Genetic Information Research Institute

Abstract Crop and varietal diversification are essential for African smallholder farmers to adapt to the complex and unprecedented challenges posed by climate change. Although African genebanks maintain seed collections of numerous crops, with thousands of varieties collected from their countries’ farmers, the direct use of these collections by farmers is very limited. Five African national genebanks therefore explored ways to strengthen farmers’ access to and use of these collections through a longer-term collaborative process. The genebanks and their partners engaged with ‘Germplasm User Groups’ as a basis for facilitating sustained joint learning with farmers for use of conserved germplasm. The structure of these groups and the methods they used for identifying and testing germplasm accessions, although differing by country context, all enabled a diversity of farmers to learn about a wide range of germplasm under relevant field conditions. The large number of accessions that farmers selected, their diverse advantages and the requests by numerous farmer groups to continue exploring additional crops and varieties indicated the usefulness of these approaches. These experiences revealed the feasibility and unique roles and opportunities for national genebanks to facilitate farmers’ direct use of the diversity conserved in their crop collections. National genebanks thus have unique responsibilities for adapting their operating procedures and partnering with research and development practitioners to facilitate farmers’ discovery and use of their conserved crop diversity.

Abstract Glioblastoma (GBM) is the most aggressive primary tumor of the central nervous system, with a median survival of approximately 14 months despite standard-of-care treatment consisting of maximal surgical resection followed by radiotherapy and temozolomide (TMZ) chemotherapy. Although TMZ remains the most commonly used chemotherapeutic agent for GBM, patient responses vary widely. In clinical practice, its benefit is often more limited in older patients (≥65 years) and in those with poorer performance status, who also tend to experience greater treatment-related toxicity. These observations suggest that age-related differences in tumor biology and cellular stress responses may influence therapeutic outcomes and highlight the need for molecular markers that better predict TMZ sensitivity. To explore age-associated transcriptional differences following TMZ treatment, the public bulk RNA-sequencing dataset GSE263890 was reanalyzed, a transcriptomic dataset of GBM tumors from younger and senior patients after TMZ. Raw gene expression data were processed, normalized, and log-transformed, with low-expression and unannotated transcripts removal to improve data quality. Differentially expressed genes (DEGs) were identified using thresholds of |log2 fold change| > 0.2 and FDR < 0.05. Heatmaps and volcano plots were used to visualize expression patterns, and Gene Ontology (GO) enrichment analysis was performed to identify biological pathways. DEGs analysis between younger and older patients revealed 402 up-regulated genes and 522 down-regulated genes in tumors from senior patients. Prominent up-regulated genes included ZYG11A, HMX1, AP1M2, KERA, GARIL6, USP6, SFTPA1, PAX9, TSPAN19, and TPH2, whereas down-regulated genes included MEST, FLNC, H3C12, NDUFB2, CAV1, GAS2L1, ID4, ATP6V1F, POLR2J, DENND2A, EDNRB, TREM2, RARRES2, and CDC42EP1. Gene Ontology enrichment analysis showed that up-regulated genes were significantly associated with pathways related to cilium organization, microtubule bundle formation, axoneme assembly, ciliary movement, and calcium ion transport, pointing to changes in cytoskeletal structure and intracellular signaling in older patients following TMZ exposure. In contrast, down-regulated genes were enriched in pathways involved in cytoplasmic ribosome biogenesis, peptide chain elongation, eukaryotic translation initiation and termination, nonsense-mediated mRNA decay, and EIF2AK4 (GCN2)-mediated amino acid stress responses, suggesting an overall reduction in protein synthesis and translational activity. In conclusion, these results reveal age-associated transcriptional differences in GBM tumors following TMZ treatment. The observed alteration markers in cellular structure, signaling pathways, and translational regulation may help explain differences in therapeutic response and tolerance between younger and older patients. This study provides molecular insight into age-related variability in TMZ efficacy and supports the development of age-informed biomarkers to improve outcomes for patients with GBM. Citation Format: Catherine Chen, Wlliam Xu, Qian Wang. Age-Associated Transcriptomic Alterations in Glioblastoma Following Temozolomide Treatment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Brain Cancer; 2026 Mar 23-25; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(6_Suppl):Abstract nr A049.

Epigenetic DNA modification is a key component of the defense system against invading nucleic acids such as transposons. TET/JBP dioxygenases oxidize 5-methylcytosine and lead to its replacement by cytosine in mammals. Expansion of TET/JBP genes and their association with DNA transposons were previously reported in Basidiomycota fungi. In this study, a thorough bioinformatics investigation of TET/JBP genes revealed that diverse groups of DNA transposons have captured a TET/JBP dioxygenase in three lineages of fungi: Pucciniomycetes (rusts) and Agaricomycetes (mushrooms) in Basidiomycota, and Pezizomycetes (morels and truffles) in Ascomycota. TET/JBP genes encoded by DNA transposons can be classified into three types, designated as PU, AG, and PE here. The PU type is distributed in Pucciniomycetes and encoded by seven different lineages of DNA transposons (Dileera, hAT, Harbinger, IS3EU, EnSpm, ESTA, and Helitron). The AG type is distributed in Agaricomycetes, and encoded by two lineages of DNA transposons (Kyakuja and Zisupton). The PE type is distributed in Pezizomycetes and Agaricomycetes, and encoded by five lineages of DNA transposons (Zisupton, IS3EU, EnSpm, Plavaka, and Helitron). Phylogenetic analysis indicated several transmission events from certain DNA transposon lineage to another. These transposon-encoded TET/JBP dioxygenases likely contribute to the escape of transposons from the methylation-based silencing system in fungi.

Lentinula edodes (shiitake mushroom) possesses substantial nutritional and medicinal value. Even though the genomes of several strains have been reported, some essential observations, including the exact chromosome number, still need validation. This study reports a near-telomere-to-telomere assembly of the complete diploid genome of L. edodes strain XR1, a commercially important Japanese strain. We employed the PacBio HiFi long-read sequencing technology combined with single-cell genotyping data and manual curation. The assembled diploid genome comprised 20 chromosomes (10 per haplotype), and significant inter-haplotype variation was observed. Additionally, we identified a novel Penelope-like retrotransposon-Coprina-1_LeEd-specifically localized to the telomeres. This study marks the first report of telomere elongation by the transposition of Coprina. Our findings provide a high-resolution genome resource for L. edodes, consequently elucidating its evolution, genomic structure, and breeding potential. Furthermore, this study establishes a foundation for further research on edible mushroom genetics and biotechnology.

Canine epilepsy, a prevalent neurological disorder, poses significant challenges in veterinary medicine. Traditional treatment approaches often yield variable outcomes, necessitating exploration of alternative therapies. This study investigates the efficacy of homeopathic remedies in managing canine epilepsy and explores the potential of Artificial Intelligence (AI) and Machine Learning (ML) to enhance treatment protocols. We analyzed data from 32 epileptic dogs, documenting various parameters including age, breed, sex, weight, seizure frequency and duration pre- and post-treatment, homeopathic remedies used, potency, treatment duration, and owner observations. Remedies included Agaricus mus, Belladonna, Cicuta virosa, Cina, Hyoscyamus, Cuprum met and Natrum mur, administered in potencies of 30C, 200C, 1M and 0/1 LM over treatment durations ranging from 2 to 24 months. Descriptive statistics and visualizations revealed significant findings. Bulldogs and male dogs exhibited the highest improvement levels, particularly with Agaricus mus and Natrum mur remedies. Notably, remedies administered at LM potencies (0/1 LM) and longer durations (21 months) demonstrated superior efficacy. Improvement levels during treatment showed moderate correlations with treatment duration, indicating prolonged administration enhances therapeutic outcomes. We trained 3 different ML algorithms logistic regression, random forest and xgboost. The Random Forest model emerged as the most accurate, with an accuracy of 86%. Feature importance analysis revealed that pre-treatment seizure frequency, homeopathic remedy used, and treatment duration were critical predictors of treatment success In conclusion, Integrating AI and ML can revolutionize this aspect by analyzing large datasets to predict optimal treatment protocols based on individual patient characteristics. Machine learning algorithms can identify patterns and correlations that may not be immediately apparent, offering insights into the most effective remedies, potencies, and durations for specific breeds and demographics. This approach promises to enhance the quality of life for affected dogs and provide veterinarians with robust tools for decision-making.

Abstract The ability to predict T-cell receptor (TCR) specificity computationally could revolutionize personalized immunotherapies, vaccine development, and the understanding of immunology and autoimmune diseases. While progress depends on obtaining training data that represent the vast range of possible TCR-ligand pairs, systematic assessment of modeling assumptions is equally important and can begin with existing data. We illustrate this by evaluating two ideas currently present in the field1,2: treating TCR specificity and T cell activation as distinct modeling tasks, and using unsupervised models based on sequence similarity for TCR specificity prediction. Although presented as general strategies, we argue these are exceptions rather than universally applicable principles.

BackgroundDNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal species Chondrus crispus, and one fungal species Puccinia graminis. Six Academ families from P. graminis encode a helicase in addition to putative transposase, while some other families encode a single protein which contains a putative transposase and an XPG nuclease.ResultsSystematic searches on Repbase and BLAST searches against publicly available genome sequences revealed that several species of fungi and animals contain multiple Academ transposon families encoding a helicase. These AcademH families generate 9 or 10-bp target site duplications (TSDs) while Academ families lacking helicase generate 3 or 4-bp TSDs. Phylogenetic analysis clearly shows two lineages inside of Academ, designated here as AcademH and AcademX for encoding helicase or XPG nuclease, respectively. One sublineage of AcademH in animals encodes plant homeodomain (PHD) finger in its transposase, and its remnants are found in several fish genomes.ConclusionsThe AcademH lineage of TEs is widely distributed in animals and fungi, and originated early in the evolution of Academ DNA transposons. This analysis highlights the structural diversity in one less studied superfamily of eukaryotic DNA transposons.

Nonalcoholic fatty liver disease (NAFLD) and cryptogenic cirrhosis (CC) are considered preneoplastic conditions that might progress to hepatocellular carcinoma. We evaluated parameters of telomere dysfunction in these patient groups to study the correlation between telomere length and the progression of NAFLD. We analyzed peripheral lymphocytes from 22 patients with NAFLD, 20 patients with CC, and 20 healthy, age-matched controls. Telomere length was analyzed using quantitative fluorescence in situ hybridization, and cellular senescence was evaluated by the percentage of cells with senescence-associated heterochromatin foci. The expression of telomerase reverse transcriptase (hTERT) mRNA was measured using polymerase chain reaction, and telomere capture (TC) was assessed with 2 Cytocell probes, 15qter and 13qter. Shorter telomere length and increased cellular senescence was demonstrated in patients with NAFLD, compared to the CC patients and healthy controls. While hTERT mRNA was significantly decreased, TC was increased in CC patients, compared to the NAFLD group and healthy individuals. Thus, there is a correlation between hTERT mRNA expression and telomere length in patients with NAFLD, which might be related to associated metabolic disorders and the risk of malignant transformation. Patients with CC, on the contrary, elongate their telomeres through the TC mechanism.

Ama: Pigmente purpurik dermatoz (PPD) petei ve hiperpigmente makllerle karakterize bir hastalktr. Hastaln etiyoloji tam olarak bilinmemektedir. Ortalama trombosit hacmi (OTH) trombosit fonksiyon ve aktivasyonunu gsteren bir belirtetir. Trombositler hemostaz ve koagulasyondaki rollerine ek olarak inflamasyon ve immn sistem zerinde de nemli rol oynarlar. Biz bu almada, PPD ve OHT arasndaki olas ilikiyi aratrdk. Yntemler: PPD tans olan 40 hasta almaya dahil edildi

Transposons, or transposable elements, are the major components of genomes in most eukaryotes. Some groups of transposons have developed target specificity that limits the integration sites to a specific nonessential sequence or a genomic region to avoid gene disruption caused by insertion into an essential gene. R2 is one of the most intensively investigated groups of sequence-specific non-LTR retrotransposons and is inserted at a specific site inside of 28S ribosomal RNA (rRNA) genes. R2 is known to be distributed among at least six animal phyla even though its occurrence is reported to be patchy. Here, in order to obtain a more detailed picture of the distribution of R2, we surveyed R2 using both in silico screening and degenerate PCR, particularly focusing on actinopterygian fish. We found two families of the R2C lineage from vertebrates, although it has previously only been found in platyhelminthes. We also revealed the apparent movement of insertion sites of a lineage of actinopterygian R2, which was likely concurrent with the acquisition of a 28S rRNA-derived sequence in their 3′ UTR. Outside of actinopterygian fish, we revealed the maintenance of a single R2 lineage in birds; the co-existence of four lineages of R2 in the leafcutter bee Megachile rotundata; the first examples of R2 in Ctenophora, Mollusca, and Hemichordata; and two families of R2 showing no target specificity. These findings indicate that R2 is relatively stable and universal, while differences in the distribution and maintenance of R2 lineages probably reflect characteristics of some combination of both R2 lineages and host organisms.