H3 Gene Research Articles

Detection of Uropathogenic Escherichia coli Virulence Factors’ fimH and fliC H7 in Urinary Tract Infections and Their Association with Antibiotics Resistance among Sudanese Children

Background UTIs are one of the most common pathological conditions in both community and hospital settings. A broad spectrum of pathogens causes UTIs, it has been estimated that about 80% to 90% of cases worldwide develop UTI each year. However, the most frequent agent of community-acquired UTI is Uropathogenic Escherichia coli (UPEC), Some of UPEC genes have been associated with disease and antibiotic resistance. The presence of multidrug-resistant UPEC harboring several virulence factors, is a major risk factor for inpatients. This study aimed to detect the presence of virulence factors; fimH and fliC H7 genes and their possible association with antibiotic resistance, to evaluate the relation between virulence factors and antibiotic resistance among UPEC isolated from Sudanese symptomatic children’s patients with UTI, in Khartoum State- Sudan. Methods Sixty-six urine samples from study participants with symptomatic UTIs have been identified by clinician from two hospitals as UPEC using the conventional microbiological tests. All the isolates were subjected to antimicrobial sensitivity test using disk diffusion and polymerase chain reaction (PCR) assay to identify the presence of two putative virulence factors; fimH and fliC H7, and their association with antimicrobial resistance. Results Our results have shown that Amoxcacillin (penicillin group) was consistently the most resistance active (90.9%) of the systemically active antimicrobials, followed by Sulfamethoxazole (89.4%). On the other hand, sensitivity to nitrofurantoin (nitrofuran) was found to be the highest (89.4%). FimH gene has the highest prevalence among E. coli isolates (63.6%), followed by fliC gene (53.0%). A statistically significant association was found between the presence of fimH gene and resistance of E. coli to Polynaphethol with Chi-square p-value = 0.016 and odds ratio =5.353. Another significant association was found with resistance of E. coli to Chloramphenicol (Chi-Square p-value = 0.038, odds ratio = 3.103) and presence of fimH gene, also there was a significant association between the presence of fliC H7 gene and resistance of E. coli to Cephalexin with a (Chi-Square p-value = 0.001 and odds ratio = 5.869) Conclusions The study highlighted the prevalence of UPEC isolates which harbored the virulence factors and their association with antibiotic resistance which possibly cause the urine disease. The outcome of the study may represent targets for improving the regimen used and therapeutics against UPEC in Sudan.

CSIG-13. TARGETING GENETIC DEPENDENCIES EXPOSES DIFFUSE MIDLINE GLIOMA CELL OF ORIGIN VULNERABILITIES

Abstract Diffuse midline glioma (DMG), including diffuse intrinsic pontine glioma (DIPG), are uniformly fatal brain cancers affecting children, adolescents, and young adults. These tumors are characterized by ‘oncohistone’ mutations in histone H3 genes (H3F3A, HIST1H3B, HIST1H3C), resulting in the substitution of lysine 27 to methionine (H3K27M), resulting in dominant negative hypomethylation at lysine 27 (H3K27) and a global loss of gene silencing. CRISPR-Cas9 loss-of-function gene deletion screens identified mutation-independent dependencies on PIK3CA and MTOR genes for tumor growth and proliferation, highlighting a targetable molecular dependency across DMG patient-derived models (n=38). However, systemic PI3K/mTOR inhibition increased blood glucose and insulin levels, promoting hyperinsulinemia/hyperglycemia and reduced efficacy in vivo. To exploit genetic dependencies while maintaining compliance and therapeutic benefit, we optimized combinations of clinically relevant PI3K inhibitors (paxalisib, GCT007, everolimus) with the antiglycemic drug metformin to restore glucose homeostasis and decrease DMG insulin receptor activity in vivo, extending the survival of DIPG xenograft models. Phosphoproteomic profiling of DIPG models treated with PI3K/mTOR inhibitors promoted calcium-activated PKC signaling. The brain-penetrant PKC inhibitor enzastaurin in combination with paxalisib, synergistically extended the survival of DIPG xenograft models, including those mimicking disease progression, with further benefits potentiated using metformin in a multimodality approach. Combined PI3K-PKC inhibition in vivo promoted differentiation of OPC-like DMG to more OC-like cells, enhancing PDGFRA-JAK/STAT proinflammatory signaling, showing features of demyelination and MHC-II+ antigen expression, including PD1/PDL1. In parallel, combined PI3K/mTOR and PDGFRA inhibition using paxalisib and avapritinib synergistically extended the survival of patient-derived xenograft models, showing the preclinical relevance of simultaneously targeting these vulnerabilities. Together, we reveal that therapeutic inhibition of PI3K/mTOR and compensatory PKC signaling, while mitigating side effects with metformin, altered the chromatin architecture, leading to cellular differentiation and opening the door for clinically relevant checkpoint inhibitors. This combination strategy addresses DMG genetic dependencies, cellular and systemic responses to precision therapies, while harnessing the immune system for potential clinical translation.

ГЕНЕТИЧЕСКИЙ СКРИНИНГ ПЕРСПЕКТИВНЫХ ГИБРИДОВ КАРТОФЕЛЯ РЕСПУБЛИКИ КОМИ

The studies were conducted with the aim of genetic screening of promising selection hybrids of potatoes to identify genotypes resistant to a complex of phytopathogens. The study was carried out at A.V.Zhuravskiy Institute of Agrobiotechnology of Komi Scientific Center of the Ural Branch of the Russian Academy of Sciences and Sintol company (Moscow) using the GenExpert reagent kit “Markers of potato resistance genes” (“Syntol”). For the study, 10 markers of genes encoding resistance to potato cancer, golden potato cyst nematode, pale potato cyst nematode, X-virus and Y-virus were selected (genes H1, Gro1-4 were detected using markers TG-689, 57R, N195 and Gro1-4-1, gene Sen1 – using marker NL25, gene Gpa2 – Gpa2-2). The objects of the study were leaves of plants of five potato hybrids undergoing selection testing in breeding nurseries: 2341-265 (Amur × Gala), 2339-8 (Oksania × Gala), 2339-9 (Oksania × Gala), 1992-14 (Udacha × Elmundo), 2000-60 (Colette × FZ 1867). The maximum number of markers (five in each) linked to resistance genes was revealed in samples 2339-8 and 1992-14: TG-689, 57R, N195 and NL25 in both hybrids; Gro1-4-1 marker in 2339-8 and Gpa2-2 in 1992-14. Only the marker of potato wart resistance gene, NL25, was noted in selection number 2341-265. Sample 2339-8 was characterized as a valuable source of R-genes, having in its genome the genes of resistance to golden potato cyst nematode (H1, Gro1-4) and potato wart (Sen1). The genotype of the 1992-14 hybrid, carrying the Gpa2 gene, is recommended for breeding new potato varieties resistant to various types of nematodes.

Analysis of Stress Response Genes in Microtuberization of Potato Solanum tuberosum L.: Contributions to Osmotic and Combined Abiotic Stress Tolerance.

Wild Solanum species have contributed many introgressed genes during domestication into current cultivated potatoes, enhancing their biotic and abiotic stress resistance and facilitating global expansion. Abiotic stress negatively impacts potato physiology and productivity. Understanding the molecular mechanisms regulating tuber development may help solve this global problem. We made a transcriptomic analysis of potato microtuberization under darkness, cytokinins, and osmotic stress conditions. A protein-protein interaction (PPI) network analysis identified 404 genes with high confidence. These genes were involved in important processes like oxidative stress, carbon metabolism, sterol biosynthesis, starch and sucrose metabolism, fatty acid biosynthesis, and nucleosome assembly. From this network, we selected nine ancestral genes along with eight additional stress-related genes. We used qPCR to analyze the expression of the selected genes under osmotic, heat-osmotic, cold-osmotic, salt-osmotic, and combined-stress conditions. The principal component analysis (PCA) revealed that 60.61% of the genes analyzed were associated with osmotic, cold-osmotic, and heat-osmotic stress. Seven out of ten introgression/domestication genes showed the highest variance in the analysis. The genes H3.2 and GAPCP1 were involved in osmotic, cold-osmotic, and heat-osmotic stress. Under combined-all stress, TPI and RPL4 were significant, while in salt-osmotic stress conditions, ENO1, HSP70-8, and PER were significant. This indicates the importance of ancestral genes for potato survival during evolution. The targeted manipulation of these genes could improve combined-stress tolerance in potatoes, providing a genetic basis for enhancing crop resilience.

H3K27me3 Loss in Central Nervous System Tumors: Diagnostic, Prognostic, and Therapeutic Implications.

Central nervous system (CNS) tumors represent a formidable clinical challenge due to their molecular complexity and varied prognostic outcomes. This review delves into the pivotal role of the epigenetic marker H3K27me3 in the development and treatment of CNS tumors. H3K27me3, specifically the trimethylation of lysine 27 on the histone H3 protein, plays a crucial role in regulating gene expression and maintaining chromatin architecture (e.g., in X-chromosome inactivation). Notably, a reduction in H3K27me3 levels, frequently tied to mutations in the H3 gene family such as H3F3A and HIST1H3B, is evident in diverse brain tumor variants, including the diffuse midline glioma characterized by the H3K27M mutation and certain pediatric high-grade gliomas. The loss of H3K27me3 has been linked to more aggressive behavior in meningiomas, with the trimethylation loss associated with significantly shorter recurrence-free survival (RFS) among grade 2 meningiomas, albeit not within grade 1 tumors. Pediatric posterior fossa ependymomas characterized by a lowered H3K27me3 and DNA hypomethylation exhibit poor prognosis, underscoring the prognostic significance of these epigenetic alterations in CNS tumors. Comprehending the role of H3K27me3 in CNS tumors is vital for advancing diagnostic tools and therapeutic interventions, with the goal of enhancing patient outcomes and quality of life. This review underscores the importance of ongoing investigations into H3K27me to refine and optimize management strategies for CNS tumors, paving the way for improved personalized medicine practices in oncology.

New data on the polyphyletic Marionina genus (Annelida, Enchytraeidae): description of three new species from European shore habitats

Marionina (Michaelsen in Pfeffer, 1890) is a worldwide distributed genus of small enchytraeids living in mainly aquatic habitats. The genus is polyphyletic, including about 100 species with diverse morphological characters and cryptic lineages; therefore, taxonomic revisions were performed recently, and further actions are needed in the future. In our study, Marionina individuals were investigated from decaying seagrass debris collected from seashores in Croatia and Italy using morphological characters and molecular markers involving the COI and H3 genes and the ITS region. Descriptions of two new Marionina species, M. puntaalanensissp. nov. and M. orbiferasp. nov., are presented in this paper, and in addition, the description of a third new Marionina species, M. reichartisp. nov., from the shore of the freshwater Lake Balaton (Hungary) is provided here. All three new species are small (2–3.5 mm in vivo with less than 30 segments), their clitellum is saddle-shaped, the dorsal anterior blood vessel bifurcation is in III, and the spermatheca is attached to the oesophagus. The main diagnostic features of M. puntaalanensissp. nov. are: brain incised posteriorly; dorsal vessel from the clitellar region; two chaetae in all bundles; three pairs of preclitellar nephridia; small subneural glands in XIII–XIV; seminal vesicle absent or small; ectal duct of spermatheca surrounded along the length by glands and one larger. The main features of M. orbiferasp. nov. are: brain truncate posteriorly; dorsal vessel from the clitellar region; two chaetae in all bundles; two pairs of preclitellar nephridia; subneural glands in XIII–XIV; seminal vesicle well developed; the lumen of the spermathecal ampulla is characteristically full with many spherical sperm rolls. In M. reichartisp. nov.: brain incised posteriorly, dorsal vessel origin in XII, maximum five chaetae per bundle, often the middle chaetae slightly smaller than the ental ones, three pairs of preclitellar nephridia, subneural glands absent, spermathecal ampulla globular, ectal duct surrounded along the length by glands, and one large sessile gland at the orifice.

Diversity and Pathogenicity of Six Diaporthe Species from Juglans regia in China.

Walnut (Juglans regia L.) is cultivated extensively in China for its substantial economic potential as a woody oil species. However, many diseases caused by Diaporthe greatly affect the health of Juglans regia trees. The present study revealed the presence of Diaporthe species from Juglans regia. A total of six species of Diaporthe were isolated from twigs of Juglans regia in three provinces in China, including two known species (Diaporthe gammata and D. tibetensis) and four novel species (D. chaotianensis, D. olivacea, D. shangluoensis and D. shangrilaensis). Phylogenetic relationships of the new species were determined by multilocus phylogenetic analyses based on partial sequences of the internal transcribed spacer (ITS) region, calmodulin (cal) gene, histone H3 (his3) gene, translation elongation factor 1-α (tef1-α) gene and β-tubulin (tub2) gene. Pathogenicity tests indicated that all Diaporthe species obtained in this study were confirmed as pathogens of Juglans regia. This study deepens the understanding of species associated with several disease symptoms in Juglans regia and provides useful information for effective disease control.

A targeted gene phylogenetic framework to investigate diversification in the highly diverse yet geographically restricted red devil spiders (Araneae, Dysderidae).

The family Dysderidae is a highly diverse group of nocturnal ground-dwelling and active-hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased-80% of its 644 documented species belong to just two genera, Dysdera (326) and Harpactea (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi-locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post-dated the break-up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus Dysdera. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis.

Identification and analysis of flavonoid pathway genes in responsive to drought and salinity stress in Medicago truncatula

Flavonoid compounds are widely present in various organs and tissues of different plants, playing important roles when plants are exposed to abiotic stresses. Different types of flavonoids are biosynthesized by a series of enzymes that are encoded by a range of gene families. In this study, a total of 63 flavonoid pathway genes were identified from the genome of Medicago truncatula. Gene structure analysis revealed that they all have different gene structure, with most CHS genes containing only one intron. Additionally, analysis of promoter sequences revealed that many cis-acting elements responsive to abiotic stress are located in the promoter region of flavonoid pathway genes. Furthermore, analysis on M. truncatula gene chip data revealed significant changes in expression level of most flavonoid pathway genes under the induction of salt or drought treatment. qRT-PCR further confirmed significant increase in expression level of several flavonoid pathway genes under NaCl and mannitol treatments, with CHS1, CHS9, CHS10, F3′H4 and F3′H5 genes showing significant up-regulation, indicating they are key genes in response to abiotic stress in M. truncatula. In summary, our study identified key flavonoid pathway genes that were involved in salt and drought response, which provides important insights into possible modification of flavonoid pathway genes for molecular breeding of forage grass with improved abiotic resistance.

A new species of planthopper in the genus Myxia (Hemiptera: Auchenorrhyncha: Fulgoromorpha: Delphacoidea: Cixiidae) from the cloud forest in Costa Rica.

A new species of Myxia is described from light collecting in Villa Blanca, Costa Rica. The new species possesses an unusual large areolet on the anterior portion of the vertex. Maximum Likelihood analyses based on the 18S rRNA gene, D9-D10 expansion region of the 28S gene, H3 gene and 5' region of the COI gene support the monophyly of Myxia, with the new species nested deeply within the genus.

First Report of Leaf Blight of Osmanthus fragrans Caused by Diaporthe eres in China.

Osmanthus fragrans is an evergreen garden tree species, with high ecological, social, and economic benefits (Lan et al. 2023), which is widely planted in Guizhou Province. From late April to June 2023, a leaf blight disease was observed on O. fragrans in a bauxite mining area in Qingzhen City, with an incidence of ~50%. Symptoms first appeared at the leaf tip or margin, as irregular brown spots, which gradually coalesced into dark brown patches until the leaves withered and fell off. Symptomatic leaves were collected and surface disinfected with 2% NaClO for 30 s, 75% ethanol for 30 s, rinsed 3 times in sterile ddH2O, air-dried and placed on potato dextrose agar (PDA) medium and incubated at 25°C for 7 d. Fungal colonies on PDA of 9 similar obtained isolates were white, with at least one concentric ring. The reverse was light yellow and gradually turned brown. At 12 d, the pycnidia on PDA was gray to black, spherical or conical, with a diameter of 305.15 μm (n=20). The conidial horns oozed out from pycnidia after 25 d of incubation on Pinus massoniana needles. The alpha conidia were unicellular, fusiform, hyaline, had a guttule at each end, and measured 6.24 ± 0.10 μm × 2.48 ± 0.04 μm (n=50). No beta or gamma conidia were observed. The morphological characteristics were likely to Diaporthe spp. (Gomes et al. 2013). DNA of isolates GH02, GH06 and GH08 was extracted. The internal transcribed spacer region (ITS) and partial sequences of translation elongation factor 1-alpha (TEF1-α), calmodulin (CAL), beta-tubulin (TUB2), and histone H3 (HIS) genes were amplified with primers ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R, CAL228F/CAL737R (Carbone and Kohn, 1999), βt2a/βt2b and CYLH3F/H3-1b (Crous et al. 2004; Glass and Donaldson, 1995), respectively. The sequences of ITS, TEF-1α, TUB2, CAL and HIS were deposited in GenBank (GH02: PP813499, PP813844, PP813846, PP813848 and PP813850; GH06: PP813500, PP813845, PP813847, PP813849 and PP813851; GH08: PP507168 and PP529956 to PP529959). BLAST results showed the sequences of GH08 were highly identical to sequences of Phomopsis mahothocarpi (NR147522 [ITS], 527/530), P. mahothocarpi (MW700277 [TEF-1α], 367/372), D. eres (OR885862 [TUB], 513/513), D. celeris (ON221721 [CAL], 484/486), and D. eres (OP968956 [HIS], 477/477). A phylogenetic tree constructed with MEGA X using Neighbor-Joining algorithm (Felsenstein, 1985) indicated the isolate GH02, GH06 and GH08 separated from D. eres CBS 297.77 previously reported from O. aquifolium in Netherlands, as well as D. osmanthi and D. fusicola from O. fragrans in China (Gomes et al. 2013; Long et al. 2019; Si et al. 2021). Based on these results, the three isolates were identified as D. eres (Chaisiri et al., 2021). The isolate GH08 was deposited in the Forest Protection Laboratory, Guizhou University. To confirm pathogenicity, spore suspensions (1×105 spores/mL) of GH08 were sprayed on healthy detached leaves (n=10) and leaves of 3-year-old potted O. fragrans seedlings (n=8). An equal volume of sterile water was sprayed for the control. Then they were placed at 20°C and 70-80% RH. Similar leaf blight symptoms appeared after 5 and 15d on the inoculated leaves and seedlings, respectively. The re-isolated fungus, was identical to D. eres based on morphological and molecular analysis, thus fulfilling Koch's postulates. To our knowledge, this is the first report of D. eres causing leaf blight of O. fragrans in China, supporting a basis for developing effective methods to manage this disease.

NtWIN1 regulates the biosynthesis of scopoletin and chlorogenic acid by targeting NtF6′H1 and NtCCoAMT genes in Nicotiana tabacum

Scopoletin and chlorogenic acid (CGA) are important polyphenols that regulate plant growth, development, and stress resistance. The ERF transcription factor WAX INDUCER1 (WIN1) promotes the biosynthesis of cutin, suberine, and wax. However, its full roles in regulating the accumulation of plant secondary metabolites still remain to be further clarified. In this study, NtWIN1 gene encoding a SHINE-type AP2/ERF transcription factor of the Va subgroup was identified from N. tabacum. NtWIN1 showed high expression levels in tobacco stems, sepals, and pistils. Overexpression (OE) and knock-out of NtWIN1 showed that it promoted the accumulation of total polyphenols and altered their composition. Compare to that of WT plants, the CGA contents significantly increased by 25%–50% in the leaves, flowers, and capsules of OE lines, while the scopoletin contents in the OE plants significantly decreased by 30%–67%. In contrast, the CGA contents in ntwin1 lines reduced by 23%–26%, and the scopoletin contents in ntwin1 increased by 38%–75% compare to that of WT plants. Chromatin immunoprecipitation and Dual-Luc transcription activation assays showed that NtWIN1 could bind to the promoters of NtF6′H1 and NtCCoAMT, thereby modulating their expression. The scopoletin content in ntwin1/ntf6′h1 double mutant was significantly lower than that in ntwin1 and WT plants, but showed no significant differences with that in ntf6′h1 mutant, further indicating that the inhibition of NtWIN1 on scopoletin accumulation depends on the activity of NtF6′H1. Our study illustrates the new roles of NtWIN1, and provides a possible target for regulating the synthesis of polyphenols in tobacco.

Virulence genes and pulsed-field gel electrophoresis profiles of Shiga toxin-producing Escherichia coli isolated from different food samples and patients with acute diarrhea.

Escherichia coli O157: H7 is one of the most important causes of hemorrhagic colitis, and hemolytic uremic syndrome. The present study aimed to isolate E. coli O157: H7 from foods and patients with hemorrhagic colitis, and identify Shiga toxin genes, phylogenetic comparison, and antibiotic resistance of the isolates. In total 400 samples, including patients stool and food were taken in Isfahan-Iran province. Phenotypic tests and PCR were performed to identify Shiga toxin-producing E. coli. The isolated strains were compared phylogenetically by PFGE. Agar disk diffusion was performed to identify the antibiotic resistance of the isolates. Totally, 5 isolates of fecal samples were E. coli O157, but only 2 isolates carried H7 gene. Also, 9 isolates of E. coli O157 were isolated from food samples that 3 isolates were E. coli O157: H7. The isolates carried stx1, stx2, hlyA and eaeA genes. Also, E. coli non-O157: H7 identified from samples that contained stx1, stx2, hlyA genes. The highest susceptibility to imipenem and the highest resistance to ampicillin and ciprofloxacin were observed. There was a similarity of 100% between the E. coli O157: H7 strains isolated from patients and raw milk and minced beef samples. Serotypes other than the O157 of E. coli are more prevalent in patients and food. The E. coli O157: H7 isolates from patients had 100% genetic similarity with minced meat and cow milk isolates, which indicates cattle are the most important reservoir of this bacterium in Iran.

The Anti-Obesogenic Effects of Muscadine Grapes through Ciliary Neurotrophic Factor Receptor (Cntfr) and Histamine Receptor H1 (Hrh1) Genes in 3T3-L1 Differentiated Mouse Cells.

Obesity and type 2 diabetes are prevalent metabolic diseases that have significant links to several chronic diseases, including cancer, diabetes, hypertension, and cardiovascular disease. Muscadine grape extracts have shown the potential to reduce adiposity and improve insulin sensitivity and glucose control. Thus, this study was designed to determine the potential of muscadine grape berries extract (Pineapple and Southern Home) for its antiobesity properties in 3T3-L1 cells as a model for obesity research. The current study's data indicated the total phenolic content (TPC) and 2,2-diphenyl-1-picrylhydraziyl (DPPH) activity were higher in cultivar (CV) Southern Home, meanwhile, elevated the total flavonoid content (TFC) in Pineapple. Both extracts were safe across the tested range (0-5 mg/mL). A noticeable reduction in lipid accumulation was also found in extract-treated cells. In preadipocytes and adipocytes, the tested extracts showed significant alterations in various genes involved in glucose homeostasis and obesity. The most remarkable findings of the current study are the upregulation of two genes, Cntfr (+712.715-fold) and Hrh1 (+270.11-fold) in CV Pineapple extract-treated adipocytes 3T3-L1 and the high fold increase in Ramp3 induced by both Pineapple and Southern Home in pre-adipose cells. Furthermore, the tested extracts showed a potential to alter the mRNA of various genes, including Zfp91, B2m, Nr3c1, Insr, Atrn, Il6ra, Hsp90ab1, Sort1, and Npy1r. In conclusion, the data generated from the current study suggested that the two extracts under investigation are considered potential candidates for controlling insulin levels and managing obesity.

Combined metabolome and transcriptome reveal HmF6’H1 regulating simple coumarin accumulation against powdery mildew infection in Heracleum moellendorffii Hance

BackgroundPowdery mildew, caused by Eeysiphe heraclei, seriously threatens Heracleum moellendorffii Hance. Plant secondary metabolites are essential to many activities and are necessary for defense against biotic stress. In order to clarify the functions of these metabolites in response to the pathogen, our work concentrated on the variations in the accumulation of secondary metabolites in H. moellendorffii during E. heraclei infection.ResultsFollowing E. heraclei infection, a significant upregulation of coumarin metabolites—particularly simple coumarins and associated genes was detected by RNA-seq and UPLC-MS/MS association analysis. Identifying HmF6’H1, a Feruloyl CoA 6’-hydroxylase pivotal in the biosynthesis of the coumarin basic skeleton through ortho-hydroxylation, was a significant outcome. The cytoplasmic HmF6’H1 protein was shown to be able to catalyze the ortho-hydroxylation of p-coumaroyl-CoA and caffeoyl-CoA, resulting in the formation of umbelliferone and esculetin, respectively. Over-expression of the HmF6’H1 gene resulted in increased levels of simple coumarins, inhibiting the biosynthesis of furanocoumarins and pyranocoumarins by suppressing PT gene expression, enhancing H. moellendorffii resistance to powdery mildew.ConclusionsThese results established HmF6’H1 as a resistance gene aiding H. moellendorffii in combatting E. heraclei infection, offering additional evidence of feruloyl-CoA 6’-hydroxylase role in catalyzing various types of simple coumarins. Therefore, this work contributes to our understanding of the function of simple coumarins in plants’ defense against powdery mildew infection.

Pediatric Diffuse Midline Glioma H3K27-Altered: From Developmental Origins to Therapeutic Challenges.

Diffuse intrinsic pontine glioma (DIPG), now referred to as diffuse midline glioma (DMG), is a highly aggressive pediatric cancer primarily affecting children aged 4 to 9 years old. Despite the research and clinical trials conducted to identify a possible treatment for DIPG, no effective drug is currently available. These tumors often affect deep midline brain structures in young children, suggesting a connection to early brain development's epigenetic regulation targets, possibly affecting neural progenitor functions and differentiation. The H3K27M mutation is a known DIPG trigger, but the exact mechanisms beyond epigenetic regulation remain unclear. After thoroughly examining the available literature, we found that over 85% of DIPG tumors contain a somatic missense mutation, K27M, in genes encoding histone H3.3 and H3.1, leading to abnormal gene expression that drives tumor growth and spread. This mutation impacts crucial brain development processes, including the epithelial-mesenchymal transition (EMT) pathway, and may explain differences between H3K27M and non-K27M pediatric gliomas. Effects on stem cells show increased proliferation and disrupted differentiation. The genomic organization of H3 gene family members in the developing brain has revealed variations in their expression patterns. All these observations suggest a need for global efforts to understand developmental origins and potential treatments.

Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine.

Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily. In this study, a novel family of Tourist-like MITE was characterized in wild soybean species Glycine falcata. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in G. falcata. Using polymerase chain reaction, cloning and sequencing approaches, we showed a high number of copies of the GftoMITE1 family. Extensive bioinformatic analyses revealed the genome-level distribution and locus-specific mapping of GftoMITE1 members in Glycine species. Our results provide the first extensive characterization of the GftoMITE1 family and contribute to the understanding of the evolution of MITEs in the Glycine genus. Genome-specific GftoMITE1 was prominent in perennial wild soybean species, but not in annual cultivated soybean (Glycine max) or its progenitor (Glycine soja). We discuss that the GftoMITE1 family reveals a single rapid amplification in G. falcata and could have potential implications for gene regulation and soybean breeding as an efficient genetic marker for germplasm utilization in the future.

Development and evaluation of a multiplex real-time RT-PCR assay for simultaneous detection of H5, H7, and H9 subtype avian influenza viruses

H5, H7 and H9 are the major subtypes of avian influenza virus (AIV) that cause economic losses in the poultry industry and sporadic zoonotic infection. Early detection of AIV is essential for preventing disease spread. Therefore, molecular diagnosis and subtyping of AIV via real-time RT-PCR (rRT-PCR) is preferred over other classical diagnostic methods, such as egg inoculation, RT-PCR and HI test, due to its high sensitivity, specificity and convenience. The singleplex rRT-PCRs for the Matrix, H5 and H7 gene used for the national surveillance program in Korea have been developed in 2017; however, these methods were not designed for multiplexing, and does not reflect the sequences of currently circulating strains completely. In this study, the multiplex H5/7/9 rRT-PCR assay was developed with sets of primers and probe updated or newly designed to simultaneously detect the H5, H7 and H9 genes. Multiplex H5/7/9 rRT-PCR showed 100% specificity without cross-reactivity with other subtypes of AIVs and avian disease-causing viruses or bacteria, and the limit of detection was 1–10 EID50/0.1 ml (50% egg infectious dose). Artificial mixed infections with the three different subtypes could be detected accurately with high analytical sensitivity even under highly biased relative molecular ratios by balancing the reactivities of each subtype by modifying the concentration of the primers and probes. The multiplex H5/7/9 rRT-PCR assay developed in this study could be a useful tool for large-scale surveillance programs for viral detection as well as subtyping due to its high specificity, sensitivity and robustness in discriminating viruses in mixed infections, and this approach would greatly decrease the time, cost, effort and chance of cross-contamination compared to the conventional method of testing three subtypes by different singleplex rRT-PCR methods in parallel or in series.

National trends in the treatment of adult diffuse midline gliomas: a rare clinical scenario.

Diffuse midline gliomas (DMG) include all midline gliomas with a point mutation to the histone H3 gene resulting in the substitution of a lysine with a methionine (K27M). These tumors are classified as World Health Organization grade 4 with a mean survival between 9- and 19-months following diagnosis. There is currently no standard of care for DMG, and palliative radiation therapy has been proven to only extend survival by months. Our current study aims to report current treatment trends and predictors of the overall survival of DMG. We searched the National Cancer Database for adult patients treated for DMG from 2016 to 2020. Patients were required to have been treated with primary radiation directed at the brain with or without concurrent chemotherapy. Univariable and multivariable Cox regressions were used to determine predictors of overall survival. Of the 131 patients meeting the inclusion criteria, 113 (86%) received radiation and chemotherapy. Based on multivariable Cox regression, significant predictors of survival were Charlson-Deyo comorbidity index and race. Patients with a Charlson-Deyo score of 1 had 2.72 times higher odds of mortality than those with a score of 0. Patients not identifying as White or Black had 2.67 times higher odds of mortality than those identifying as White. The median survival for all patients was 19 months. Despite being considered ineffective, chemotherapy is still administered in most adult patients diagnosed with DMG. Significant predictors of survival were Charlson-Deyo comorbidity index and race.

Pediatric-type high-grade gliomas with PDGFRA amplification in adult patients with Li-Fraumeni syndrome: clinical and molecular characterization of three cases

Li-Fraumeni syndrome (LFS) is an autosomal dominant tumor predisposition syndrome caused by heterozygous germline mutations or deletions in the TP53 tumor suppressor gene. Central nervous system tumors, such as choroid plexus tumors, medulloblastomas, and diffuse gliomas, are frequently found in patients with LFS. Although molecular profiles of diffuse gliomas that develop in pediatric patients with LFS have been elucidated, those in adults are limited. Recently, diffuse gliomas have been divided into pediatric- and adult-type gliomas, based on their distinct molecular profiles. In the present study, we investigated the molecular profiles of high-grade gliomas in three adults with LFS. These tumors revealed characteristic histopathological findings of high-grade glioma or glioblastoma and harbored wild-type IDH1/2 according to whole exome sequencing (WES). However, these tumors did not exhibit the key molecular alterations of glioblastoma, IDH-wildtype such as TERT promoter mutation, EGFR amplification, or chromosome 7 gain and 10 loss. Although WES revealed no other characteristic gene mutations or copy number alterations in high-grade gliomas, such as those in histone H3 genes, PDGFRA amplification was found in all three cases together with uniparental disomy of chromosome 17p, where the TP53 gene is located. DNA methylation analyses revealed that all tumors exhibited DNA methylation profiles similar to those of pediatric-type high-grade glioma H3-wildtype and IDH-wildtype (pHGG H3-/IDH-wt), RTK1 subtype. These data suggest that high-grade gliomas developed in adult patients with LFS may be involved in pHGG H3-/IDH-wt. PDGFRA and homozygous alterations in TP53 may play pivotal roles in the development of this type of glioma in adult patients with LFS.