Analysis Of Gene Function Research Articles

Metagenomic and Physicochemical Characterization of Diesel Contaminated Soil from University of Calabar Power Plant: In-Sights to Bacterial Diversity and Community Function

Petroleum-contaminated soils provide an ideal environment for hydrocarbon-degrading bacteria, necessitating the study of their microbial ecology and community changes. This research compared diesel-impacted power plant soil (PPS) from the University of Calabar with pristine soil (CSS) as a control, the samples (50 g) were randomly collected from depths of 0–15 cm, 15–30 cm, and 30–45 cm. Physicochemical and metagenomic analyses were conducted. Taxonomic profiling with functional gene analyses via COG and PRK frameworks performed. PPS displayed higher concentrations of organic carbon (7.02%), total petroleum hydrocarbons (8500 mg/kg), nitrogen (0.51%), phosphorus (3.65 g/kg), lead (175 mg/kg), iron (2619 mg/kg), and copper (196.55 mg/kg) than CSS. Conversely, CSS had higher pH, temperature, conductivity, and moisture content. Bacterial abundance was slightly higher in CSS (89.24%) than in PPS (87.47%), with distinct dominant microbial taxa between samples. Functional analysis identified COG Class I (lipid transport and metabolism) as the most abundant in PPS (32.37%), linked to the predominant hydrocarbon-degrading bacterium Bacillus amyloliquefaciens (26.24%), absent in CSS. In contrast, CSS had COG Class O (posttranslational modification) as the highest (94%). These results demonstrate that petroleum pollution promotes the growth of hydrocarbon-degrading bacteria, underscoring the ecological impacts of contamination on soil microbial communities.

Characteristics of gut microbiota of premature infants in the early postnatal period and their relationship with intraventricular hemorrhage

BackgroundStudies have shown correlations between gut microbiota and neurocognitive function, but little was known about the early postnatal gut microbiota and intraventricular hemorrhage (IVH). We aimed to explore the characteristics of gut microbiota in premature infants and their relationship with IVH, further exploring potential therapeutic targets.MethodsPremature infants delivered at Peking University First Hospital from February 2023 to August 2023 were recruited as a cohort. Feces samples were collected on postnatal days 1, 3, and 5. Premature infants were divided into normal, mild IVH, and severe IVH groups based on cranial ultrasound. 16S rRNA amplicon sequencing technology was used to determine the fecal microbiota, and the results were analyzed.ResultsThirty-eight premature infants were enrolled. There was a significant difference in alpha and beta diversity among the three groups. The relative abundance of E. coli and A. muciniphila was different among the three groups. Further random forest analysis indicated that S. lutetiensis, L. mirabilis, and N. macacae can effectively distinguish premature infants with IVH. Finally, the phylogenetic investigation of communities by reconstruction of unobserved states2 (PICRUSt2) functional gene analysis predicted significant differences in energy metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and membrane transport between normal and severe IVH groups.ConclusionsThe gut microbiota in the early postnatal period of premature infants is closely associated with the IVH status. As age increases, the differences in gut microbiota of premature infants with different degrees of IVH continue to increase, and the trend of changes with severity of IVH becomes more and more obvious. E. coli, A. muciniphila, S. lutetiensis, L. mirabilis, N. macacae, G. haemolysans, and S. oralis can effectively distinguish between IVH infants and normal premature infants. The results indicate that gut microbiota is expected to provide effective therapeutic targets for the diagnosis and treatment of IVH.

Ubiquitin Ligase U-Box51 Positively Regulates Drought Stress in Potato (Solanum tuberosum L.)

The ubiquitin-proteasome system (UPS) is a key protein degradation pathway in eukaryotes, in which E3 ubiquitin ligases mediate protein ubiquitination, directly or indirectly targeting substrate proteins to regulate various biological processes, including plant growth, hormone signaling, immune responses, and adaptation to abiotic stress. In this study, we identified plant U-box protein 51 in Solanum tuberosum (StPUB51) as an E3 ubiquitin ligase through transcriptomic analysis, and used it as a candidate gene for gene-function analysis. Quantitative real-time PCR (qRT-PCR) was used to examine StPUB51 expression across different tissues, and its expression patterns under simulated drought stress induced by polyethylene glycol (PEG 6000) were assessed. Transgenic plants overexpressing StPUB51 and plants with down-regulated StPUB51 expression were generated to evaluate drought tolerance. The activities of key antioxidant enzymes-superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) as well as malondialdehyde (MDA) content in transgenic plants’ leaves were measured under drought conditions. Protein–protein interactions involving StPUB51 were explored via yeast two-hybrid (Y2H) screening, with interaction verification by bimolecular fluorescence complementation (BiFC). StPUB51 was predominantly expressed in stems, with lower expression observed in tubers, and its expression was significantly upregulated in response to 20% PEG-6000 simulated drought. Subcellular localization assays revealed nuclear localization of the StPUB51 protein. Under drought stress, StPUB51-overexpressing plants exhibited enhanced SOD, POD, and CAT activities and reduced MDA levels, in contrast to plants with suppressed StPUB51 expression. Y2H and BiFC analyses identified two interacting proteins, StSKP2A and StGATA1, which may be functionally linked to StPUB51. Collectively, these findings suggest that StPUB51 plays a positive regulatory role in drought tolerance, enhancing resilience in potato growth and stress adaptation.

Phosphorus removal performance of Sulfide-Based autotrophic denitrification process

Sulfide-based Autotrophic Denitrification (SAD) Process can simultaneous remove sulfurous and nitrogenous pollutants, showing a promising prospect. Beyond our expectation, it also has an efficient phosphorus (P) removal performance. The operation results demonstrated that when the influent concentration of nitrate, sulfide and phosphate was 80.55 ± 2.98 mg N/L, 380.15 ± 20.83 mg S/L and 47.70 ± 4.35 mg P/L respectively, their removal efficiency was 87.63 ± 3.12 %, 99.61 ± 1.02 % and 85.38 ± 4.07 % at the HRT of 8.8 h. However, the phosphorus removal performance disappeared once the effluent pH dropped below 8.0. The random forest regression model revealed that effluent pH had the most significant impact on phosphorus removal performance. This finding was corroborated by a mathematical model that related the phosphate removal load to effluent pHs. The combination of batch test, Standard Measurements and Testing (SMT) and X-Ray Diffraction (XRD) method revealed that the phosphorus removal performance of SAD process came from the synergies of biological phosphorus removal (29.71 ± 3.21 %) and bio-induced phosphate precipitation (70.29 ± 3.21 %). The analysis of key functional genes coding for nitrogen, sulfur and phosphorus metabolism offered an explanation for their metabolic pathways especially the phosphorus removal pathway. The study would provide some new information for the development of SAD process.

Establishment and Validation of an Efficient Agrobacterium Tumefaciens-Mediated Transient Transformation System for Salix Psammophila

Salix psammophila, C. Wang & Chang Y. Yang, a desert-adapted shrub, is recognized for its exceptional drought tolerance and plays a vital role in ecosystem maintenance. However, research on S. psammophila has been limited due to the lack of an efficient and reliable genetic transformation method, including gene functional studies. The Agrobacterium-mediated transient overexpression assay is a rapid and powerful tool for analyzing gene function in plant vivo. In this study, tissue culture seedlings of S. psammophila were utilized as the recipient materials, and the plant expression vector pCAMBIA1301, containing the GUS reporter gene, was transferred into the seedlings via an Agrobacterium-mediated method. To enhance the efficiency of the system, the effects of secondary culture time, Agrobacterium concentration, infection time, and co-culture duration on the transient transformation efficiency of S. psammophila were explored. The optimal combination for the instantaneous transformation of S. psammophila tissue culture seedlings mediated by Agrobacterium was determined as follows: a secondary culture time of 30 d, a value of OD600 of 0.8, an infection time of 3 h, and a co-culture duration of 48 h. Subsequently, the effectiveness of the transformation system was validated using the S. psammophila drought response gene SpPP2C80. To further confirm the accuracy of the system, SpPP2C80-overexpressing Arabidopsis was constructed and drought resistance analysis was performed. The results were consistent with the transient overexpression of SpPP2C80 in S. psammophila tissue culture seedlings, indicating that this system can be effectively employed for studying gene function in S. psammophila. These findings provide essential information for investigating gene function in non-model plants and pave the way for advancements in molecular biology research in S. psammophila.

Comprehensive analysis of the PbrTBL gene family and functional analysis of PbrTBL43 under Botryosphaeria dothidea infection in Pyrus bretschneideri

The TBL (Trichome Birefringence-Like) gene family, which participates in the initiation of trichomes and the acetylation of xylan in a variety of plant species, plays a significant role in plant biology. However, there is little information regarding TBL family members in pear (Pyrus bretschneideri Rehd). Here, 65 PbrTBL genes were identified in Pyrus bretschneideri genome. Phylogenetic, gene structure, expression pattern and cis-element of promoter analysis were performed and compared. Expression profiling across different tissues and in response to Botryosphaeria dothidea (B. dothidea) infection highlighted the dynamic and coordinated response of PbrTBL genes, with PbrTBL43 showing significant upregulation. Subcellular localization of PbrTBL43 to the plasma membrane and the enhanced susceptibility to B. dothidea infection upon PbrTBL43 silencing further support its role in pathogen resistance. This study enhances our understanding of the PbrTBL gene family's multifaceted involvement in pear biology and provides a foundation for future research aimed at improving pear resistance to diseases and environmental challenges.

Novel serous effusion-related risk models and biomarkers for predicting prognosis in T-cell lymphoma patients.

T-cell lymphomas (TCLs) are a cluster of lymphoproliferative diseases with high heterogeneity, which lack accurate prognostic models and standard treatment regimen at present. Serous effusion (SE) is a relatively common manifestation and poses more challenges for risk stratification in TCLs. In this study, entire of 518 newly diagnosed TCLs patients were included. SE was found to be tightly correlated to clinical characteristics and prognosis in TCL patients, and SE volume (SEV) > 1000ml was identified as a potential prognostic factor. Novel AEBS risk model, including age > 60, ECOG PS > 1, β2-microglobulin (BMG) > 3.0mg/L and SEV > 1000ml, which exerted superior efficacy for risk stratification compared to the current risk systems in TCL patients with SE. Besides, multiple RNA-seq datasets were used for the identification and function analysis of SE-related genes (SERGs). TCL patients in different SERGs-associated subgroups exhibited discrepancy in the infiltration of immunocytes and the expression of immune checkpoints. SERGs signature, including HIF1A, FERMT2, NFATC1 and COL1A1, was established and demonstrated to have distinguishing capacity for predicting prognosis in TCL patients. Moreover, immunohistochemistry revealed that SE-related molecule HIF1A was reductively expressed and related to inferior prognosis in TCL patients, especially in SE group. Pan-cancer analysis found HIF1A expression was decreased in several tumors, and chemosensitivity analysis revealed that HIF1A was associated with sensitivity of several anti-tumor drugs, such as Sorafenib, Navitoclax, and Venetoclax. Our findings provide evidence for identifying high-risk population and facilitating individualized treatment in TCL patients with SE.

Identification of the EXORDIUM gene family and functional analysis of VaEXO2a during cold stress response in Vitis amurensis

Identification of the EXORDIUM gene family and functional analysis of VaEXO2a during cold stress response in Vitis amurensis

Identification of gastric cancer biomarkers through in-silico analysis of microarray based datasets

Gastric cancer is among the most prevalent cancers worldwide including in Pakistan. Late diagnosis of gastric cancer leads to reduced survival. The present study aimed to investigate biomarkers for early diagnosis and prognosis of gastric cancer. For this purpose, the ten microarray-based gene expression datasets (GSE54129, GSE79973, GSE161533, GSE103236, GSE33651, GSE19826, GSE118916, GSE112369, GSE13911, and GSE81948) were retrieved from GEO database and analyzed by GEO2R to identify differentially expressed genes. Datasets were arranged in subsets of different dataset combinations to identify common DEGs. The gene ontology and functional pathway enrichment analysis of common DEGs was performed by DAVID tool. Pan-cancer analysis was conducted by UALCAN database. Survival analysis of common DEGs was done by Kaplan-Meier plotter. A total of 71 common DEGs were identified in different combinations of datasets. Among them, only 5 DEGs namely ATP4B, ATP4A, CCKBR, KCNJ15, and KCNJ16 were detected to be common in all the datasets. The GO and pathway analysis represented that the identified DEGs are involved in gastric acid secretion and collecting duct acid secretion pathways. Further expression validation of these five genes using three additional datasets (GSE31811, GSE26899, and GSE26272) confirmed their differential expression in gastric cancer samples. The pan-cancer analysis also revealed aberrant expression of DEGs in various cancers. The survival analysis showed the association of these 5 DEGs with poor survival of gastric cancer patients. To conclude, this study revealed a panel of 5 genes, which can be employed as diagnostic and prognostic biomarkers of gastric cancer patients.

A Comprehensive Transcriptomic and Proteomics Analysis of Candidate Secretory Proteins in Rose Grain Aphid, Metopolophium dirhodum (Walker)

The Rose grain aphid, a notable agricultural pest, releases saliva while feeding. Yet, there is a need for a comprehensive understanding of the specific identity and role of secretory proteins released during probing and feeding. Therefore, a combined transcriptomic and proteomic approach was employed in this study to identify putative secretory proteins. The transcriptomic sequencing result led to the assembly of 18,030 unigenes out of 31,344 transcripts. Among these, 705 potential secretory proteins were predicted and functionally annotated against publicly accessible protein databases. Notably, a substantial proportion of secretory genes (71.5%, 69.08%, and 60.85%) were predicted to encode known proteins in Nr, Pfam, and Swiss-Prot databases, respectively. Conversely, 27.37% and 0.99% of gene transcripts were predicted to encode known proteins with unspecified functions in the Nr and Swiss-Prot databases, respectively. Meanwhile, the proteomic analysis result identified, 15 salivary proteins. Interestingly, most salivary proteins (i.e., 60% of the proteins) showed close similarity to A. craccivora, while 46.67% showed close similarity to A. glycines, M. sacchari and S. flava. However, to verify the expression of these secretory genes and characterize the biological function of salivary proteins further investigation should be geared towards gene expression and functional analysis.

A machine learning model revealed that exosome small RNAs may participate in the development of breast cancer through the chemokine signaling pathway

BackgroundExosome small RNAs are believed to be involved in the pathogenesis of cancer, but their role in breast cancer is still unclear. This study utilized machine learning models to screen for key exosome small RNAs and analyzed and validated them.MethodPeripheral blood samples from breast cancer screening positive and negative people were used for small RNA sequencing of plasma exosomes. The differences in the expression of small RNAs between the two groups were compared. We used machine learning algorithms to analyze small RNAs with significant differences between the two groups, fit the model through training sets, and optimize the model through testing sets. We recruited new research subjects as validation samples and used PCR-based quantitative detection to validate the key small RNAs screened by the machine learning model. Finally, target gene prediction and functional enrichment analysis were performed on these key RNAs.ResultsThe machine learning model incorporates six small RNAs: piR-36,340, piR-33,161, miR-484, miR-548ah-5p, miR-4282, and miR-6853-3p. The area under the ROC curve (AUC) of the machine learning model in the training set was 0.985 (95% CI = 0.948-1), while the AUC in the test set was 0.972 (95% CI = 0.882–0.995). RT-qPCR was used to detect the expression levels of these key small RNAs in the validation samples, and the results revealed that their expression levels were significantly different between the two groups (P < 0.05). Through target gene prediction and functional enrichment analysis, it was found that the functions of the target genes were enriched mainly in the chemokine signaling pathway.ConclusionThe combination of six plasma exosome small RNAs has good prognostic value for women with positive breast cancer by imaging screening. The chemokine signaling pathway may be involved in the early stage of breast cancer. It is worth further exploring whether small RNAs mediate chemokine signaling pathways in the pathogenesis of breast cancer through the delivery of exosomes.

Comprehensive Genome-Wide Analysis of the Receptor-like Protein Gene Family and Functional Analysis of PeRLP8 Associated with Crown Rot Resistance in Passiflora edulis

Comprehensive Genome-Wide Analysis of the Receptor-like Protein Gene Family and Functional Analysis of PeRLP8 Associated with Crown Rot Resistance in Passiflora edulis

Identification and expression analysis of the SPL gene family during flower bud differentiation in Rhododendron molle.

The family of SQUAMOSA promoter binding protein-like (SPL) transcription factors is essential for regulating plant growth and development. While this SPL gene functional research has been limited in Rhododendron molle (R. molle). To preliminarily explore the regulatory mechanism of the SPL gene in flower bud development of R. molle. In this study, for R. molle, the flower bud differentiation period was determined by observing the morphological anatomy of the flower bud. The SPL gene family members were identified based on the R. molle genome, Additionally, the expressions of RmSPL genes at five flower bud differentiation stages were analyzed via Quantitative reverse transcription PCR (RT-qPCR). We first characterized 20 SPL family members in the reference genome of R. molle. The phylogenetic analysis of plant SPL proteins separated them into eight subfamilies (G1-G8) according to conserved gene structures and protein motifs. Cis-elements of promoter region analysis showed that RmSPL genes were regulated by light, phytohormones, stress response, and plant growth and development and may play a critical role in the photoresponse, abasic acid, anaerobic induction, and meristematic expression. Gene expression analysis showed that 18 RmSPL genes were differentially expressed in different developing flower buds. In particular, RmSPL1/7/8/12/13 exhibited significantly different expressions, suggesting that they were likely essential genes for regulating the differentiation of flower buds. In conclusion, our analysis of RmSPL genes provides a theoretical basis and reference for future functional analysis of RmSPL genes in the flower bud differentiation of R. molle.

Comprehensive analysis identifies endocrine fibroblast growth factors as promising prognostic markers for colorectal carcinoma

Endocrine fibroblast growth factors (eFGFs) play essential roles in cellular signaling processes, including development and differentiation, and are implicated in various cancers. However, their precise involvement in colon neoplasia and colon adenocarcinoma (COAD) remains incompletely understood. Here, we conducted a comprehensive investigation utilizing multiple databases to explore the multifaceted characteristics of eFGFs. Through integrated analyses of diverse databases, including TIMER2.0, UALCAN, OncoDB, cBioPortal, LinkedOmics, STRING, htfTarget, mirTarBase, circBank, and DGIdb, we explored eFGFs’ gene expression, DNA methylation, prognostic significance, genetic alterations, gene regulatory networks, functional analysis, and drug interactions in COAD patients. Our findings revealed elevated expression levels of eFGFs in COAD, with aberrant gene expression potentially linked to promoter methylation. Importantly, hypermethylation of FGF21 and FGF23 and downregulation of FGF23 correlated with poor survival outcomes in COAD patients. Functional analyses highlighted the involvement of eFGF genes in Ras signaling, PI3K-Akt signaling, and cancer pathways. Furthermore, we validated our findings through a cross-sectional study by quantitative real-time polymerase chain reaction (qRT-PCR), confirming significant overexpression of FGF21 in colon polyps compared to normal mucosa. Additionally, we observed elevated RNA expression of FGF21 and FGF23 in adenomatous polyps compared to hyperplastic polyps. This study sheds new light on the critical roles of eFGFs in COAD tumorigenesis and underscores their potential as promising prognostic markers for COAD, as well as discriminative markers for distinguishing high-risk from low-risk polyps. These findings provide valuable insights into the complex molecular mechanisms underlying colorectal neoplasia and offer potential avenues for targeted therapeutic strategies.

Whole-Genome Identification of the Flax Fatty Acid Desaturase Gene Family and Functional Analysis of the LuFAD2.1 Gene Under Cold Stress Conditions.

Fatty acid desaturase (FAD) is essential for plant growth and development and plant defence response. Although flax (Linum usitatissimum L.) is an important oil and fibre crop, but its FAD gene remains understudied. This study identified 43 LuFAD genes in the flax genome. The phylogenetic analysis divided the FAD genes into seven subfamilies. LuFAD is unevenly distributed on 15 chromosomes, and fragment duplication is the only driving force for the amplification of the LuFAD gene family. In the LuFAD gene promoter region, most elements respond to plant hormones (MeJA, ABA) and abiotic stresses (anaerobic and low temperature). The expression pattern analysis showed that the temporal and spatial expression patterns of all LuFAD genes in different tissues and the response patterns to abiotic stresses (heat and salt) were identified. Subcellular localisation showed that all LuFAD2-GFP were expressed in the endoplasmic reticulum membrane. RT-qPCR analysis revealed that LuFAD2 was significantly upregulated under cold, salt and drought stress, and its overexpression in Arabidopsis thaliana enhanced cold tolerance genes and reduced ROS accumulation. This study offers key insights into the FAD gene family's role in flax development and stress adaptation.

Transcriptomic and Metabolomics Joint Analyses Reveal the Influence of Gene and Metabolite Expression in Blood on the Lactation Performance of Dual-Purpose Cattle (Bos taurus).

Blood is an important component for maintaining animal lives and synthesizing sugars, lipids, and proteins in organs. Revealing the relationship between genes and metabolite expression and milk somatic cell count (SCC), milk fat percentage, milk protein percentage, and lactose percentage in blood is helpful for understanding the molecular regulation mechanism of milk formation. Therefore, we separated the buffy coat and plasma from the blood of Xinjiang Brown cattle (XJBC) and Chinese Simmental cattle (CSC), which exhibit high and low SCC/milk fat percentage/milk protein percentage/lactose percentages, respectively. The expression of genes in blood and the metabolites in plasma was detected via RNA-Seq and LC-MS/MS, respectively. Based on the weighted gene coexpression network analysis (WGCNA) and functional enrichment analysis of differentially expressed genes (DEGs), we further found that the expression of genes in the blood mainly affected the SCC and milk fat percentage. Immune or inflammatory-response-related pathways were involved in the regulation of SCC, milk fat percentage, milk protein percentage, and lactose percentage. The joint analysis of the metabolome and transcriptome further indicated that, in blood, the metabolism pathways of purine, glutathione, glycerophospholipid, glycine, arginine, and proline are also associated with SCC, while lipid metabolism and amino-acid-related metabolism pathways are associated with milk fat percentage and milk protein percentage, respectively. Finally, related SCC, milk fat percentage, and milk protein percentage DEGs and DEMs were mainly identified in the blood.

Gene Co-Expression Network Analysis Associated with Endometrial Cancer Tumorigenesis and Survival Outcomes.

Endometrial cancer (EC) presents a substantial health challenge, with increasing incidence and mortality rates. Despite advances in diagnosis and treatment, understanding the molecular underpinnings of EC progression remains unknown. In this study, we conducted a comprehensive investigation utilizing The Cancer Genome Atlas (TCGA-UCEC n = 588) data to analyze gene co-expression patterns, elucidate biological process pathways, and identify potential prognostic and diagnostic biomarkers for EC, using weighted gene co-expression network analysis (WGCNA), differential gene expression, survival analysis, and functional analysis, respectively. We determined that the Green module (M5) was significantly correlated with patient survival. Functional analysis of the genes in module M5 indicates involvement in cell cycle regulation, mitotic spindle assembly, and intercellular signaling. TPX2, BUB1, and ESPL1 were among the top differentially expressed genes in the Green module, suggesting their involvement in critical pathways that contribute to disease progression and patient survival outcomes. The biological and clinical assessments of our findings provide an understanding of the molecular landscape of EC and identified several potential prognostic markers for patient risk stratification and treatment selection.

Developing and applying a virus-induced gene silencing system for functional genomics in walnut (Juglans regia L.) mediated by tobacco rattle virus

Walnut (Juglans regia L.) is a high-value tree species planted worldwide, but the incomplete less developed genetic transformation system limits its gene function analysis. In this study, virus-induced gene silencing (VIGS) mediated by tobacco rattle virus (TRV) technology was applied to walnut seedlings to degrade the transcript of target gene. Different infiltration methods were used to explore the effects of infection mode, Agrobacterium cell density, silencing fragment length, and walnut cultivars. The results showed that spray infiltration of seedlings resulted in a photobleaching phenotype of the whole plant. Leaf injection was a more effective way of infiltration. The optimal combination was the Agrobacterium cell density at OD600 = 1.1 with target fragment = 255 bp for the treatment of walnut early-fruiting cultivar ’Xiangling.’ This combination can reach up to 48 % of gene silencing efficiency. Based on this optimized VIGS system, silencing a walnut chlorophyll synthesis-related gene, JrPOR (Protochlorophyllide reductase), to further validate the system’s effect. The results showed that the expression of JrPOR was significantly repressed, and the chlorophyll level of the silenced plants was significantly decreased compared with the control. The above results indicate that the walnut TRV-VIGS system has been successfully established and can be used for reverse genetic studies, providing an option for verifying gene function in walnut.

Genome editing of an oxalyl-CoA synthetase gene in Lathyrus sativus reveals its role in oxalate metabolism.

Established an Agrobacterium-mediated hairy root transformation system for gene function analysis in Lathyrus sativus. Arabidopsis mutant complementation and genome editing in Lathyrus confirmed role of LsOCS in the oxalate metabolism. Grass pea (Lathyrus sativus) is a resilient legume cultivated for its protein-rich seeds and fodder. However, the presence of a naturally occurring neurotoxin, β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which causes neurolathyrism, limits its extensive cultivation. This paper reports the in-planta characterization of oxalyl-CoA synthetase (OCS), an enzyme involved in oxalate metabolism and important in the oxalylating step leading to β-ODAP production in Lathyrus. For this, we used complementation experiments in an Arabidopsis OCS mutant. The LsOCS-complemented lines showed oxalate content similar to wild-type levels, and the analysis of seeds by field emission scanning electron microscope (FESEM) showed that the LsOCS-complemented lines were rescued from seed-coat defects found in the mutant seeds. We used genome editing of LsOCS in Lathyrus hairy roots to further characterize LsOCS function. The mutations in LsOCS resulted in the accumulation of oxalate in the hairy roots of Lathyrus, as observed in Arabidopsis mutants, but did not affect the ODAP levels. The hairy root genome editing system could serve as a rapid tool for functional studies of Lathyrus genes and optimizing the agronomic traits.

CNSC-48. DIFFERENTIAL GENE EXPRESSION UNDERLYING EPILEPTOGENICITY IN PATIENTS WITH GLIOMAS

Abstract BACKGROUND Seizures are a common sequela for patients suffering from gliomas. Molecular properties are known to influence the initiation of seizures that may influence tumor growth. Different levels of gene expression associated with seizures related to gliomas remain unclear. We analyzed RNA sequencing of gliomas to further probe these differences. METHODS Total RNA sequencing was obtained from The Cancer Genome Atlas - Lower Grade Glioma project, comprised of 2021 WHO classification low grade gliomas, including IDH-mutant and IDH-wild type, to distinguish differential expression in patients who did and did not experience seizures. Utilizing QIAGEN Ingenuity Pathways Analysis, we identified canonical and functional pathways to further characterize differential expression. RESULTS Of 289 patients with gliomas, 83 (28.7%) had available information regarding seizure occurrence prior to intervention and other pertinent variables of interest. Of these, 50 (60.2%) were allocated to the seizure group. When comparing the level of RNA expression from these tumors between the seizure and non-seizure groups, 52 genes that were significantly differentially regulated were identified. We found canonical pathways that were altered, most significantly RhoGDI and Semaphorin Neuronal Repulsive signaling. Functional gene analysis revealed tumors that promoted seizures had significantly increased functional gene sets involving neuronal differentiation and synaptogenesis. CONCLUSIONS In the setting of gliomas, differences in tumor gene expression exist between individuals with and without seizures, despite similarities in patient demographics and other tumor characteristics. There are significant differences in gene expression associated with neuron development and synaptogenesis, ultimately suggesting a mechanistic role of a tumor-neuron synapse in seizure initiation.