunit (RPB2) gene, and β-tubulin gene (Jewell et al., 2013). BLAST analysis showed high similarity (≥ 99.58%) with the corresponding sequences of LSU (KP858937, 832/832 bp), ITS (OM949048, 509/509 bp), RPB2 (MZ734201, 727/727 bp) and β-tubulin (JX280568, 717~719/720) of M. majus in the database. The new sequences were deposited in GenBank as follows: LSU: PQ319764 to PQ319775; ITS: PQ252935 to PQ252946; RPB2: PQ261093 to PQ261104; β-tubulin: PQ261081 to PQ261092. To assess the pathogenicity of the isolates, germinated seeds of the susceptible wheat cultivar Mingxian169 were grown in test tubes containing Murashige and Skoog medium, each inoculated with a 0.8 mm diameter plug of M. majus. Of the 12 isolates, seven were selected for pathogenicity test. In the control group, seeds were cultivated without the fungal inoculum. The test tubes were incubated at 20°C under a 16-hour photoperiod for 20 days, with 10 replicates per isolate (Gorshkov et al., 2020). The control showed no symptoms, whereas all inoculated treatments resulted in wheat seedlings with brown discoloration at the stem base, watery leaf spots, and dusky-pink mold in severe cases, leading to plant death. No pathogens were isolated from the control, whereas M. majus was reisolated from the symptomatic leaves, confirmed morphologically and molecularly, fulfilling Koch's postulates. In conclusion, this study provides the first confirmation of M. majus as the causal agent of PSM in Xinjiang. Future efforts should prioritize monitoring and managing the occurrence and spread of M. majus-induced PSM in wheat to mitigate its potential threat to wheat production and prevent significant economic losses.

Molecular characterization and phylogenetic analyses of the mitogenome of Wan-Xi white goose, a native goose breed in China

BackgroundThe Wan-Xi white goose (WXG), an indigenous Chinese waterfowl (Anserini: Anserinae), is crucial for goose germplasm conservation. This study aimed to sequence and analyze the complete mitochondrial DNA (mtDNA) of WXG using the BGISEQ-500 platform. The mtDNA's structure and function were investigated to gain insights into its genetic diversity and population structure.ResultsThe mtDNA was found to be 16,743 bp long and comprised 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes, a complement of 13 protein-coding genes (PCGs), as well as a single noncoding control region known as the D-loop. Notably, all tRNA genes, except for trnS1-tRNA which lacked the dihydrouridine stem, were predicted to adopt the typical cloverleaf structure. Given the genetic variability across the mtDNA of Anser spp. and the intergenic gaps identified by codon analysis, the codon usage patterns were comprehensively examined via comparative analysis of the mtDNAs of WXG and 24 other Anser spp. The relative synonymous codon usage (RSCU) values of the 13 mitochondrial PCGs of WXG were consistent with those of the mitochondrial PCGs of the 24 other Anser spp. Analysis of the neutrality (GC3-GC12), the effective number of codons (ENCs)-GC3, and parity rule 2-bias plots further revealed that natural selection emerged as the primary factor influencing codon bias in Anser sp. High nucleotide diversity (Pi > 0.02) was observed in several regions, including the D-loop, ATP6, 12S rRNA, ND1, 16S rRNA_ND1, COX2, and ND5. Furthermore, the results of nonsynonymous (Ka)/synonymous (Ks) analysis of the 13 mitochondrial PCGs of the 25 species under Anser revealed that the genes were subject to strong purifying selection. The findings of phylogenetic analysis further revealed that WXG and 10 other members of Anser cygnoides clustered into a single branch to form a monophyletic group.ConclusionThis research provides valuable insights into the mtDNA of WXG, highlighting its genetic diversity and population structure. The identified mutation hotspots and purifying selection on mitochondrial PCGs suggest potential areas for future research on Anser cygnoides. The findings contribute to our understanding of this rare species and its conservation efforts.

The impact of dietary salt on the development of hypertension and gut microbiome dysbiosis in captive-bred vervet monkeys (Chlorocebus aethiops)

BackgroundThe study was designed to establish a hypertensive nonhuman primate model to evaluate the role of dietary salt intake on blood pressure levels and gut microbiome regulation. Sixteen adult vervet monkeys were selected and assigned into two groups (control and experimental). The control group was given a maintenance diet (100 g), whereas the diet of the experimental group was supplemented with 1.5 g/day of dietary salt in the mornings for six months (T0-T6), thereafter, the dose was increased to 2 g/day for additional six months (T9-T12). Blood and stool samples were collected for biochemical and 16 S ribosomal RNA gene sequencing.ResultsThe control group was borderline hypertensive (134.7/62.9 mmHg), whereas elevated blood pressure levels (171.3/81.3 mmHg) were observed at T12 indicating the experimental group to be salt sensitive. Furthermore, gut microbiome analysis showed two main phyla, Bacteroidetes and Firmicutes. However, there was no significant difference for alpha and beta diversity for both groups.ConclusionThese findings suggested that dietary salt intake (1.5–2 g/day) caused alterations in systolic blood pressure levels, chloride and alkaline phosphatase (ALP). However, these changes were not associated with gut microbiome dysbiosis even though significant changes were observed over time for the individual groups.

Nephropathy II Decoction Attenuates Renal Fibrosis via Regulating TLR4 and Gut Microbiota Along the Gut-Kidney Axis.

Nephropathy II Decoction (NED) is a widely used Chinese medicinal formulation for managing chronic kidney disease (CKD). Despite its extensive application, the precise mechanisms underlying its therapeutic effects remain poorly understood. This study aims to elucidate the role of NED in attenuating renal fibrosis and to explore its impact on the gut-kidney axis. The principal constituents of NED were analyzed using ultra-performance LC-tandem mass spectrometry (UPLC-MS/MS). A bilateral renal ischemia-reperfusion injury (bIRI) model was employed to induce fibrosis. RT-qPCR was utilized to assess the expression of mRNA related to the toll-like receptor 4 (TLR4) and myeloid differentiation factor 88 (MyD88) and nuclear factor-κB (NF-κB) signaling pathway. Western blotting analysis was performed to identify changes in renal fibrosis markers, TLR4/MyD88/NF-κB pathway proteins, and the colon proteins ZO-1 and Occludin-1. Serum levels of uremic toxins were quantified using enzyme-linked immunosorbent assay (ELISA), and 16S ribosomal RNA (rRNA) gene sequencing was conducted to explore changes in the gut microbiome of the mice. Our study demonstrated that mice in the NED group exhibited reduced serum creatinine, blood urea nitrogen, and urinary protein levels, alongside improvements in kidney damage and a decrease in renal fibrosis markers. In the bIRI group, TLR4/MyD88/NF-κB protein and mRNA levels, as well as intestinal tight junction proteins and enterogenic uremic toxins, were significantly reduced. NED treatment reversed these changes and modified the gut microbiota. Furthermore, fecal microbial transplantation (FMT) alleviated kidney damage and fibrosis in bIRI mice. In summary, NED ameliorates kidney injury and fibrosis by modulating the gut microbiota and may further attenuate fibrosis through the inhibition of TLR4 expression, thereby influencing the gut-kidney axis.

AmrProfiler: a comprehensive tool for identifying antimicrobial resistance genes and mutations across species.

Antimicrobial resistance (AMR) remains a critical challenge in public health and research. AmrProfiler is a comprehensive tool with three specialized modules: identifying acquired AMR genes, resistance-associated mutations, and ribosomal RNA (rRNA) gene mutations across nearly 18 000 bacterial species. By integrating and refining data from established databases, it provides a robust framework for AMR analysis. AmrProfiler is the first to systematically report mutations in rRNA genes, offering in-depth analysis of rRNA copy numbers and mutations-key for identifying potential rRNA-associated resistance mechanisms. Its curated database includes 7600 unique AMR gene entries and over 4300 resistance-related mutations. Supporting genome assemblies in multiple formats, AmrProfiler allows users to customize detection thresholds for AMR genes, mutations, and rRNA analysis. Validation with Acinetobacter baumannii,Escherichia coli,Klebsiella pneumoniae,Staphylococcus aureus, and Staphylococcus epidermidis demonstrated that AmrProfiler accurately identified all AMR genes and mutations reported by other tools while also detecting additional resistance markers and mutations not previously recognized. By bridging AMR genotypes and phenotypes, AmrProfiler provides actionable insights that advance both research and clinical applications in AMR. AmrProfiler is freely available as an open-access web server without login at https://dianalab.e-ce.uth.gr/amrprofiler.

Alterations in scalp microorganisms after Er: YAG laser treatment for Shanghai androgenetic alopecia patients.

Androgenetic alopecia (AGA) is associated with the scalp microbiota, but the role of microflora during hair loss has not been fully characterized. Erbium: yttrium aluminum garnet (Er: Yag) is a microablative laser treatment for hair regeneration that can cause minimal damage to the skin surface. This investigation aimed to evaluate the effects of microtrauma caused by the Er: Yag laser of AGA on scalp microorganisms. Thirteen AGA patients in this study received Er: Yag laser treatment (3.3Hz frequency and 7.00J/cm2 pulse fluence). Scanning electron microscope (SEM) was used to observe the scalp bacteria. Before treatment, microflora samples were collected 2 hours and 48hours after shampooing. Samples were also collected on the third, seventh, and fourteenth days following laser treatment. Scalp microorganisms coding the 16S ribosomal RNA V3/V4 region were analysed by high-throughput DNA sequencing. Globular bacteria were detected through the SEM images on the epidermis at the junction of the hair shaft and hair follicle. The results of the 16S sequencing revealed that the most abundant genera observed across all samples prior to laser treatment were Cutibacterium species (spp.) (53%) and Staphylococcus spp. (13%) in 13 AGA patients. Three days after laser treatment, Firmicutes, Staphylococcus spp., and Staphylococcus capitis were significantly more abundant at the phylum, genus, and species levels than before, respectively. These data suggest that the presence of Staphylococcus spp. significantly increased after microtrauma caused by Er: Yag laser treatment, indicating that the Er: Yag laser might play an essential role in modulating and restoring the balance of scalp microbiota.

Phlebia formosana Strain SMF410-5-1 and Auricularia cornea Strain ME1-1 Display Potential in Wood Degradation and Forest Waste Reutilization

Wood waste, primarily composed of lignin, cellulose, and hemicellulose, which is typically disposed of through burning and crushing, poses environmental challenges. However, conventional wood waste disposal methods present critical limitations, such as environmental pollution and resource waste. To develop sustainable processing strategies to dispose wood waste, we identified two fungal isolates, SMF410-5-1 and ME1-1, from decayed wood trunks, demonstrating high lignocellulose-degrading enzyme activities, including laccase (Lac, 125.7 U/mL), manganese peroxidase (MnP, 89.3 U/mL), and lignin peroxidase (LiP, 67.9 U/mL). Isolates of ME1-1 and SMF410-5-1 both exhibited superior poplar lignin degradation, while SMF410-5-1 excelled in coniferous wood weight losses, which reached 19.7% for pine after 180 days post inoculation. Moreover, biochemical analyses revealed that isolates of ME1-1 and SMF410-5-1 accelerated the degradation by producing various lignocellulose-degrading enzymes to hydrolyze wood waste. In addition, through multi-locus phylogenetic analysis using sequences of the internal transcribed spacer (ITS), large subunit ribosomal RNA (LSU), and RNA polymerase II second largest subunit (RPB2), SMF410-5-1 and ME1-1 were identified as Phlebia formosana and Auricularia cornea, respectively. This study provides novel insights into fungal-driven biodegradation, offering eco-friendly solutions for forest waste recycling and supporting circular bioeconomy strategies.

Unveiling species diversity within early-diverging fungi from China V: Five new species of Absidia (Cunninghamellaceae, Mucoromycota)

Absidia is widely distributed in soil, koji, and various types of feces. A multi-locus phylogeny covering the small subunit (SSU), internal transcribed spacer (ITS), and large subunit of ribosomal RNA gene (LSU rDNA), translation elongation factor 1-alpha (TEF1α), and actin (Act), combined with morphological characteristics, revealed five new species in this genus. This study provides their descriptions and illustrations and discusses their differences from morphological allies and phylogenetic relatives. Absidia collariatasp. nov. is distinguished from other species in terms of the length of collars. A. hainanensissp. nov. is named after the geographical location Hainan, distinctive with a higher maximum growing temperature. A. pyriformissp. nov. is different from other species in terms of sporangial shape. A. tardivasp. nov. is characterized by slow growth. And A. tibetensissp. nov. is named after the geographical location Tibet and differentiated by more ampulliform swellings. This study further enriches the species diversity of Absidia as the latest discovery of early-diverging fungi in China.

Complete mitochondrial genome of the Korean endemic earthworm Amynthas bubonis (Clitellata: Megascolecidae): mitogenome characterization and phylogenetic positioning

Amynthas bubonis Hong & James, 2001 is an earthworm species endemic to Korea. This species is typically found in mountainous forests at low altitudes. Specimens were collected from Mt. Deogyu in South Korea, and the complete A. bubonis mitogenome was sequenced, assembled, and annotated. The A. bubonic mitogenome is a 15,095 bp circular DNA molecule with 64.85% A + T content. It contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding region (control region). Phylogenetic analysis revealed that A. bubonis clustered with A. jiriensis, A. yunoshimensis, and M. hilgendorfi in the well-supported Megascolecidae family.

Alteration of gut microbiota associated with hypertension in children

BackgroundThe association of disturbance in gut microbiota with hypertension (HTN) defined on three separate occasions among children and adolescents remains unclear. In this study, we aimed to compare the differences in gut microbiota composition and diversity between children with HTN and those with normal blood pressure (BP).MethodsData and stool samples were collected from the second follow-up of a childhood cardiovascular health cohort study in 2021. 16 S ribosomal RNA gene sequencing was conducted to determine the relative abundance of microbial taxa in 51 children aged 10–14 years with HTN and 51 children with normal BP.ResultsCompared with children with normal BP, those with HTN had decreased gut microbiome diversity. At the genus level, after adjusting for the false discovery rate (FDR), the proportions of several gut microbiota such as Blautia (PFDR=0.042), Coprococcus (PFDR=0.042), Eubacterium_ventriosum_group (PFDR=0.027), Christensenellaceae_R-7_group (PFDR=0.027), and norank_f__Lachnospiraceae (PFDR=0.015) significantly decreased in children with HTN compared to those with normal BP. Receiver operating characteristic analysis, net reclassification improvement (NRI) and integrated discrimination improvement (IDI) were performed and showed that the genera norank_f__Lachnospiraceae and Dorea significantly enhanced the ability of body mass index to differentiate between children with HTN and those with normal BP (area under the receiver operating characteristic curve: 0.95, 95% confidence interval 0.91–0.99; NRI > 0; IDI = 0.12, P < 0.05). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States showed that the mean proportions of cofactors and vitamins metabolism pathway and the glycan anabolism pathway were higher in children with HTN.ConclusionsDisturbances in the abundance and diversity of gut microbiota may contribute to the development of HTN in children. Gut microbiota biomarkers may be of significant importance in the early identification and diagnosis of childhood HTN.Clinical trial numberNot applicable.

Weakened priming effect along soil profile in alpine grasslands on the Tibetan Plateau.

Subsoils hold a substantial reservoir of organic carbon (C), and its dynamics can be greatly influenced by fresh C inputs through priming effect, potentially altering the magnitude of soil C-climate feedback. Despite the importance of soil C dynamics in regulating this feedback, our understanding of how soil C release and the priming effect vary along the soil profile remains limited, especially in alpine grasslands on the Tibetan Plateau. In particular, the relative importance of abiotic and biotic factors, such as soil physicochemical properties, aggregate and mineral protection, substrate quantity and quality, and plant and microbial properties (e.g., microbial biomass and diversity), in mediating vertical variations in soil C release and the priming effect is still unclear. Using 1-meter-deep soil profiles from five sites on the plateau, our 13C isotope labeling incubation experiments revealed a significant decline in both C release and the priming effect with increasing soil depth. We found that variations in soil C release along the profile were primarily influenced by soil properties (soil moisture and pH), mineral protection (the molar ratios of amorphous Fe/Al oxides to soil organic C (SOC) and soil mineral specific surface area), and hydrolase activity. In addition, vertical variations in the priming effect were dominantly affected by soil properties (soil moisture and pH), mineral and aggregate protection (the molar ratio of exchangeable Ca to SOC and the proportion of C occluded in clay+silt fractions), and microbial properties (oxidase activity and the copy number of bacterial ribosomal RNA gene operons). These findings provide valuable insights into the complex soil C cycling across profiles and its feedback to climate change.

Association of the gut microbiota with type 2 diabetes: Links to disease and remission in the Japanese population.

Although the gut microbiota is associated with type 2 diabetes (T2D) and its remission in clinical settings, their relationship in the general population remains unclear. This study aimed to investigate the association between the gut microbiota and T2D and its remission in a population-based setting. A cross-sectional study was conducted on 1,639 Japanese participants with (n = 106) or without (n = 1,533) T2D. The gut microbiota was compared between the two groups using multivariable-adjusted logistic regression. The relative abundance of the gut microbiota in fecal samples was calculated using 16S ribosomal RNA amplification. The association between the gut microbiota and T2D remission was determined via longitudinal analyses. Six genera were independently associated with T2D; a higher abundance of Faecalibacterium, Blautia, Roseburia, and Oscillibacter was significantly associated with a lower odds ratio for T2D, whereas a higher abundance of Megasphaera and Lactobacillus was significantly associated with a higher odds ratio for T2D. Of these, only Blautia abundance was significantly increased in the remission group compared with that in the non-remission group. In the remission group, an increase in Blautia abundance was significantly correlated with an increase in adiponectin level and skeletal muscle mass. Specific gut microbes were significantly associated with T2D and its remission. The gut microbiota may represent a potential area for further exploration in T2D treatment and prevention. However, additional large-scale cohort studies or intervention studies using a probiotic or prebiotic approach are needed to validate these findings.

First Report of Nigrospora oryzae Causing Basal Rot on Siberian lily (Lilium spp.) Ornamental hybrids in China.

Lilium 'Siberia', is extensively cultivated and has high economical value in China due to its popularity as an ornamental lily. In August 2023, lily basal rot was observed on about 60% of two-year-old plants at the Liaoning Academy of Agricultural Sciences Multiplex greenhouse ( in an area of about 2000 m2 ) . Initial symptoms appeared on the base of the bulbs as brown lesions that expanded over time, and later the leaves turned yellow and about one month latter the whole plant died. To isolate the causal pathogen, tissues were collected from 5 symptomatic plants with basal rot. The infected bulbs were surface-sterilized with 75 % ethanol solution for 30 s after initial rinsing, followed by triple sterile-water washes, specimens were dried aseptically prior to pathogen isolation. Tissue sections 5 mm × 5 mm were transferred from plant lesion margins onto potato dextrose agar (PDA) medium after surface sterilization. Cultures were maintained at 25℃ for pathogen isolation. After 7 days, 3 consistent surface morphology strains(H1, H2 and H3) were prepared based on single spore isolates. After 10 to 15 days, mycelium had fully covered the plates. The hyphae were branched, septate, smooth, hyaline, Conidia were black, solitary, globose or subglobose, glossy aseptate of 8.3 - 11.4 μm × 12.4 - 14.9 μm (n=50) in size, and produced at the tips of hyaline and ampulliform conidiophores. The fungus showed similar morphological characteristics to Nigrospora oryzae (Wang et al. 2017). For molecular confirmation of the species identity, genomic DNA of three isolates (H1, H2 and H3) were extracted by the CTAB method (O'Donnell et al., 1998), and portions of three genes, the Intemal Transcribed Spacer (ITS) of the ribosomal RNA, the Translation Elongation Factor subunit 1-alpha (TEF1-ɑ) and the beta-tubulin (TUB2) genes were amplified by the PCR using the primers ITS1/ITS4,EF1-728F/EF-2 and Bt-2a/Bt-2b (Wang et al. 2017). A BLASTn analysis showed that the identity of the nucleotide sequences of isolates (H1, H2 and H3) were 99%(500/501bp; 488/488 bp; 495/499bp) for ITS, 99% (461/461 bp;466/467 bp;467/467 bp) for TEF1- ɑ; and 99% (331/333 bp; 376/384 bp; 381/388 bp) for the TUB2 sequences, with N. oryzae LC2702 in GenBank. The resulting sequences were submitted to GenBank under accession numbers PP203296, PP784618, PP784619 for ITS; PP417827, PP869279, PP886084, for TEF1-ɑ; PP448183, PP869277, PP869278 for TUB2 of isolates H1, H2 and H3 respectively. A neighbor-joining phylogenetic tree showed that the three isolates from Siberian lily clustered with the N.oryzae clade.Therefore, the isolates H1, H2 and H3 were identified as N. oryzae based on morphology and molecular evidence. One representative isolate(H1) was used for completing the Koch's postulates. A pathogenicity test was made on 1-year-old healthy Siberia lily bulbs, the bulbs were disinfected, using a sterile needle to prick the base of the bulbs, then they were planted in sterilized soil. A conidial suspension (1 × 106 conidia/ml) was used to water the planted lily bulbs once every 5 days, and the controls were watered with sterile water. Each treatment contained 30 bulbs, and experiment was repeated three times. After 15 days of inoculation at 25℃, the bulbs inoculated with H1 began to turn black and to rot, and black perithecia were visible. The control plants did not show disease and no pathogen was isolated from them. We reisolated the pathogen from infected tissues, after observation of the morphological characteristics and ITS sequence ( PQ686265 ) the reisolated fungus was identified as Nigrospora oryzae. According to Koch's Postulates, Nigrospora oryza was the pathogen causing lily basal rot. To our knowledge, this is the first report of basal rot on Lilium'Siberia'(Lilium spp.) caused by Nigrospora oryzae in China.

The complete mitochondrial genome of Sinojackia microcarpa: evolutionary insights and gene transfer

BackgroundAs a dicotyledonous plant within the Styracaceae family, Sinojackia microcarpa (S. microcarpa) is notable for its library-shaped fruit and sparse distribution, serving as a model system for studying the entire tree family. However, the scarcity of genomic data, particularly concerning the mitochondrial and nuclear sequences of S. microcarpa, has substantially impeded our understanding of its evolutionary traits and fundamental biological mechanisms.ResultsThis study presents the first complete mitochondrial genome sequence of S. microcarpa and conducts a comparative analysis of its protein-encoding genes across eight plant species. Our analysis revealed that the mitochondrial genome of S. microcarpa spans 687,378 base pairs and contains a total of 59 genes, which include 37 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Sixteen plastid-derived fragments strongly linked with mitochondrial genes, including one intact plastid-related gene (rps7), were identified. Additionally, Ka/Ks ratio analysis revealed that most mitochondrial genes are under purifying selection, with a few genes, such as nad9 and ccmB, showing signs of relaxed or adaptive evolution. An analysis of twenty-nine protein-coding genes from twenty-four plant species reveals that S. microcarpa exhibits a closer evolutionary relationship with species belonging to the genus Camellia. The findings of this study provide new genomic data that enhance our understanding of S. microcarpa, and reveal its mitochondrial genome’s evolutionary proximity to other dicotyledonous species.ConclusionsOverall, this research enhances our understanding of the evolutionary and comparative genomics of S. microcarpa and other plants in the Styracaceae family and lays the foundation for future genetic studies and evolutionary analyses in the Styracaceae family.

Unraveling Unbreakable Hairpins: Characterizing RNA secondary structures that are persistent after dinucleotide shuffling.

The sequence of nucleotides that make up an RNA determines its structure, which determines its function. The RNA hairpin, also known as a stem-loop, is a ubiquitous and fundamental feature of RNA secondary structure. A common method of randomizing an RNA sequence is dinucleotide shuffling with the Altschul-Erickson algorithm, which preserves the dinucleotide content of the sequence. This algorithm generates randomized sequences by sampling Eulerian paths through the de Bruijn graph representation of the original sequence. We identified a subset of RNA hairpins in the bpRNA-1m meta-database that always form hairpins after repeated application of dinucleotide shuffling. We investigated these "unbreakable hairpins" and found several common properties. First, we found that unbreakable hairpins had on average similar folding energies compared to other hairpins of similar lengths, although they frequently contained ultra-stable hairpin loops. We found that they tend to be split by purines and pyrimidines on opposite sides of the stem. Furthermore, we found that this specific sequence feature restricts the number of distinct Eulerian paths through their de Bruijn graph representation, resulting in a small number of distinguishable dinucleotide-shuffled sequences. Beyond this algorithmic means of identification, these distinct sequences may have biological significance because we found that a significant percentage occur in a specific location of 16S ribosomal RNAs. Finally, we present a formula to calculate the number of possible unique dinucleotide shuffled sequences for an input RNA sequence, which has utility for the general application of the Altschul-Erickson algorithm.

Association of Multi-Kingdom Skin Microbiota With Radiation Dermatitis in Patients With Breast Cancer After Reconstructive Surgery: A Prospective, Longitudinal Study.

Association of Multi-Kingdom Skin Microbiota With Radiation Dermatitis in Patients With Breast Cancer After Reconstructive Surgery: A Prospective, Longitudinal Study.

Complete mitochondrial genome of the brain coral Platygyra daedalea (Ellis & Solander, 1786)

Platygyra daedalea Ellis & Solander, 1786, is a dominant species within the world’s warmest reefs, making it a critical model for investigating coral stress resistance and adaptive evolutionary mechanisms. This study presents the first sequenced and annotated mitogenome of the reef-building coral P. daedalea. The mitogenome is 16,363 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes, and two transfer RNA genes. The base composition is 24.8% adenine (A), 13% cytosine (C), 20.4% guanine (G), and 41.8% thymine (T), with a G-C content of 33.4%. We conducted a comparative analysis between P. daedalea and P. carnosa. Notably, genetic variations in the ND5 and COXI genes emerge as potential markers for distinguishing species within the Platygyra genus. Additionally, the protein-coding gene ND6 has been subjected to strong selective pressure. Phylogenetic analysis based on the complete mitogenome aligns with the internal clade structure of Scleractinia reported in previous studies, reinforcing the evolutionary insights provided by this dataset.

Morphology, Molecular Characterization, and Phylogeny of Travassosius rufus Khalil, 1922 (Strongylidea: Trichostrongylidae), a Parasite from Endangered Sino-Mongolian Beaver (Castor fiber birulai) in Xinjiang, China.

The genus Travassosius Khalil, 1922, the smallest genus in the subfamily Trichostrongylinae (family Trichostrongylidae), primarily infects the only two extant beaver species worldwide and can be lethal in severe infections. However, the mitochondrial genome evolution of Travassosius remains poorly understood, and its phylogenetic placement within Trichostrongylinae is still unresolved. In this study, we applied both morphological techniques (differential interference contrast microscopy) and molecular tools (nuclear ITS2 and mitochondrial genome) to examine T. rufus Khalil, 1922. Specimens were collected from the Sino-Mongolian beaver, a subspecies of the Eurasian beaver native to the Ulungur River Basin in northern Xinjiang, China. This work presents the first complete mitochondrial genome sequence and annotation of T. rufus, and it is also the first mitochondrial genome reported for the genus Travassosius. The mitochondrial genome of T. rufus measures 13,646 bp and contains 36 genes, including 12 protein-coding genes (PCGs) (excluding atp8), 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic analysis based on amino acid sequences of 12 mitochondrial PCGs strongly supports the distinctiveness of the genus Travassosius. Additionally, T. rufus appears to be closely related to Nematodirus within Trichostrongylinae. This study also addresses the possible consequences of parasitic infection for the Sino-Mongolian beaver and offers a scientific foundation for conserving this endangered subspecies and managing parasitic diseases in its population.

Muscle-specific isoforms of FXR1 are necessary for miR-1-mediated repression of connexin 43 and are down-regulated in pediatric dilated cardiomyopathy.

The Fragile-X (FraX) protein family regulates RNA metabolism, muscle development, and neuronal plasticity. These proteins are crucial for translation regulation, interacting with ribosomal subunits and RNA through specific domains. FXR1 has seven isoforms, including isoforms mostly expressed in skeletal and cardiac tissue, and play a significant role in heart development and function. Additionally, FXR1 modulates microRNA function, impacting gene expression. Given FXR1's crucial role in cardiac differentiation, we evaluated if expression of the muscle-specific isoforms of FXR1 was dysregulated in pediatric dilated cardiomyopathy (DCM) and sought to determine the impact of these isoforms on the function of miR-1, an important cardiac miRNA, and its regulation of the 3'UTR of the gap junction protein, connexin 43 (Cx43). Our results show that FXR1 protein levels are decreased in pediatric DCM left ventricular tissue when compared to age-matched non-failing controls. We investigated the function of muscle-specific isoforms FXR1-G and FXR1-E in an in vitro model of myocyte differentiation. H9c2 cells, differentiated to cardiomyocyte-like cells, show a significant increase in FXR1-G/E protein expression compared to H9c2 myoblasts. Furthermore, we show that FXR1G/E are essential for miR-1-mediated repression of Cx43 3'UTR, emphasizing the importance of miR binding proteins in myocyte homeostasis. Lastly, we show that FXR1-G promotes interaction between miR-1 and the Cx43 3'UTR. Overall, we demonstrate miR-1 regulation of the Cx43 3'UTR relies on muscle-specific isoforms of FXR1. Significantly, we are the first to report a reduction in the muscle-specific isoforms of FXR1 in pediatric DCM patients, underscoring an age-specific regulation of FXR1 expression.