Ribosomal DNA Research Articles

First Report of Powdery Mildew on Cardamine violifolia in China.

Cardamine violifolia, also called Cardamine hupingshanensis, is an economically important medicinal plant renowned for accumulating selenium (Guo et al., 2022). Selenium is an essential trace element with anti-oxidant, anti-inflammatory, anti-cancer, and immune regulatory functions. In July 2023, an outbreak of powdery mildew was detected, infecting the leaves of numerous C. violifolia plants in Enshi (30°11'5.27''N; 109°48'48.45''E), Hubei Province, China. This disease caused severe damage to plant leaves and stems, starting as individual spots and merging into a large mold that covers the entire leaf. It affected nearly 25% all C. violifolia plants, resulting in significant yield loss, disruption of normal metabolism, and premature aging. The lower leaf blades and underside of the leaves were particularly vulnerable. The affected leaves were collected and subjected to morphological diagnostic analysis (Mori et al., 2000) (Fig. S1). The powdery mildew species aggressively spread throughout the leaves, pedicels, and pods, persisting until present and often covering the entire surface. The conidiophores were upright, cylindrical, composed of 3 to 4 cells, and measured 92.3 ± 12.9 × 9.2 ± 0.6 μm (n = 30). Conidial pedicels had 21.6 ± 3.4 μm (n = 50) long cylindrical podocytes. The monoconidia were columnar or barrel-columnar, 30.60-55.59 × 9.11-20.00 μm in size. Conidia lacked an obvious cellulose body. The bud tubes formed from the end of conidia, and papillary appressoria developed on the epiphytic mycelia. ITS region sequences were amplified using the specific powdery mildew universal primers ITS1 (5'-TCCGTAGGTGAACCTGCGG-3'), PM6 (5'-GYCRCYCTGTCGCGAG-3') for partial sequences of 18S and 28S ribosomal DNA genes (Takamatsu et al., 2001). The sequence was deposited in the GenBank under the accession number OR506156 and aligned with available sequences on NCBI, which were 99.2%(528/532) identical to the E. cruciferarum (MT309701, MF192845, and KY660929) sequences (Fig. S2). The ITS sequence from GenBank was used to conduct maximum likelihood phylogenetic analysis using MEGA 11.0. The analysis results showed both the strain and E. cruciferarum clustered on the same branch. To confirm Koch's postulates, pathogenicity testing was carried out using an illuminating incubator. Infected leaves were attached to healthy leaves of C. violifolia seedlings (n=8). All the plants were incubated under 25℃ and >80% relative humidity. After one month, all inoculated plants presented the same symptoms as those initially observed in the field. Morphological and molecular analysis confirmed the isolated fungi's identity as the same pathogen. Therefore, C. violifolia is a suitable host for E. cruciferarum in China. The growers must be informed of these findings to prevent serious economic losses caused by this pathogenic white powder and to prepare for proper management practices. To our knowledge, this is the first report of E. cruciferarum infecting C. violifolia in China.

PTDP-43 levels correlate with cell type specific molecular alterations in the prefrontal cortex of C9orf72 ALS/FTD patients.

Repeat expansions in the C9orf72 gene are the most common genetic cause of amyotrophic lateral sclerosis and familial frontotemporal dementia (ALS/FTD). To identify molecular defects that take place in the dorsolateral frontal cortex of patients with C9orf72 ALS/FTD, we compared healthy controls with C9orf72 ALS/FTD donor samples staged based on the levels of cortical phosphorylated TAR DNA binding protein (pTDP-43), a neuropathological hallmark of disease progression. We identified distinct molecular changes in different cell types that take place during FTD development. Loss of neurosurveillance microglia and activation of the complement cascade take place early, when pTDP-43 aggregates are absent or very low, and become more pronounced in late stages, suggesting an initial involvement of microglia in disease progression. Reduction of layer 2-3 cortical projection neurons with high expression of CUX2/LAMP5 also occurs early, and the reduction becomes more pronounced as pTDP-43 accumulates. Several unique features were observed only in samples with high levels of pTDP-43, including global alteration of chromatin accessibility in oligodendrocytes, microglia, and astrocytes; higher ratios of premature oligodendrocytes; increased levels of the noncoding RNA NEAT1 in astrocytes and neurons, and higher amount of phosphorylated ribosomal protein S6. Our findings reveal previously unknown progressive functional changes in major cell types found in the frontal cortex of C9orf72 ALS/FTD patients that shed light on the mechanisms underlying the pathology of this disease.

Identification and fungicide sensitivity of Fusarium spp. associated with root rot of Scutellaria baicalensis in Shanxi Province, China.

Fusarium root rot is usually classified as an extremely destructive soil-borne disease in the world. 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 internal transcribed spacer region (ITS) of ribosomal DNA and translation elongation factor 1-alpha (TEF-1α) sequences, 68 Fusarium isolates obtained in this work were identified as F. oxysporum (52.94%), F. acuminatum (20.59%), F. solani (16.17%), F. proliferatum (5.88%), F. incarnatum (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. incarnatum. According to fungicide sensitivity tests, Fusarium isolates were more sensitive to fudioxonil 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. incarnatum and F. brachygibbosum) as causal agents of S. baicalensis root rot in Shanxi Province, China. The fungicide sensitivity results will be helpful for formulating management strategies of S. baicalensis root rot.

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.

Fast growth phenotypes are achieved through optimal transcriptomic allocation, in which cells must balance tradeoffs in resource allocation between diverse functions. One such balance between stress readiness and unbridled growth in E. coli has been termed the fear versus greed (f/g) tradeoff. Two specific RNA polymerase (RNAP) mutations observed in adaptation to fast growth have been previously shown to affect the f/g tradeoff, suggesting that genetic adaptations may be primed to control f/g resource allocation. Here, we conduct a greatly expanded study of the genetic control of the f/g tradeoff across diverse conditions. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and obtained expression profiles of each. We found that these single RNAP mutation strains resulted in large shifts in the f/g tradeoff primarily in the RpoS regulon and ribosomal genes, likely through modifying RNAP-DNA interactions. Two of these mutations additionally caused condition-specific transcriptional adaptations. While this tradeoff was previously characterized by the RpoS regulon and ribosomal expression, we find that the GAD regulon plays an important role in stress readiness and ppGpp in translation activity, expanding the scope of the tradeoff. A phylogenetic analysis found the greed-related genes of the tradeoff present in numerous bacterial species. The results suggest that the f/g tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.IMPORTANCETo increase growth, E. coli must raise ribosomal content at the expense of non-growth functions. Previous studies have linked RNAP mutations to this transcriptional shift and increased growth but were focused on only two mutations found in the protein's central region. RNAP mutations, however, commonly occur over a large structural range. To explore RNAP mutations' impact, we have introduced 12 RNAP mutations found in laboratory evolution experiments and obtained expression profiles of each. The mutations nearly universally increased growth rates by adjusting said tradeoff away from non-growth functions. In addition to this shift, a few caused condition-specific adaptations. We explored the prevalence of this tradeoff across phylogeny and found it to be a widespread and conserved trend among bacteria.

First report of Stagonosporopsis cucurbitacearum Causing Gummy Stem Blight on Trichosanthes kirilowii Maxim. in China.

Trichosanthes kirilowii Maxim. (Cucurbitaceae), one of the Chinese herbal medicines, is an economically important crop in Anhui Province, China. In recent years, gummy stem blight disease, a major disease of cucurbits, was widespread in many T. kirilowii plantations. The initial symptoms on the naturally infected stems appeared as dark brown water-soaked lesions, and as the disease progressed, vines of T. kirilowii gradually withered. On leaves, brown water-soaked lesions were visible initially, and then lesions enlarged and coalesced, resulting in extensive necrosis of leaves. On fruit, lesions covered with the white mycelium were nearly circular and tan to brown initially. Subsequently, the diseased fruit turned black and rotten commonly known as fruit rot or black rot. A Stagonosporopsis-like organism was consistently isolated from symptomatic stems, leaves and fruits. Fungal isolates were initially white and later turned dark grey or black with woolly to floccose aerial mycelium on PDA medium. Twenty-four isolates from different plantations were selected for further morphological studies. Pycnidia and conidia were formed after inoculating on cucumber fruit for 3 days. Pycnidia were globose to sub-globose, brown, ostiolate and 106.7 to 213.6 μm (average 160.1 μm, n = 50) in diameter. Conidia were hyaline, ellipsoidal, aseptate or one-septate, slightly constricted at the septa, 6.1 to 13.6 × 3.5 to 4.8 μm (average 9.9 × 4.1 μm, n = 50), and contained two or more oil drops. Three different loci of the genomic DNA, including the nuclear ribosome DNA internal transcribed spacer (ITS), RNA polymerase II second-largest subunit (RPB2), and β-tubulin (TUB2) genes., were amplified using primers ITS1/ITS4 (White et al. 1990), RBP2DF/RBP2DR (Lawrence et al. 2013), and T1/β-Sandy-R (O' Donnell and Cigelnik 1997; Stukenbrock et al. 2012), respectively and sequenced. A phylogenetic tree was built based on analysis of ITS, RPB2, and TUB2 sequences that deposited in GenBank (MW485497-MW485502 for ITS, MW531661-MW531666 for RPB2, and MW531667-MW531672 for TUB2), using the maximum likelihood method. The phylogenetic tree showed that the isolates fell into a single clade with S. cucurbitacearum. On the basis of morphological and molecular characteristics, the isolates obtained from T. kirilowii were identified as Stagonosporopsis cucurbitacearum. Pathogenicity tests were carried out on stems and leaves of 4-week-old T. kirilowii seedlings and on immature fruit collected from adult T. kirilowii plants. The epidermis, previously injured with a syringe needle, was inoculated with 5-mm-diameter mycelial plugs, and the inoculated areas were then wrapped in water-soaked cotton. Controls were similarly inoculated with agar plugs. The diameters of lesions were measured in two perpendicular directions. Re-isolations from the stem and leaf lesions were performed on the PDA medium. Stagonosporopsis cucurbitacearum, was re-identified based on its colony and conidial characteristics and, therefore, completed Koch's postulates. Gummy stem blight caused by S. cucurbitacearum has been reported in a wide range of hosts, including cucumber, luffa, pumpkin, gourd, muskmelon, cantaloupe, and watermelon (Jiang et al. 2015; Keinath 2011; Zhao et al. 2019). To our knowledge, this is the first report of gummy Stem blight disease on T. kirilowii caused by S. cucurbitacearum in China. The research provides a basis for the development and implementation of effective management strategies. Pathogenicity tests were carried out on stems and leaves of 4-week-old T. kirilowii seedlings and on immature fruits collected from adult T. kirilowii plants. The epidermis, previously injured with a syringe needle, was inoculated with 5-mm-diameter mycelial plugs, and the inoculated areas were then wrapped in water-soaked cotton. Controls were treated similarly but inoculated with agar plugs. Diameters of lesions were measured in two mutually perpendicular directions. Reisolations from the lesions were performed on PDA medium, and was re-identified based on its colony and conidial characteristics to complete Koch's postulates. Gummy stem blight caused by S. cucurbitacearum have been reported in a wide range of hosts, including cucumber, luffa, pumpkin, gourd, muskmelon, cantaloupe, and watermelon (Jiang et al. 2015; Keinath 2011; Zhao et al. 2019). To our knowledge, this is the first report of gummy Stem blight disease on T. kirilowii caused by S. cucurbitacearum in China. The research provides a basis for the development and implementation of effective management strategies.

Poaceascoma zborayi sp. nov. and Agrorhizomyces patris gen. et spec. nov. – Two novel dark septate endophytes colonizing wheat (Triticum aestivum) roots from a cropland in Hungary

In this study, we investigated two distinct new phylogenetic lineages of root-colonizing dark septate endophytic fungi colonizing wheat (Triticum aestivum) roots from a long-term agricultural experimental site in Hungary. According to four-locus (internal transcribed spacer, partial large and small subunit regions of nuclear ribosomal DNA, and partial translation elongation factor 1-alpha) phylogenetic analyses, the isolates belong to the Lentitheciaceae and Didymosphaeriaceae of the Pleosporales (Dothideomycetes). We studied the morphology and culture characteristics of the strains. We carried out in vitro resynthesis pot experiments with their original hosts and found no overall negative effect of the inoculation with different isolates of the new taxa. One of the lineages belonged to the genus Poaceascoma (Lentitheciaceae) and represented a novel species described here as Poaceascoma zborayi. We could describe conidia-like structures from this species. Isolates of the other lineage represented a monotypic novel genus in the Didymosphaeriaceae. Accordingly, the new genus, Agrorhizomyces, represented by the species A. patris, is introduced. Sterile, globose structures resembling immature sporocarps were detected. Sequence similarity searches indicated that P. zborayi might be widely distributed, while no sequence similar to A. patris was found outside the sampling area.

Characterization of the intestinal microbiota in MSM with HIV infection

BackgroundHIV-infected persons demonstrate notable disturbances in their intestinal microbiota; however, the impact of intestinal microbiota on HIV susceptibility in men who have sex with men (MSM), as well as the effects of HIV and antiretroviral therapy (ART) on their gut microbiota, remains under active study. Thus, our research focuses on clarifying the distinctions in intestinal microbiota composition among uninfected MSM and non-MSM healthy controls, investigating the alterations in early-stage intestinal microbial communities following HIV infection, and assessing how ART affects the intestinal microbiota.MethodsThis study enrolled four participant groups: uninfected MSM, Recent HIV-1 infection (RHI) MSM, MSM on ART, and non-MSM healthy controls, with 30 individuals in each group. We utilized 16S ribosomal DNA (16S rDNA) amplicon sequencing to analyze fecal microbiota and employed Luminex multiplex assays to measure plasma markers for microbial translocation (LBP, sCD14) and the inflammatory marker CRP.FindingsComparing uninfected MSM to non-MSM healthy controls, no substantial variances were observed in α and β diversity. Uninfected MSM had higher average relative abundances of Bacteroidetes, Prevotella, and Alloprevotella, while Bacteroides, Firmicutes, and Faecalibacterium had lower average relative abundances. MSM on ART had lower intestinal microbiota diversity than RHI MSM and uninfected MSM. In MSM on ART, Megasphaera and Fusobacterium increased, while Faecalibacterium and Roseburia decreased at genus level. Additionally, treatment with a non-nucleoside reverse transcriptase inhibitor (NNRTI) led to significant alterations in intestinal microbiota diversity and composition compared to RHI MSM. The random forest model showed that HIV infection biomarkers effectively distinguished between newly diagnosed HIV-infected MSM and HIV-negative MSM, with an ROC AUC of 76.24% (95% CI: 61.17-91.31%).ConclusionsMSM showed early intestinal microbiota imbalances after new HIV infection. MSM on ART experienced worsened dysbiosis, indicating a combined effect of HIV and ART. NNRTI-based treatment notably changed intestinal microbiota, suggesting a potential direct impact of NNRTI drugs on intestinal microbiota.

Effect of oral tryptamines on the gut microbiome of rats—a preliminary study

Background Psilocybin and related tryptamines have come into the spotlight in recent years as potential therapeutics for depression. Research on the mechanisms of these effects has historically focused on the direct effects of these drugs on neural processes. However, in addition to such neural effects, alterations in peripheral physiology may also contribute to their therapeutic effects. In particular, substantial support exists for a gut microbiome-mediated pathway for the antidepressant efficacy of other drug classes, but no prior studies have determined the effects of tryptamines on microbiota. Methods To address this gap, in this preliminary study, male Long Evans rats were treated with varying dosages of oral psilocybin (0.2 or 2 mg/kg), norbaeocystin (0.25 or 2.52 mg/kg), or vehicle and their fecal samples were collected 1 week and 3 weeks after exposure for microbiome analysis using integrated 16S ribosomal DNA sequencing to determine gut microbiome composition. Results We found that although treatment with neither psilocybin nor norbaeocystin significantly affected overall microbiome diversity, it did cause significant dose- and time-dependent changes in bacterial abundance at the phylum level, including increases in Verrucomicrobia and Actinobacteria, and decreases in Proteobacteria. Conclusion and Implications These preliminary findings support the idea that psilocybin and other tryptamines may act on the gut microbiome in a dose- and time-dependent manner, potentially identifying a novel peripheral mechanism for their antidepressant activity. The results from this preliminary study also suggest that norbaeocystin may warrant further investigation as a potential antidepressant, given the similarity of its effects to psilocybin.

Decoding chromosome organization using CheC-PLS: chromosome conformation by proximity labeling and long-read sequencing.

Genomic approaches have provided detailed insight into chromosome architecture. However, commonly deployed techniques do not preserve connectivity-based information, leaving large-scale genome organization poorly characterized. Here, we developed CheC-PLS: a proximity-labeling technique that indelibly marks, and then decodes, protein-associated sites. CheC-PLS tethers dam methyltransferase to a protein of interest, followed by Nanopore sequencing to identify methylated bases - indicative of in vivo proximity - along reads >100kb. As proof-of-concept we analyzed, in budding yeast, a cohesin-based meiotic backbone that organizes chromatin into an array of loops. Our data recapitulates previously obtained association patterns, and, importantly, exposes variability between cells. Single read data reveals cohesin translocation on DNA and, by anchoring reads onto unique regions, we define the internal organization of the ribosomal DNA locus. Our versatile technique, which we also deployed on isolated nuclei with nanobodies, promises to illuminate diverse chromosomal processes by describing the in vivo conformations of single chromosomes.

Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages.

Mitochondrial biogenesis requires precise regulation of both mitochondrial-encoded and nuclear-encoded genes. Nuclear receptor Nur77 is known to regulate mitochondrial metabolism in macrophages and skeletal muscle. Here, we compared genome-wide Nur77 binding site and target gene expression in these two cell types, which revealed conserved regulation of mitochondrial genes and enrichment of motifs for the transcription factor Yin-Yang 1 (YY1). We show that Nur77 and YY1 interact, that YY1 increases Nur77 activity, and that their binding sites are co-enriched at mitochondrial ribosomal protein gene loci in macrophages. Nur77 and YY1 co-expression synergistically increases Mrpl1 expression as well as mitochondrial abundance and activity in macrophages but not skeletal muscle. As such, we identify a macrophage-specific Nur77-YY1 interaction that enhances mitochondrial metabolism.

Screening and Identification of Soil Selenium-Enriched Strains and Application in Auricularia auricula.

Selenium (Se) is an essential trace element for human physiological metabolism. The application of organic Se as a source to cultivate Se-rich plants for micronutrient supplementation has been receiving increasing attention. In our study, a bacterial strain named H1 was isolated from the soil in Heilongjiang Province, China, and under optimal culture conditions, the unit Se content could reach 3000 μg·g-1 and its 16S ribosomal DNA sequence seemed to be a new molecular record of an Enterobacter species. After the domestication of Se tolerance and Se-rich experiments, H1 can be used as a Se source for cultivation of Se-rich Auricularia auricula. The results showed that soluble protein, soluble sugar, free amino acid and vitamin C contents in Auricularia auricula were notably increased by 28.7%, 21.8%, 32.5% and 39.2% under the treatment of Se concentration of 0.24 mg·kg-1, respectively. These findings enhance our understanding that H1 is more conducive to Se uptake and nutrient accumulation.

Factors associated with seedling establishment on logs of different fungal decay types-A seed-sowing experiment.

Wood decay fungi alter the abiotic and biotic properties of deadwood, which are important as nurse logs for seedling regeneration. However, the relationship between fungal decay type and seedling performance has not been evaluated experimentally. In this study, we examined the germination, growth, and survival of six arbuscular mycorrhizal (AM) and six ectomycorrhizal (ECM) tree species on three substrates (pine logs with brown and white rot and soil) by conducting seed-sowing experiments in a mixed forest dominated by Pinus densiflora and Quercus serrata. Analysis using ribosomal DNA internal transcribed spacer 1 (rDNA ITS1) sequencing revealed that the fungal community was significantly different across three substrates. The richness of operational taxonomic units (OTUs) of AM and ECM fungi was the largest on brown rot logs and soil, respectively. The substrate significantly affected the seedling performance when comparing wood decay types, but these were not consistent across the mycorrhizal status of the seedlings. Nevertheless, seedlings of some AM trees showed better growth and enhanced mycorrhizal colonization on brown rot logs than on white rot logs. The wood decay type influenced fungal communities in the logs and the performance of some seedling species partly by different mycorrhizal colonization rates. However, the effect was seedling species dependent and showed no apparent difference between AM and ECM trees.

Psychoneurological symptoms, inflammatory biomarkers and gut microbiome richness and diversity in individuals receiving hematopoietic cell transplantation (HCT).

e24053 Background: Hematopoietic Stem Cell Transplantation (HCT) is a potentially curative treatment for certain hematologic cancers. Although survival rates are markedly higher than in the past, there are a growing number of long-term HCT survivors who are at risk for short and long-term sequela, which can negatively affect quality of life. Psychoneurological (PN) symptoms are common occurrences associated with heightened inflammation in other cancers and chronic conditions. Emerging research links the gut microbiota to inflammatory biomarkers and suggests that gut-microbiota-brain crosstalk impacts the severity of psychoneurological symptoms among HCT recipients. Methods: This longitudinal descriptive study investigated the relationship among a cluster of PN symptoms (pain, fatigue, and depression), inflammatory biomarkers (IL-6, IL-10, C-reactive protein (CRP), and microbiota diversity measures (Shannon and Chao Beta diversity indexes) in 55 individuals receiving HCT for a hematologic malignancy. The time periods examined covered pre-transplant, 30-days, and 100-days following transplant. The PN symptoms were collected through self-reported questionnaires via computer with assistance from study staff, along with blood samples and stool specimens obtained at each study visit. Inflammatory marker values were log-transformed when used as dependent variables. Gut microbiota samples were analyzed using 16S ribosomal gene (V4 region) amplicons using Illumina MiSeq. Data analysis was performed using SAS 9.4, with PROC MIXED used for the mixed model analyses. Results: The analysis characterized mean changes in microbiota diversity over time for both Shannon and Chao indexes. IL6 levels were consistent over time, with an inverse association with Chao but not Shannon index. IL10 and CRP levels changed over time, but without associations with either Shannon or Chao. Pain severity and interference changed over time, but with no associations with inflammatory markers or gut microbiome beta diversity. Fatigue severity and interference changed over time and were positively associated with IL10. Depression did not change over time and was not associated with inflammatory markers or diversity. Conclusions: This study provides preliminary information related to associations between PN symptoms, inflammatory markers, and selected measures of gut microbiome diversity in HCT recipients. Further research is needed to explore and validate these findings to examine the implications for microbiota diversity on inflammatory factors and PN symptoms. Clinical trial information: NCT02398708 .

Predicting immunotherapy toxicity through single-cell sequencing of peripheral immune cells: A pilot study.

e14538 Background: Immune checkpoint inhibitors are widely used in oncology. However, immune-related adverse events (iRAEs) are idiosyncratic and can be severe. The overall incidence is 27%, with severe iRAEs occurring in 6% of patients. We hypothesised that distinct immune cell phenotypes (gene expression) correlate with immune-related toxicity from checkpoint inhibitor immunotherapy. Single-cell RNA sequencing (scRNA-seq) is a powerful tool that can assay the gene expression of thousands of individual cells. RPS26 expression mediates CD4/CD8 T cell activation through a known trans-expressive quantitative trait locus at rs1131017 and is linked with autoimmunity. FOS and JUN encode for c-Fos and c-Jun, which dimerise to create the activator protein-1 complex, a well-established transcriptional factor of the immune system. c-Fos is an immunoregulator known to suppress pro-inflammatory cytokines, suggesting that c-FOS deficiency plays a crucial role in developing autoimmunity. We aimed to analyse the transcriptomic differences of peripheral immune cells between patients who experienced severe checkpoint inhibitor therapy iRAE and those who did not. Methods: We identified a pilot cohort of eight patients who developed grade three or above toxicity due to immune checkpoint inhibitors and eight controls who were matched for age, cancer and treatment type. Peripheral blood mononuclear cells were collected prospectively at baseline and two subsequent treatment cycles. Cells were captured on the 10x Chromium platform, and libraries were sequenced to 30,000 reads per cell. Samples were demultiplexed, and the data was analysed with the Seurat package on R statistical software (version 4.3.0). Results: Five patients had baseline samples only, two patients had two samples from two cycles, and one patient had samples from three cycles. After quality control filtering, we identified 36,288 cells from 16 individuals and 24 samples. Immune cells were annotated with the Azimuth package into 29 subtypes. We identified differences in cell proportions of immune cell subsets in the toxicity vs control group, including B naive cells (5.57% vs 3.71% p=0.01) and reduced cytotoxic CD4 T lymphocyte cells (0.66% vs 2.26%, p=0.005). Differential gene expression analysis identified a significantly high expression of ribosomal genes, particularly RPS26, in multiple cell types at baseline (p<0.01) and reduced expression of FOS and JUN-related genes in CD14 and CD16 monocytes, CD4 and CD8 T cells in the toxicity cohort (p<0.01). Conclusions: Overexpression of ribosomal genes and reduced expression of FOS/ JUN genes amongst PBMCs at baseline are potentially predictive biomarkers of severe checkpoint inhibitor immunotherapy toxicity. Validation of these findings in a larger cohort is in progress.

Aging disrupts the coordination between mRNA and protein expression in mouse and human midbrain.

Age-related dopamine (DA) neuron loss is a primary feature of Parkinson's disease. However, it remains unclear whether similar biological processes occur during healthy aging, albeit to a lesser degree. We therefore determined whether midbrain DA neurons degenerate during aging in mice and humans. In mice, we identified no changes in midbrain neuron numbers throughout aging. Despite this, we found age-related decreases in midbrain mRNA expression of tyrosine hydroxylase (Th), the rate limiting enzyme of DA synthesis. Among midbrain glutamatergic cells, we similarly identified age-related declines in vesicular glutamate transporter 2 (Vglut2) mRNA expression. In co-transmitting Th +/Vglut2 + neurons, Th and Vglut2 transcripts decreased with aging. Importantly, striatal Th and Vglut2 protein expression remained unchanged. In translating our findings to humans, we found no midbrain neurodegeneration during aging and identified age-related decreases in TH and VGLUT2 mRNA expression similar to mouse. Unlike mice, we discovered diminished density of striatal TH+ dopaminergic terminals in aged human subjects. However, TH and VGLUT2 protein expression were unchanged in the remaining striatal boutons. Finally, in contrast to Th and Vglut2 mRNA, expression of most ribosomal genes in Th + neurons was either maintained or even upregulated during aging. This suggests a homeostatic mechanism where age-related declines in transcriptional efficiency are overcome by ongoing ribosomal translation. Overall, we demonstrate species-conserved transcriptional effects of aging in midbrain dopaminergic and glutamatergic neurons that are not accompanied by marked cell death or lower striatal protein expression. This opens the door to novel therapeutic approaches to maintain neurotransmission and bolster neuronal resilience.

Transcriptomic analysis reveals differential gene expression patterns of Lacticaseibacillus casei ATCC 393 in response to ultrasound stress

In recent years, there has been a growing interest in modulating the performance of probiotic, mainly Lactic Acid Bacteria (LAB), in the field of probiotic food. Attenuation, induced by sub-lethal stresses, delays the probiotic metabolism, and induces a metabolic shift as survival strategy. In this paper, RNA sequencing was used to uncover the transcriptional regulation in Lacticaseibacillus casei ATCC 393 after ultrasound-induced attenuation. Six (T) and 8 (ST) min of sonication induced a significant differential expression of 742 and 409 genes, respectively. We identified 198 up-regulated and 321 down-regulated genes in T, and similarly 321 up-regulated and 249 down-regulated in ST. These results revealed a strong defensive response at 6 min, followed by adaptation at 8 min. Ultrasound attenuation modified the expression of genes related to a series of crucial biomolecular processes including membrane transport, carbohydrate and purine metabolism, phage-related genes, and translation. Specifically, genes encoding PTS transporters and genes involved in the glycolytic pathway and pyruvate metabolism were up-regulated, indicating an increased need for energy supply, as also suggested by an increase in the transcription of purine biosynthetic genes. Instead, protein translation, a high-energy process, was inhibited with the down-regulation of ribosomal protein biosynthetic genes. Moreover, phage-related genes were down-regulated suggesting a tight transcriptional control on DNA structure. The observed phenomena highlight the cell need of ATP to cope with the multiple ultrasound stresses and the activation of processes to stabilize and preserve the DNA structure. Our work demonstrates that ultrasound has remarkable effects on the tested strain and elucidates the involvement of different pathways in its defensive stress-response and in the modification of its phenotype.

Chromosomal mapping of repetitive DNA and retroelement sequences and its implications for the chromosomal evolution process in Ctenoluciidae (Characiformes)

Ctenoluciidae is a Neotropical freshwater fish family composed of two genera, Ctenolucius (C. beani and C. hujeta) and Boulengerella (B. cuvieri, B. lateristriga, B. lucius, B. maculata, and B. xyrekes), which present diploid number conservation of 36 chromosomes and a strong association of telomeric sequences with ribosomal DNAs. In the present study, we performed chromosomal mapping of microsatellites and transposable elements (TEs) in Boulengerella species and Ctenolucius hujeta. We aim to understand how those sequences are distributed in these organisms’ genomes and their influence on the chromosomal evolution of the group. Our results indicate that repetitive sequences may had an active role in the karyotypic diversification of this family, especially in the formation of chromosomal hotspots that are traceable in the diversification processes of Ctenoluciidae karyotypes. We demonstrate that (GATA)n sequences also accumulate in the secondary constriction formed by the 18 S rDNA site, which shows consistent size heteromorphism between males and females in all Boulengerella species, suggesting an initial process of sex chromosome differentiation.

Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities

Research on microbial communities associated with wild animals provides a valuable reservoir of knowledge that could be used for enhancing their rehabilitation and conservation. The loggerhead sea turtle (Caretta caretta) is a globally distributed species with its Mediterranean population categorized as least concern according to the IUCN Red List of Threatened Species as a result of robust conservation efforts. In our study, we aimed to further understand their biology in relation to their associated microorganisms. We investigated epi- and endozoic bacterial and endozoic fungal communities of cloaca, oral mucosa, carapace biofilm. Samples obtained from 18 juvenile, subadult, and adult turtles as well as 8 respective enclosures, over a 3-year period, were analysed by amplicon sequencing of 16S rRNA gene and ITS2 region of nuclear ribosomal gene. Our results reveal a trend of decreasing diversity of distal gut bacterial communities with the age of turtles. Notably, Tenacibaculum species show higher relative abundance in juveniles than in adults. Differential abundances of taxa identified as Tenacibaculum, Moraxellaceae, Cardiobacteriaceae, and Campylobacter were observed in both cloacal and oral samples in addition to having distinct microbial compositions with Halioglobus taxa present only in oral samples. Fungal communities in loggerheads’ cloaca were diverse and varied significantly among individuals, differing from those of tank water. Our findings expand the known microbial diversity repertoire of loggerhead turtles, highlighting interesting taxa specific to individual body sites. This study provides a comprehensive view of the loggerhead sea turtle bacterial microbiota and marks the first report of distal gut fungal communities that contributes to establishing a baseline understanding of loggerhead sea turtle holobiont.

DNA Damage Checkpoints Govern Global Gene Transcription and Exhibit Species-Specific Regulation on HOF1 in Candida albicans.

DNA damage checkpoints are essential for coordinating cell cycle arrest and gene transcription during DNA damage response. Exploring the targets of checkpoint kinases in Saccharomyces cerevisiae and other fungi has expanded our comprehension of the downstream pathways involved in DNA damage response. While the function of checkpoint kinases, specifically Rad53, is well documented in the fungal pathogen Candida albicans, their targets remain poorly understood. In this study, we explored the impact of deleting RAD53 on the global transcription profiles and observed alterations in genes associated with ribosome biogenesis, DNA replication, and cell cycle. However, the deletion of RAD53 only affected a limited number of known DNA damage-responsive genes, including MRV6 and HMX1. Unlike S. cerevisiae, the downregulation of HOF1 transcription in C. albicans under the influence of Methyl Methanesulfonate (MMS) did not depend on Dun1 but still relied on Rad53 and Rad9. In addition, the transcription factor Mcm1 was identified as a regulator of HOF1 transcription, with evidence of dynamic binding to its promoter region; however, this dynamic binding was interrupted following the deletion of RAD53. Furthermore, Rad53 was observed to directly interact with the promoter region of HOF1, thus suggesting a potential role in governing its transcription. Overall, checkpoints regulate global gene transcription in C. albicans and show species-specific regulation on HOF1; these discoveries improve our understanding of the signaling pathway related to checkpoints in this pathogen.

Five new records of Collybiopsis (Agaricales, Omphalotaceae) in Thailand: a significant addition to the species diversity and global distribution of the genus

The genus Collybiopsis is known to be found in tropical and temperate regions throughout the world. Currently, 66 species have been validated and assigned to this genus. In this study, we have updated a brief review of the genus Collybiopsis through an overview of species diversity, geographic distribution, and recently published literature. Prior to this study, only four Collybiopsis species have been reported from Thailand. During surveys of macrofungi in northern and southern Thailand from 2018 to 2022, nine Collybiopsis specimens were collected. These nine specimens were identified as belonging to five species, namely C. gibbosa, C. indocta, C. melanopus, C. menehune, and C. nonnulla based on morphological characteristics and molecular data of the internal transcribed spacer (ITS) and large subunit (nrLSU) of nuclear ribosomal DNA sequences. The present study offers the first record of these five Collybiopsis species in Thailand. Detailed morphological descriptions, photographs, illustrations, comparisons with related taxa, and a phylogenetic tree to show the placement of these five species from Thai specimens are provided. Moreover, a new key to the species of Collybiopsis found in Thailand is presented.