Search Results (1,698)

A mutation detection strategy based on mismatch digestion was applied previously in barley seedlings carrying the chloroplast mutator (cpm) genotype through many generations. Sixty-one mutations were detected along with four large indels: a 15 bp insertion in the intergenic region between tRNA^His and rps19 genes, a 620 bp deletion in the psbA gene, a 79 bp deletion in the intergenic region between rpl33 and rps18 genes and a 45 bp deletion in the rps3 gene. The present investigation aims to understand the mechanisms producing the large indels and to better characterize the cpm mutagenic effect. Whole plastome sequencing revealed novel polymorphisms that were identified either in regions not previously examined or in regions that were explored but not detected through celery juice extract (CJE) digestion. The 620 bp deletion in the psbA gene was lethal when homoplastomic, whereas the 45 bp deletion in the rps3 gene did not affect the viability of the seedlings even in homoplastomy. The presence of direct repeats at the borders of large indels suggests that they could have originated by illegitimate recombination because of CPM protein malfunction. A truncated mismatch repair MSH1 protein identified in cpm seedlings suggests that CPM is involved in organellar genome stability maintenance. Full article

Malignant bone and soft tissue tumors are often resistant to conventional treatment, and treatment options for unresectable and metastatic cases are limited. L-type amino acid transporter 1 (LAT1) is overexpressed in several malignancies, including sarcomas, making it an attractive target for targeted alpha therapy. In this study, we investigated the therapeutic efficacy of LAT1-targeted alpha therapy using a novel modified 3-astatin-211 Astato-α-methyl-L-tyrosine (²¹¹At-AAMT) for bone and soft tissue sarcomas. LAT1 expression and the specificity of LAT1-mediated uptake of ²¹¹At-AAMT were evaluated in bone and soft tissue sarcoma cell lines. Antiproliferative effects were assessed using cell viability and colony formation assays. DNA damage was assessed using immunostaining with phosphorylated histone γH2AX. In vivo efficacy of ²¹¹At-AAMT, determined using xenograft mouse models, was compared with that of doxorubicin. LAT1 was highly expressed in all cell lines, especially MP-CCS-SY and MG-63 cells. ²¹¹At-AAMT uptake was LAT1-dependent and significant in all cell lines. It inhibited cell proliferation in a dose-dependent manner, comparable to that of doxorubicin. In xenograft models, a single administration of ²¹¹At-AAMT significantly inhibited tumor growth without systemic toxicity, whereas doxorubicin caused weight loss. Histopathological analysis showed reduced cell density, inhibited proliferation, and extensive DNA damage in tumors treated with ²¹¹At-AAMT, whereas LAT1 expression was maintained in residual tumor tissues. LAT1-targeted alpha therapy with ²¹¹At-AAMT demonstrated antitumor efficacy comparable to that of first-line chemotherapy for osteosarcoma and soft tissue sarcoma. Sustained LAT1 expression suggests the potential for repeated or combination treatments, highlighting its promise as a novel therapy for advanced, treatment-resistant sarcomas. Full article

Post-exertional malaise (PEM) is a defining symptom of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), yet its molecular underpinnings remain elusive. This study investigated the temporal–longitudinal DNA methylation changes associated with PEM using a structured two-day maximum repeated effort cardiopulmonary exercise testing (CPET) protocol involving pre- and two post-exercise blood samplings from five ME/CFS patients. Cardiopulmonary measurements revealed complex heterogeneous profiles among the patients compared to typical healthy controls, and VO₂ peak indicated all patients had poor normative fitness. The switch to anaerobic metabolism occurred at a lower workload in some patients on Day Two of the test. Reduced Representation Bisulphite Sequencing followed by analysis with Differential Methylation Analysis Package-version 2 (DMAP2) identified differentially methylated fragments (DMFs) present in the DNA genomes of all five ME/CFS patients through the exercise test compared with ‘before exercise’. With further filtering for >10% methylation differences, there were early DMFs (0–24 h after first exercise test) and late DMFs between (24–48 h after the second exercise test), as well as DMFs that changed gradually (between 0 and 48 h). Of these, 98% were ME/CFS-specific, compared with the two healthy controls accompanying the longitudinal study. Principal component analysis illustrated the three distinct clusters at the 0 h, 24 h, and 48 h timepoints, but with heterogeneity among the patients within the clusters, highlighting dynamic methylation responses to exertion in individual patients. There were 24 ME/CFS-specific DMFs at gene promoter fragments that revealed distinct patterns of temporal methylation across the timepoints. Functional enrichment of ME-specific DMFs revealed pathways involved in endothelial function, morphogenesis, inflammation, and immune regulation. These findings uncovered temporally dynamic epigenetic changes in stress/immune functions in ME/CFS during PEM and suggest molecular signatures with potential for diagnosis and of mechanistic significance. Full article

Background/Objectives: Cervical cancer (CC), a highly prevalent female neoplasia, has been prevented through repeated cervicovaginal cytology, the so-called Pap test, across women’s lifespans. The now undebatable role of Human Papillomaviruses in the etiology of CC and the development of high-throughput automated molecular amplification diagnostic platforms is allowing for the replacement of the Pap test with HPV testing. The objective of this review is to contextualize the current strategies for cervical cancer screening using molecular assays. Methods: The many existing screening tools relying on molecular markers and their advantages and drawbacks are discussed. Results: Testing for oncogenic Human Papillomavirus DNA is presently the mainstay strategy for molecular screening, replacing cervicovaginal cytology. Conclusions: The presence of HPV-DNA is the most sensitive marker for cervical cancer and its precursor lesions. However, its adoption has led to an increase in the number of screening-positive subjects, generating extra demand for triage resources. New algorithms and technologies are fast being developed to address this need, moving toward risk-based management. Full article

Background/Objectives: Pothos chinensis is commonly used as traditional medicine in China and India. Codon usage analysis is a good way to understand plants’ evolution. However, there is no report about the codon usage bias of chloroplast genomes in P. chinensis. Methods: In this study, the chloroplast genome of the medicinal plant P. chinensis was newly obtained. Comparative analyses, DNA barcoding investigation, codon usage bias, and phylogenetic reconstruction were conducted to reveal the chloroplast genome characteristics of P. chinensis. Results: The length of the chloroplast genome of P. chinensis was 165,165 bp. A total of 134 genes were annotated, i.e., 90 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Compared to its sister group Anthurium andraeanum, the length of the large single-copy region (LSC) had been expanded, while the small single-copy region (SSC) had been contracted. Within P. chinensis and P. scandens there were no obvious differences in the length of LSC, SSC, and two inverted repeat regions. Based on Pi values, seven hypervariable regions of whole plastomes were identified. The analysis of codons showed that an average frequency of the 50 candidate genes was 35.30%, and these genes preferred A/U-ending codons. The average effective number of codon (ENC) value was 45.49, which indicated weak codon usage bias. ENCs had a highly significant positive correlation with GC3. Fourteen optimal codons had been identified, 11 of which ended with A/U. The results of the neutrality plot, ENC-plot, and PR2-plot analysis indicated that natural selection might have a significant impact on codon usage patterns. Conclusions: Taken together, our study unraveled the codon usage patterns in P. chinensis and provided valuable genetic information for the genus Pothos. Full article

The interactions of leukocyte glycoproteins with adhesion and signaling molecules through glycan recognition are not well understood. We previously demonstrated that galectin-8, a tandem-repeat lectin with N- and C-terminal carbohydrate binding domains which is highly expressed in endothelial and epithelial cells, can bind to activated neutrophils to induce surface exposure of phosphatidylserine (PS) without DNA fragmentation or apoptosis, in a process termed preaparesis. However, the receptors for Gal-8 on leukocytes have not been identified. Here we report our results using both proteomics and affinity chromatography with both full-length Gal-8 and the separate Gal-8 C-terminal and N-terminal domains to identify glycoprotein ligands in HL-60 cells for Gal-8. Two of the major ligands for Gal-8 are CD45RA and CD45RC (Protein Tyrosine Phosphatase, PTP) and basigin (CD147). Both CD45 and basigin are integral membrane glycoproteins that carry poly-N-acetyllactosamine modifications on N- and/or O-glycans, required for Gal-8 binding. Inhibition of the phosphatase activity of CD45 reduced Gal-8-induced PS exposure, indicating a possible role of CD45 in Gal-8 signaling of preaparesis in human leukocytes. These results demonstrate unique glycoprotein recognition by Gal-8 involved in cell recognition and signaling. Full article

Sequencing cyanobacteria from xenic cultures is often challenging when their DNA extracts are confounded by DNA from their heterotrophic microbiome. Using an iterative DNA lysis protocol can fractionate between DNA from the cyanobacterium and the heterotrophic strains. To further demonstrate the utility of this protocol, it was used to sequence another xenic culture of cyanobacteria. This effort led to the assembly of a megabase-length cyanobacterial chromosome; however, repeated ribosomal regions created assembly issues even after adding data from another sequencing run to improve coverage. A separate DNA preparation from a single cell lysis step was also run for comparison but yielded a markedly lower proportion of cyanobacterial reads (<2%). Instead, the circular cyanobacterial chromosome was closed with targeted amplicon sequencing. Phylogenetic analysis assigned this strain to the genus Pseudanabaena. Within the metagenomic assembly were the genomes of six heterotrophic strains, preliminarily assigned as belonging to the genera Acidovorax, Hydrogenophaga, Lysobacter, Novosphingobium, Sediminicoccus, and Tabrizicola. Lysobacter sp. BL-A-41-H3’s chromosome was also assembled as a closed circular contig. This study demonstrates that iterative lysis enriches for cyanobacterial DNA and enables concurrent genome assembly of cohabitating heterotrophs alongside the host cyanobacterium. Full article

Pyrola decorata Andres (P. decorata) is a traditional medicinal plant in China. However, its chloroplast genome and the deep evolutionary relationships among its genus remain unexplored. This study identified the samples as P. decorata using morphological observations from Flora of China (FOC) and ITS sequences. It is the first to analyze the complete chloroplast genome of P. decorata using Illumina and Nanopore sequencing technologies, confirming a typical chloroplast dumbbell structure. The chloroplast DNA (cpDNA) of P. decorata is 179,999 bp in length, consisting of a large single copy (LSC) (62.3% of total length (112,150 bp)), a small single copy (SSC) (6.5% of total length (11,701 bp)), and two inverted repeat regions (IRA and IRB) (31.2% combined (28,074 bp × 2)). Functional annotation revealed 128 genes: 77 conserved coding sequences (CDS) genes, 43 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis placed P. decorata, Pyrola atropurpurea (P. atropurpurea), Pyrola rotundifolia (P. rotundifolia), and Chimaphila japonica within Group I, with P. decorata exhibiting the closest chloroplast genomic affinity to P. atropurpurea. These findings integrate morphological and molecular evidence to facilitate further identification, classification, and evolutionary analysis of this genus. Full article

The Naozhou stock of large yellow croakers (Larimichthys crocea) exhibits unique phenotypic traits and high genetic diversity, making it a valuable resource for selective breeding and genetic conservation in aquaculture. Despite its importance, simple sequence repeat (SSR) markers have not been developed for this stock, which limits efforts in genetic evaluation, breeding optimization, and sustainable utilization of this commercially important species. In this study, 195,263 SSRs were identified from the genome of the Naozhou stock of large yellow croaker, covering a total length of 16,578,990 bp with a density of 288 bp/Mb. Dinucleotide repeats were the most common, with the AC motif being the most prevalent. The frequency of SSR markers ranged from 245.63 to 346.60 per Mb. A total of 30 primer pairs were synthesized, of which 28 pairs (93.3%) successfully amplified clear and reproducible bands in PCR assays. Among these, 28 SSR markers exhibited distinct and reproducible bands following gel electrophoresis. For eight SSR loci, the number of alleles (Na) ranged from 4 to 22 (mean = 11.375), while the effective number of alleles (Ne) ranged from 1.5401 to 10.4727 (mean = 5.6475). The assembled mitochondrial genome (mtDNA) was 16,467 bp in length and comprised 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The total sequence length of the PCGs was 11,431 bp, accounting for 69.4% of the mtDNA. A large portion of the PCGs (5) used incomplete stop codons (e.g., nad2, nad3, cox2), while others used TAA stop codons (e.g., nad6, nad5, TrnT). The mtDNA encoded a total of 3808 codons, with UAA showing the highest relative synonymous codon usage value. The SSR markers and mtDNA data generated in this study provide valuable tools for future genetic breeding and genomic research on the Naozhou stock of large yellow croakers. Full article

The bidirectional relationship between epilepsy and depression illustrates shared neurobiological mechanisms of neuroinflammation, hypothalamic–pituitary–adrenal axis dysregulation, and glutamatergic dysfunction. Depression is present in 20–55% of people with epilepsy, far greater than in the general population, while depression doubles epilepsy risk 2.5-fold, indicating shared pathophysiology. Neuroinflammatory mediators (interleukin-6, tumor necrosis factor alpha, high-mobility group box 1) establish a vicious cycle: seizures exacerbate inflammation and mood disruption, and stress lowers seizure thresholds. Hippocampal damage and cortisol toxicity also link these disorders, with early life stress imprinting lifelong risk via epigenetic alteration. Genetic studies identify pleiotropic genes (brain-derived neurotrophic factor) that regulate synaptic plasticity, serotonin activity, and immune responses. New treatments target shared pathways: ketamine and AMPAkines normalize glutamate tone; mGluR5 antagonists attenuate hyperexcitability and inflammation; DNA methyltransferase inhibitors reverse aberrant DNA methylation; and probiotics manipulate the gut–brain axis by boosting neuroprotective metabolites like butyrate. Despite challenges—transient effects, precision dosing, and blood–brain barrier penetration—these advances constitute a paradigm shift toward mechanistic repair rather than symptom management. The way forward includes clustered regularly interspaced short palindromic repeats (CRISPR)-based epigenome editing, biomarker-led therapies, and combination approaches (e.g., ketamine and probiotics). Such comorbidity needs to be managed holistically through integrated neuropsychiatry care, offering hope to patients with treatment-refractory symptoms. Full article

Echinostomatidae is a taxonomically complex group with substantial species diversity and richness. The vast majority of species in this family parasitize birds and mammals, including humans, causing significant economic losses and medical costs. In this study, Echinostoma miyagawai (Digenea, Echinostomatidae) and Patagifer bilobus (Digenea, Echinostomatidae) were isolated from domestic duck and Grus japonensis, respectively. The nearly complete ribosomal transcription unit (rTU) sequences of two echinostomes were obtained, with the rTU for P. bilobus being obtained for the first time. The nearly complete rTU sequence of P. bilobus (6790 bp) and E. miyagawai (6893 bp) encompass the small-subunit (18S) ribosomal DNA (rDNA), internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), and large-subunit (28S) rDNA. The complete lengths of 18S, ITS1, 5.8S, ITS2, and 28S sequences for E. miyagawai are 1989 bp, 444 bp, 162 bp, 431 bp, and 3858 bp, respectively. For P. bilobus, complete or nearly complete lengths of these sequences are 1929 bp (nearly complete), 419 bp, 162 bp, 432 bp, and 3848 bp (nearly complete), respectively. The 18S, ITS, and 28S sequences of E. miyagawai show the highest sequence similarity with other E. miyagawai. The ITS and 28S sequences of P. bilobus show the highest sequence similarity with other P. bilobus, while 18S sequence shows the highest similarity with E. miyagawai. This is likely due to the unavailability of the 18S sequence of P. bilobus in GenBank. Repeat sequences were identified in 18S, ITS1, ITS2, and 28S sequences, with the 28S sequence containing the most repeats and the 5.8S sequence having none. The results of phylogenetic reconstruction indicated that E. miyagawai clusters with other Echinostoma spp., while P. bilobus clusters with other Patagifer spp., forming sister taxa. This study not only provides the first rTU sequence for P. bilobus but also reinforces the sister group status of Patagifer to Echinostoma through phylogenetic evidence. Finally, this study represents the first record of the G. japonensis as a new host for P. bilobus and the first report of a bird from the crane family (Gruidae) as a host for any echinostome species. These findings are significant as they expand our understanding of the host range and ecological interactions of Echinostomatidae. The data obtained provide a valuable resource of molecular markers for studying the taxonomy, population genetics, and systematics of the family Echinostomatoidea. This research contributes to a more comprehensive understanding of the evolutionary relationships and biodiversity within this complex group of parasites, which is crucial for developing effective strategies to mitigate their impact on both wildlife and human health. Full article

Background: Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumour, associated with poor survival outcomes and significant clinical challenges. Conventional diagnostic methods, including MRI, CT, and histopathological analysis of tissue biopsies, are limited by their inability to reliably distinguish treatment effects from true tumour progression, often resulting in misdiagnosis and delayed intervention. Repeated tissue biopsies are also invasive and unsuitable for longitudinal monitoring. Liquid biopsy, a minimally invasive approach analysing tumour-derived material in biofluids such as blood and cerebrospinal fluid (CSF), offers a promising alternative. This review aims to evaluate current evidence on circulating biomarkers including circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), microRNAs (miRNAs), extracellular vesicles (EVs), and proteins in GBM diagnosis and monitoring, and to assess the potential role of artificial intelligence (AI) in enhancing their clinical application. Methods: A narrative synthesis of the literature was undertaken, focusing on studies that have investigated blood- and CSF-derived biomarkers in GBM patients. Key aspects evaluated included biomarker biology, detection techniques, diagnostic and prognostic value, current technical challenges, and progress towards clinical translation. Studies exploring AI and machine learning (ML) approaches for biomarker integration and analysis were also reviewed. Results: Liquid biopsy enables repeated and minimally invasive sampling of tumour-derived material, reflecting the genetic, epigenetic, proteomic, and metabolomic landscape of GBM. Although promising, its translation into routine clinical practice is hindered by the low abundance of circulating biomarkers and lack of standardised collection and analysis protocols. Evidence suggests that combining multiple biomarkers improves sensitivity and specificity compared with single-marker approaches. Emerging AI and ML tools show significant potential for improving biomarker discovery, integrating multi-omic datasets, and enhancing diagnostic and prognostic accuracy. Conclusions: Liquid biopsy represents a transformative tool for GBM management, with the capacity to overcome limitations of conventional diagnostics and provide real-time insights into tumour biology. By integrating multiple circulating biomarkers and leveraging AI-driven approaches, liquid biopsy could enhance diagnostic precision, enable dynamic disease monitoring, and improve clinical decision-making. However, large-scale validation and standardisation are required before routine clinical adoption can be achieved. Full article

Myriophyllum heterophyllum is an aquatic macrophyte that is invasive to the northeastern United States and several western European countries. Spreading by vegetative clonal propagation, especially fragmentation, extensive resources are devoted to limiting its growth and spread; however, genetic assessments are not typically included in management strategies. Reduction in genetic (clonal) diversity should accompany biomass reduction, yet without genetic assessment, the efficacy of plant removal remains unclear. This paper is the first to describe a microsatellite marker library and its use in the characterization of Myriophyllum heterophyllum. Eighty-seven tissue samples were collected across the invasive distribution of Myriophyllum heterophyllum in Maine, USA. DNA was extracted, and PCR amplification was employed to screen 13 published microsatellites. Sequencing of the amplified loci was performed to characterize repeat motifs and confirm primer binding sites. Fragment sizing of PCR amplicons was employed to determine microsatellite lengths across the 87 samples. A total of 7 of the 13 tested markers were amplified, with six of those seven found to be variable. Polyploidy was evident from allelic diversity within individuals, although precise ploidy could not be determined. Observed heterozygosity ranged from 0.16 to 1.00 across variable markers. This seven-marker library was effective in characterizing the genetic diversity of both newly discovered (<5 years) and older (>50 years) infestations and is expected to be suitable for assessment of genetic diversity in populations within the native range of M. heterophyllum. The marker library also shows potential for use in several other Myriophyllum species. Full article

Abrus bottae belongs to the subfamily Papilionoideae DC. and the family Fabaceae Lind., endemic to the Arabian Peninsula. This genus encounters numerous taxonomic issues concerning both the quantity of species within the genus and the systematic relationships among its species. Notably, there is a complete absence of sequence data in the GenBank database for this species. A molecular and phylogenetic study of the chloroplast genome of the species A. bottae was performed in this work. The chloroplast genome is 152,540 bp in size and exhibits a typical quadripartite structure, consisting of a substantial single-copy region of 83,507 bp, a small single-copy region of 17,681 bp, and a pair of inverted repeat regions of 25,676 bp each. The chloroplast genome of Abrus bottae encompasses 130 genes. An analysis of nucleoside diversity revealed 26 nucleotide polymorphism sites with Pi values (a measure of genetic variation within species) ≥ 0.04, serving as hotspots of variation. This work represents the first molecular phylogenetic study on the endemic species Abrus bottae and presents a comparative and phylogenetic analysis of the cp genomes of related taxa within the tribe Abreae. These outcomes can be used to develop DNA barcodes to study variation among the Abrus species. Full article

The objective of this work was to analyse the genetic diversity of a population of Citrus spp. in the south of the State of Espírito Santo, Brazil, for pre-breeding studies. For that, a total of sixty genotypes were analysed, including ten citrus varieties from four species of the Citrus genus. The methodology involved DNA extraction, amplification via polymerase chain reaction, and the use of a set of 16 Simple Sequence Repeat markers. These markers identified 42 alleles, with a variation of one to four alleles per locus, an average heterozygosity value of 0.53, and an average polymorphic information content of up to 0.29 per species. After the analysis, a dissimilarity matrix was generated using Jaccard distance and a dendrogram, revealing the formation of two groups: Group I, comprising Citrus sinensis varieties, and Group II, comprising varieties of Citrus latifolia, Citrus aurantifolia, and Citrus reticulata. Our study demonstrated that the combination of these markers allowed for the differentiation of genotypes within the collection. The results obtained are valuable for the future management of the collection and the efficient use of genetic diversity estimation in Citrus spp. Full article