A newly developed free software tool set for averaging electroencephalogram implemented in the Perl programming language

Phylogenetic placement of the monotypic Baolia (Amaranthaceae s.l.) based on morphological and molecular evidence

BACKGROUND

Baolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences.

RESULTS

We sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade and sister to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat.

CONCLUSIONS

Comparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia).

Prognostic Model and Tumor Immune Microenvironment Analysis of Complement-Related Genes in Gastric Cancer

Introduction

The complement system is integral to the innate and adaptive immune response, helping antibodies eliminate pathogens. However, the potential role of complement and its modulators in the tumor microenvironment (TME) of gastric cancer (GC) remains unclear.

Methods

This study assessed the expression, frequency of somatic mutations, and copy number variations of complement family genes in GC derived from The Cancer Genome Atlas (TCGA). Lasso and Cox regression analyses were conducted to develop a prognostic model based on the complement genes family, with the training and validation sets taken from the TCGA-GC cohort (n=371) and the International Gene Expression Omnibus (GEO) cohort (n=433), correspondingly. The nomogram assessment model was used to predict patient outcomes. Additionally, the link between immune checkpoints, immune cells, and the prognostic model was investigated.

Results

In contrast to patients at low risk, those at high risk had a less favorable outcome. The prognostic model-derived risk score was shown to serve as a prognostic marker of GC independently, as per the multivariate Cox analysis. Nomogram assessment showed that the model had high reliability for predicting the survival of patients with GC in the 1, 3, 5 years. Additionally, the risk score was positively linked to the expression of immune checkpoints, notably CTLA4, LAG3, PDCD1, and CD274, according to an analysis of immune processes. The core gene C5aR1 in the prognostic model was found to be upregulated in GC tissues in contrast to adjoining normal tissues, and patients with elevated expressed levels of C5aR1 had lower 10-year overall survival (OS) rates.

Conclusion

Our work reveals that complement genes are associated with the diversity and complexity of TME. The complement prognosis model help improves our understanding of TME infiltration characteristics and makes immunotherapeutic strategies more effective.

Exploring the Correlation Between GPR176, a Potential Target Gene of Gastric Cancer, and Immune Cell Infiltration

Introduction

GPR176, an orphan G protein-coupled receptor (GPCR), is essential for the progression of gastrointestinal cancers. However, it is still unclear how GPR176 affects tumor immunity and patient prognosis in gastric cancer (GC).

Methods

The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were searched in this investigation to assess the expression patterns of GPR176 in GC tissues and normal gastric mucosa. The findings were further verified using immunohistochemical tests and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). The Kaplan-Meier method, univariate logistic regression, and Cox regression were then used to investigate the relationship between GPR176 and clinical traits. Additionally, the potential correlation between GPR176, immune checkpoint genes, and immune cell infiltration levels was investigated.

Results

As per the research findings, GC tissues had higher levels of GPR176 than normal tissues. Additionally, individuals with high expression of GPR176 had a worse 10-year overall survival (OS), in contrast with those having a low expression of GPR176 (p < 0.001). The OS of GC can be predicted using a validated nomogram model. The expression of GPR176 demonstrated a negative correlation with CD8+ T cells. When compared to the low-expression group of GPR176, Tumor Immune Dysfunction and Exclusion (TIDE) analysis demonstrated that the high-expression group had a considerably higher risk of immune evasion. A remarkable difference (variation) was observed in the levels of GPR176 expression across both groups, ie, low and high-risk groups, as determined by the immune phenomenon scores (IPS) immunotherapy assessment.

Conclusion

By examining GPR176 from various biological perspectives, it was determined that GPR176 can act as a predictive biomarker for poor patient prognosis in GC. Additionally, it was observed that GPR176 is capable of suppressing the proliferation of CD8+ T cells and facilitating immune evasion.

Identify an innovative ferroptosis-related gene in hepatocellular carcinoma

Background

SLC1A5 has been demonstrated to be associated with the progression of other tumors; however, studies are lacking in hepatocellular carcinoma (HCC). Here, we identify SLC1A5, as a novel ferroptosis factor, for HCC patients.

Methods

The core biomarkers were identified by univariate and multivariate Cox regression analysis, and the genes present in liver cancer were validated using the public database. Then, gene set enrichment analysis (GSEA) was performed to explore the underlying molecular mechanisms. In addition, we explore the relationship between SLC1A5 and clinical factors. Finally, we determine the effect of SLC1A5 on HCC cells using real‐time PCR, cell scratch analysis, transwell analysis, and CCK8 analysis in molecular biology experiments.

Results

Cox regression model shows that SLC1A5 was an independent risk factor for HCC patients. GSEA results indicated high expression of SLC1A5 related to the fatty acid metabolism pathway. Clinical correlation analysis demonstrates that alpha‐fetoprotein (AFP) expression was positively correlated with SLC1A5 (p = 8e−05), and the higher tumor stage means the higher expression of SLC1A5 (p = .02). In addition, SLC1A5 expression was also positively correlated with vascular infiltration of HCC (p = .04). Furthermore, the SLC1A5 function deficiency experiment explored its underlying impact on the biological function of HCC. qPCR, also called quantitative polymerase chain reaction, confirmed that SLC1A5 was highly expressed in liver cancer when compared with normal tissues. Studies have also shown that downregulation of SLC1A5 can inhibit wound healing, invasion, and proliferation of HCC cells.

Conclusion

In conclusion, ferroptosis factor SLC1A5 is a new therapeutic target for hepatocellular carcinoma.

Event-related potentials using the auditory novel paradigm in patients with myotonic dystrophy

Many neuropsychological disorders, especially attentional abnormality, are present in patients with myotonic dystrophy type 1 (DM1), but the underlying mechanisms remain unclear. This study aimed to evaluate attention function by auditory event-related potential (ERP) P3a (novelty paradigm) in DM1 patients. A total of 10 young DM1 patients (mean age 30.4 years) and 14 age-matched normal controls participated in this study. ERPs were recorded using an auditory novel paradigm, consisting of three types of stimuli, i.e., standard sound (70%), target sound (20%), and various novel sounds (10%), and participants pressed buttons to the target sounds. ERP components P3b after the target stimuli and P3a following the novel stimuli were analyzed. Correlations of neuropsychological evaluations with the amplitudes and latencies of P3b and P3a were analyzed in DM1 patients. We found that P3a latency was significantly delayed in patients with DM1 compared with normal controls, although the latency and amplitude of P3b in DM1 patients were comparable with those in normal controls. The achievement rates of both the Symbol Digit Modality Test and the Paced Auditory Serial Addition Test were significantly correlated with P3a amplitude, as well as P3b amplitude. These results suggest that ERPs, including P3a and P3b, provide important insights into the physiological basis of neuropsychological abnormalities in patients with DM1, especially from the viewpoint of the frontal lobe and attention function.