Diagnostic Molecular Markers Research Articles

Retraction Note: Molecular mechanism and diagnostic marker investigation of endoplasmic reticulum stress on periodontitis

Retraction Note: Molecular mechanism and diagnostic marker investigation of endoplasmic reticulum stress on periodontitis

Exploring IRGs as a Biomarker of Pulmonary Hypertension Using Multiple Machine Learning Algorithms.

Pulmonary arterial hypertension (PAH) is a severe disease with poor prognosis and high mortality, lacking simple and sensitive diagnostic biomarkers in clinical practice. This study aims to identify novel diagnostic biomarkers for PAH using genomics research. We conducted a comprehensive analysis of a large transcriptome dataset, including PAH and inflammatory response genes (IRGs), integrated with 113 machine learning models to assess diagnostic potential. We developed a clinical diagnostic model based on hub genes, evaluating their effectiveness through calibration curves, clinical decision curves, and ROC curves. An animal model of PAH was also established to validate hub gene expression patterns. Among the 113 machine learning algorithms, the Lasso + LDA model achieved the highest AUC of 0.741. Differential expression profiles of hub genes CTGF, DDR2, FGFR2, MYH10, and YAP1 were observed between the PAH and normal control groups. A diagnostic model utilizing these hub genes was developed, showing high accuracy with an AUC of 0.87. MYH10 demonstrated the most favorable diagnostic performance with an AUC of 0.8. Animal experiments confirmed the differential expression of CTGF, DDR2, FGFR2, MYH10, and YAP1 between the PAH and control groups (p < 0.05); Conclusions: We successfully established a diagnostic model for PAH using IRGs, demonstrating excellent diagnostic performance. CTGF, DDR2, FGFR2, MYH10, and YAP1 may serve as novel molecular diagnostic markers for PAH.

A prospective diagnostic model for breast cancer utilizing machine learning to examine the molecular immune infiltrate in HSPB6

BackgroundBreast cancer is a significant public health issue worldwide, being the most prevalent cancer among women and a leading cause of death related to this disease. The molecular processes that propel breast cancer progression are not fully elucidated, highlighting the intricate nature of the underlying biology and its crucial impact on global health. The objective of this research was to perform bioinformatics analyses on breast cancer-related datasets to gain a comprehensive understanding of the molecular mechanisms at play and to identify key genes associated with the disease.MethodsThe toolkit analyses involve techniques such as differential gene expression analysis, Gene Set Enrichment Analysis (GSEA), Weighted Co-Expression Network Analysis (WGCNA), and Machine Learning algorithms. Furthermore, in vitro cell experiments have demonstrated the impact of HSPB6 on cell migration, proliferation, and apoptosis.ResultsThe study identified multiple genes that displayed differential expression in breast cancer, notably FHL1 and HSPB6. A machine learning model was developed in this study and specifically trained for breast cancer diagnosis using these genes, achieving high precision. Furthermore, analysis of immune cell infiltration revealed an enrichment of Tregs and M2 macrophages in the treated group, showcasing its significant impact on the tumor’s immunological context. A temporal analysis of breast cancer cells using single-cell RNA sequencing provided insights into cellular developmental trajectories and highlighted changes in expression patterns across key genes during disease progression. The upregulation of HSPB6 in MCF7 cells significantly inhibited both cell migration and proliferation abilities, suggesting that promoting HSPB6 expression could induce ferroptosis in breast cancer cells.ConclusionOur findings have identified compelling molecular targets and distinctive diagnostic markers for the clinical management of breast cancer. This data will serve as crucial guidance for further research in the field.

Landscape of the immune infiltration and identification of molecular diagnostic markers associated with immune cells in patients with kidney transplantation

Rejection seriously affects the success of kidney transplantations. However, the molecular mechanisms underlying this rejection remain unclear. The GSE21374 and GSE36059 datasets were downloaded from the Gene Expression Omnibus (GEO) database. Next, the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was used to infer the proportions of 22 immune cells. Moreover, infiltrating immune cell-related genes were identified using weighted gene co-expression network analysis (WGCNA), and enrichment analysis was conducted to observe their biological functions. Extreme Gradient Boosting (XGBoost) and Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression algorithms were used to screen hub genes. Quantitative real-time PCR was conducted to verify the number of immune cells and hub gene expression levels. The rejection and non-rejection groups showed significantly different distributions (P < 0.05) of eight immune cells (B cell memory, Plasma cells, mast cells, follicular helper T cells, T CD8 cells, Macrophages M1, T Cells CD4 memory activated, and gamma delta T cells). Subsequently, CD8A, CRTAM, GBP2, WARS, and VAMP5 were screened as hub genes using the XGBoost and LASSO algorithms and could be used as diagnostic biomarkers. Finally, differential analysis and quantitative real-time PCR suggested that CD8A, CRTAM, GBP2, WARS, and VAMP5 were upregulated in rejection samples compared to non-rejection samples. The present study identified five key infiltrating immune cell-related genes (CD8A, CRTAM, GBP2,WARS, and VAMP5) involved in kidney transplant rejection, which may explain the molecular mechanism of rejection in kidney transplantation development.

The diagnostic challenge of a Papillary lesion of the breast in a patient with Peutz-Jeghers syndrome

Abstract Introduction/Objective Peutz-Jeghers syndrome (PJS) is an autosomal dominant disorder with elevated risk of various neoplasms, including breast cancer. The incidence of cancer among PJS patients is estimated to be 15-fold higher than the general population. The spectrum of breast lesions in PJS varies from benign papillomas to invasive carcinomas, presenting significant diagnostic complexities. The case presented here revolves around a unique papillary lesion in a PJS patient. Methods/Case Report A 40-year-old African American female, with PJS presented with a palpable abnormality in the right subareolar region with sanguineous nipple discharge. Multiple prior biopsies revealed intraductal papillomas with no atypia. Imaging showed a 7.0 cm complex solid and cystic subareolar mass, which had increased in size by 42% within a short period. Given the rapid increase in size, malignant transformation was clinically suspected. The patient underwent bilateral mastectomy. Macroscopic examination showed a 9.0 cm tan firm subareolar nodule with solid and cystic components. Histopathology revealed areas consistent with intraductal papilloma, however, additional complexities, including epithelial and myoepithelial proliferations with mild cytologic atypia, squamous, apocrine, and sebaceous metaplasia made the diagnosis challenging. No necrosis or increased mitotic activity was identified. Immunostaining for CK5/6 and p63 highlighted the myoepithelial layer, while estrogen receptor demonstrated heterogeneous positive staining. This picture raised suspicion of adenomyoepithelioma, but there was a significant overlap with intraductal papilloma. A final diagnosis of intraductal papillary neoplasm with epithelial and focal myoepithelial atypia was rendered. Results (if a Case Study enter NA) NA Conclusion This case presented a complex diagnostic dilemma. The rapid growth of the lesion, coupled with cytological atypia, raised significant concern necessitating precise differentiation between adenomyoepithelioma and intraductal papilloma. Further research is imperative to explore the pathophysiology of breast lesions in PJS, their impact on surveillance, management, potential for malignancy, and prognosis. Investigating additional diagnostic modalities and molecular markers to aid in accurate differentiation between benign and malignant papillary neoplasms in PJS patients warrants consideration.

Metabolomic profile of cerebrospinal fluid from patients with diffuse gliomas.

Diffuse gliomas are among the most common brain tumors in adults and are associated with a dismal prognosis, especially in patients with glioblastoma. To date, tumor tissue acquisition is mandatory for conclusive diagnosis and therapeutic decision-making. In this study, we aimed to identify possible diagnostic and prognostic biomarkers in cerebrospinal fluid (CSF) and blood. During glioma surgery at our institution, CSF and blood samples were collected from patients. Subsequently, targeted metabolomics analysis was used to detect and quantify circulating metabolites. The metabolome profiles of glioma patients were compared with those of patients in a control group who had undergone neurosurgery for other entities, such as nonglial tumors or hydrocephalus, and were correlated with established glioma diagnostic molecular markers. In this study, a total of 30 glioma patients were included, along with a control group of 21 patients without glioma. Serum metabolomic analysis did not detect any significant differences between the groups, whereas CSF-metabolome analysis revealed increased levels of six metabolites in glioma patients. Among these, the most pronounced differences were found for the biogenic amine putrescine (p = 0.00005). p-Cresol sulfate was identified as a potential CSF marker for determining isocitrate dehydrogenase (IDH) status in glioma patients (p = 0.0037). CSF-metabolome profiling, unlike blood profiling, shows promise as a diagnostic tool for glioma patients with the potential to assign molecular subtypes. The next step will involve a larger multicenter study to validate these findings, with the ultimate objective of integrating CSF metabolomics analysis into clinical practice.

The role of IQCB1 in liver cancer: a bioinformatics analysis.

Liver hepatocellular carcinoma (LIHC) is a prevalent malignancy globally, exhibiting substantial incidence and mortality rates. Early diagnosis and prevention of metastasis are crucial for the benefit of patients with liver cancer. The present study aimed to elucidate the involvement of IQCB1 in liver cancer through the utilization of bioinformatics. The samples utilized in this study were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Initially, the TCGA-LIHC dataset was employed to examine the expression of IQCB1, and its validation was performed on the GSE25097 dataset. Subsequently, Kaplan-Meier (KM) analysis was conducted to evaluate the prognostic significance of IQCB1 in LIHC, and its correlation with clinical pathological features was also investigated. Furthermore, a protein-protein interaction (PPI) network consisting of 20 proteins associated with IQCB1 was constructed using data from the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out. A risk model was formulated to assess the prognostic significance and its prognostic value was compared to that of IQCB1 in isolation. Furthermore, an examination was conducted to explore the correlation between IQCB1 and immune infiltration, along with the involvement of immunological checkpoints. A drug sensitivity assessment of IQCB1 was performed using the Genomics of Drug Sensitivity in Cancer (GDSC) database. Additionally, the Tumor Immune Single-cell Hub (TISCH) database was utilized to investigate the association between IQCB1 and the tumor microenvironment (TME). The expression of IQCB1 was observed to be significantly elevated in tumor samples. Furthermore, patients with high expression levels of IQCB1 demonstrated a poorer prognosis. Additionally, IQCB1 exhibited significant correlations with MKI67, hepatitis B virus (HBV), hepatitis C virus (HCV), and alpha-fetoprotein (AFP). GO and KEGG analyses revealed enrichment of multiple signaling pathways. Subsequently, an investigation was conducted to examine the association between IQCB1 and the activity of ten signaling pathways related to tumor development. A positive correlation was observed between IQCB1 expression and T-helper 2 (Th2) cells, whereas a negative correlation was observed between IQCB1 expression and Th17 cells. Furthermore, a positive association was found between IQCB1 and immune checkpoints, particularly with CD276. Analysis of single-cell data from the TISCH database revealed widespread expression of IQCB1 in the TME. Additionally, screening revealed that among 12 drugs related to IQCB1, a subset of 10 drugs demonstrated negative correlations, whereas two drugs exhibited positive correlations. IQCB1 has the potential to function as a diagnostic and prognostic molecular marker, and its association with immune infiltration and checkpoint mechanisms has been observed.

Progress of Exosomal LncRNAs in Pancreatic Cancer.

Pancreatic cancer is a prevalent malignant tumor with rising medication resistance and mortality. Due to a dearth of specific and trustworthy biomarkers and therapeutic targets, pancreatic cancer early detection and treatment are still not at their best. Exosomal LncRNAs have been found to be plentiful and persistent within exosomes, and they are capable of functioning whether the exosomes are traveling to close or distant cells. Furthermore, increasing evidence suggests that exosomal LncRNA, identified as an oncogene or tumor suppressor-control the growth, metastasis, and susceptibility of pancreatic cancer to chemotherapy and radiation therapy. Promising prospects for both antitumor targets and diagnostic biomarkers are exosomal LncRNAs. The primary features of exosomal LncRNAs, their biological roles in the onset and progression of pancreatic cancer, and their potential as therapeutic targets and diagnostic molecular markers are outlined in this review.

The Influence of miR-3149 on the Malignancy Progression of Gastric Cancer by Negatively Regulating CEACAM5

Background: There are some reports indicating that carcinoembryonic antigen associated cell adhesion molecule 5 (CEACAM5) can act as a diagnostic indicator or molecular marker for GC, but its upstream regulatory pathway still needs to be explored. microRNAs (miRNAs) regulate gene expression at the translation level and fulfil a crucial role in GC physiologyin, whether miR-3149 in family members can affect GC progression by regulating CEACAM5 is still unclear. Methods: miR-3149 and CEACAM5 expressions in GC tissues and cells (N87, AGS, and HGC-27) were observed by RT-qPCR or Western blot. Intervened the miR-3149 and CEACAM5 expression in GC cells, CCK8, Wound healing, Transwell and flow cytometry assays evaluated cell activity and function separately, while detecting related proteins. Predicted the target of miR-3149 and the expression of CEACAM5 in tumor tissue through bioinformatics analysis and evaluated the correlation between both using Spearman analysis. Verified the targeting relationship between the two through the Luciferase reporter assay. Conducted another rescue experiment on CEACAM5 overexpression to further verify this relationship. Results: In GC tissues and cells, miR-3149 and CEACAM5 expression levels were respectively down-regulated and up-regulated. Transfection of miR-3149 mimics or inhibitors respectively reduced or increased GC cell apoptosis and inhibited or encouraged cell proliferation, migration and invasion, which were shown to be enhanced or inhibited respectively by transfection of OE-CEACAM5/Si-CEACAM5, while their apoptosis rate decreased or increased. miR-3149 could target regulating CEACAM5, and showed an inverse correlation with the expression of CEACAM5. The impacts of miR-3149 mimics on the malignancy progression of GC could be partially reversed by OE-CEACAM5. Conclusion: The results indicate that miR-3149 can downregulate the expression of CEACAM5 to inhibit the malignancy progression, as a GC suppressor,which identify a new miRNA mediated tumor suppressor mechanism in GC.

Peracetic acid treatment of squid eggs infected with parasitic copepod (Ikanecator primus gen. et sp. nov.)

Having been successfully bred in semi-intensive and intensive aquaculture systems, oval squids of the Sepioteuthis lessoniana species complex are emerging as promising candidates for research and industry. Nevertheless, information about pathogens and diseases that may affect squid aquaculture remains sparse. In this study, we identify new parasitic copepod species that causes squid mortality and decreases squid hatching rates, and we also offer a solution to eliminate the pathogen during incubation of squid eggs. The newly discovered copepod Ikanecator primus gen. et sp. nov. was identified on oval squid eggs for the first time using both morphological and molecular diagnostic markers. In the genomes of the copepod and associated microbiome, we identified multiple genes for enzymes involved in cephalopod eggshell degradation in genomes of the copepod and associated microbiome. Furthermore, we conducted experiments to assess efficacy of peracetic acid in inhibiting the I. primus gen. et sp. nov. both in vitro and in vivo using immersion treatment. We established that a 2-min exposure to a concentration of 250 μl/L of peracetic acid containing product (PAA-product; 35 mg/L PAA and 15 mg/L H2O2) inhibited the development of nauplii in vitro. All parasites exposed to a concentration of 500 μl/L of PAA-product (70 mg/L PAA and 30 mg/L H2O2) were eliminated within two minutes. On top of this, the immersion treatment with 500 μl/L of PAA-product (70 mg/L PAA and 30 mg/L H2O2) improved survival of squid embryos and increased size of squid hatchlings compared with control and the immersion treatment with 125 μl/L of PAA-product (17.5 mg/L PAA and 7.5 mg/L H2O2) and the immersion treatment with 250 μl/L of PAA-product (35 mg/L PAA and 15 mg/L H2O2). These findings suggest that PAA holds a great potential as inhibitor and controller of parasitic copepod infections and for overall health management in cephalopod culture.

Multiplex PCR for Early Generation Identification of Tomato Segregants Carrying Ty-2, Ty-3 and Ph-3 Resistance Alleles Against Leaf Curl and Late Blight Diseases.

Deployment of different natural disease resistance alleles is the most sustainable and eco-friendly way for multiple disease management in tomato. Diagnostic molecular markers are indispensible in this effort as they offer early generation identification of resistance alleles in an environment-independent manner. Moreover, optimized multiplex polymerase chain reaction (PCR) for detecting different disease resistance alleles in a single reaction can speed-up the selection process with cost and labour-effectiveness. Here we report the optimized multiplex detection and stacking of leaf curl disease resistance alleles Ty-2 and Ty-3 along with late blight disease resistance allele Ph-3 in tomato genotypes and F2 segregants. The triplex assay could be replaced by a duplex assay (for Ty-2 and Ty-3 resistance alleles) followed by analysis at Ph-3 locus to achieve further cost-effectiveness. We identified two plants in F2 populations derived from the Arka Samrat (F1) x Kashi Chayan combination to carry the Ty-2, Ty-3 and Ph-3 resistance alleles in homozygous condition. Early generation genotyping also allowed us to identify a few morphologically better segregants, where further marker assisted selection (MAS) should identify superior multiple disease resistant lines. Thus we advocate the utility of multiplex PCR in MAS to address multiple disease resistance breeding in tomato.

Nasopharyngeal carcinoma cell screening based on nuclear targeting Surface-Enhanced Raman Scattering (SERS) detection

BackgroundNasopharyngeal carcinoma (NPC) is a malignant epithelial carcinoma arising from the nasopharyngeal mucosal lining. Diagnosis of NPC at early stage can improve the outcome of patients and facilitate reduction in cancer mortality. The most significant change between cancer cells and normal cells is the variation of cell nucleus. Therefore, accurately detecting the biochemical changes in nucleus between cancer cells and normal cells has great potential to explore diagnostic molecular markers for NPC. Highly sensitive surface-enhanced Raman scattering (SERS) could reflect the biochemical changes in the process of cell cancerization at the molecular level. However, rapid nuclear targeting SERS detection remains a challenge. ResultsA novel and accurate nuclear-targeting SERS detection method based on electroporation was proposed. With the assistance of electric pulses, nuclear-targeting nanoprobes were rapidly introduced into different NPC cells (including CNE1, CNE2, C666 cell lines) and normal nasopharyngeal epithelial cells (NP69 cell line), respectively. Under the action of nuclear localization signaling peptides (NLS), the nanoprobes entering cells were located to the nucleus, providing high-quality nuclear SERS signals. Hematoxylin and eosin (H&E) staining and in situ cell SERS imaging confirmed the excellent nuclear targeting performance of the nanoprobes developed in this study. The comparison of SERS signals indicated that there were subtle differences in the biochemical components between NPC cells and normal nasopharyngeal cells. Furthermore, SERS spectra combined with principal component analysis (PCA) and linear discriminant analysis (LDA) were employed to diagnose and distinguish NPC cell samples, and high sensitivity, specificity, and accuracy were obtained in the screening of NPC cells from normal nasopharyngeal epithelial cells. SignificanceTo the best of our knowledge, this is the first study that employing nuclear-targeting SERS testing to screen nasopharyngeal carcinoma cells. Based on the electroporation technology, nanoprobes can be rapidly introduced into living cells for intracellular biochemical detection. Nuclear-targeting SERS detection can analyze the biochemical changes in the nucleus of cancer cells at the molecular level, which has great potential for early cancer screening and cytotoxicity analysis of anticancer drugs.

Exploring research progress in studying serum exosomal miRNA-21 as a molecular diagnostic marker for breast cancer.

Breast cancer is one of the most prevalent malignancies affecting women globally and poses a significant public health challenge. Early clinical detection plays a pivotal role in providing optimal treatment opportunities and favorable prognoses, crucial for reducing breast cancer mortality and enhancing patients' quality of life. Therefore, the timely identification and diagnosis of breast cancer are imperative. Conventional tumor markers, such as carcinoembryonic antigen (CEA) and carbohydrate antigen 15-3 (CA15-3), serve as reliable methods for actively monitoring disease progression and have become a routine auxiliary diagnostic approach in clinical settings. However, these biomarkers exhibit limitations in sensitivity and specificity, particularly in the early screening and diagnosis of tumors, often yielding results inconsistent with clinical manifestations. In recent years, research has increasingly focused on exosomes released by tumor cells as potential new biomarkers for early stage breast cancer screening. Exosomes carry various components, including tumor-derived proteins, nucleic acids, and lipids. This paper delves into the specific utilization of serum exosomal microRNA-21 (miR-21) as a biomarker for early detection and diagnosis of breast cancer, evaluating its efficacy within this framework.

Identification of P21 (CDKN1A) Activated Kinase 4 as a Susceptibility Gene for Familial Non-Medullary Thyroid Carcinoma.

Background: Familial non-medullary thyroid carcinoma (FNMTC) is a genetically predisposed disease with unclear genetic mechanisms. This makes research on susceptibility genes important for the diagnosis and treatment options. Methods: This study included a five-member family affected by papillary thyroid carcinoma. The candidate genes were identified through whole-exome sequencing and Sanger sequencing in family members, other FNMTC patients, and sporadic non-medullary thyroid carcinoma patients. The pathogenicity of the mutation was predicted using in silico tools. Cell phenotype experiments in vitro and models of lung distant metastasis in vivo were conducted to confirm the characteristics of the mutation. Transcriptome sequencing and mechanistic validation were employed to compare the disparities between PAK4 wild-type (WT) and PAK4 mutant (MUT) cell lines. Results: This mutation alters the protein structure, potentially increasing instability by affecting hydrophobicity, intra-molecular hydrogen bonding, and phosphorylation sites. It specifically promotes phosphorylated PAK4 nuclear translocation and expression in thyroid tissue and cell lines. Compared with the WT cells line, PAK4 I417T demonstrates enhanced proliferation, invasiveness, accelerated cell division, and inhibition of cell apoptosis in vitro. In addition, it exhibits a significant propensity for metastasis in vivo. It activates tumor necrosis factor signaling through increased phosphorylation of PAK4, JNK, NFκB, and c-Jun, unlike the WT that activates it via the PAK4-NFκ-MMP9 axis. In addition, PAK4 MUT protein interacts with matrix metalloproteinase (MMP)3 and regulates MMP3 promoter activity, which is not observed in the WT. Conclusions: Our study identified PAK4: c.T1250C: p.I417T as a potential susceptibility gene for FNMTC. The study concludes that the mutant form of PAK4 exhibits oncogenic function, suggesting its potential as a novel diagnostic molecular marker for FNMTC.

A novel strategy to develop powdery mildew resistant phenotypes and diagnose reaction to Golovinomyces latisporus in sunflower (Helianthus annuus L.)

Among the various biotic stresses limiting sunflower productivity, powdery mildew incited by Golovinomyces latisporus has become a serious problem in the tropical regions. Reliable source of resistance has been identified in the diploid annual wild species Helianthus praecox (PRA-1823). Interspecific cross of cultivated sunflower (Acc. PS-2023) with PRA-1823 was advanced to develop interspecific recombinant inbred lines (IRILs) with distinct phenotypic reaction to the pathogen. The IRILs with similar morphology were subjected to molecular analysis by adopting the bulk pooling analysis (BPA) wherein DNA of eight each of susceptible and resistant IRILs were pooled to constitute the respective bulks. Fourteen sunflower specific SSR markers that showed polymorphism between the susceptible and resistant bulk IRILs, discriminated the powdery mildew resistant and susceptible samples as well. The primer ORS 485 was dominant and showed amplification only in the susceptible bulks and accessions and hence, it was converted to a multiplex reaction with actin to overrule the possibility of PCR failure. These 14 primers were successfully validated on IRIL populations and individual plants, a set of 40 breeding lines and 205 germplasm accessions with high susceptibility to the pathogen, 11 Helianthus species and three previously reported sources of resistance to powdery mildew (PM-81, IR-6, TX-16 R). This constitutes the first successful attempt at development of a diagnostic molecular marker set for distinguishing the powdery mildew resistant and susceptible genotypes in sunflower.

Detection of two homologous major QTLs and development of diagnostic molecular markers for sucrose content in peanut.

We identified two stable and homologous major QTLs for sucrose content in peanut, and developed breeder-friendly molecular markers for marker-assisted selection breeding. Sucrose content is a crucial quality trait for edible peanuts, and increasing sucrose content is a key breeding objective. However, the genetic basis of sucrose content in peanut remains unclear, and major quantitative trait loci (QTLs) for sucrose content have yet to be identified. In this study, a high-density genetic map was constructed based on whole-genome re-sequencing data from a peanut RIL population. This map consisted of 2,042 bins and 24,142 SNP markers, making it one of the most comprehensive maps to date in terms of marker density. Two major QTLs (qSCA06.2 and qSCB06.2) were identified, explaining 31.41% and 24.13% of the phenotypic variance, respectively. Notably, these two QTLs were located in homologous genomic regions between the A and B subgenomes. The elite allele of qSCA06.2 was exclusive to Valencia-type, while the elite allele of qSCB06.2 existed in other peanut types. Importantly, the distribution of alleles from two homologous QTLs in the RIL population and diverse germplasm accessions consistently demonstrated that only the combination of elite allelic genotypes from both QTLs/genes resulted in a significantly dominant phenotype, accompanied by a substantial increase in sucrose content. The newly developed diagnostic markers for these QTLs were confirmed to be reliable and could facilitate future breeding efforts to enhance sucrose content using marker-assisted selection techniques. Overall, this study highlights the co-regulation of sucrose content by two major homologous QTLs/genes and provides valuable insights into the genetic basis of sucrose in peanuts.

Molecular characterization of Haemoproteus enucleator with emphasis on the host and geographic distribution

Haemoproteus species (Haemosporida, Haemoproteidae) are cosmopolitan and highly diverse blood parasites of birds that have been neglected in avian medicine. However, recent discoveries based on molecular diagnostic markers show that these pathogens often cause marked damage to various internal organs due to exo-erythrocytic development, sometimes resulting in severe and even lethal avian haemoproteosis, including cerebral pathologies. Molecular markers are essential for haemoproteosis diagnostics, but the data is limited, particularly for parasites transmitted in tropical ecosystems. This study combined microscopic and molecular approaches to characterize Haemoproteus enucleator morphologically and molecularly. Blood samples were collected from the African pygmy kingfisher Ispidina picta in Cameroon, and the parasite was identified using morphological characters of gametocytes. The analysis of partial cytochrome b sequences (cytb) identified a new Haemoproteus lineage (hISPIC03), which was linked to the morphospecies H. enucleator. Illustrations of blood stages were provided and the phylogenetic analysis showed that the new lineage clustered with five other closely related lineages belonging to the same morphospecies (hALCLEU01, hALCLEU02, hALCLEU03, hISPIC01, and hALCQUA01), with a maximum genetic distance between these lineages of 1.5 % (7 bp difference) in the 478 bp cytb sequences. DNA haplotype network was developed and identified geographic and host distribution of all lineages belonging to H. enucleator group. These lineages were almost exclusively detected in African kingfishers from Gabon, Cameroon, South Africa, and Botswana. This study developed the molecular characterization of H. enucleator and provides opportunities for diagnostics of this pathogen at all stages of its life cycle, which remains undescribed in all its closely related lineages.

The perturbation of PAHs on mosses in Aberdeen, Scotland, as a consequence of social restrictions imposed during the COVID-19 pandemic

Air quality and the concentration of polycyclic aromatic hydrocarbons (PAHs) in urban environments are increasingly becoming a concern. Measuring air quality and PAHs, and linking these to specific activities, requires deploying and recovering sampling devices to capture and measure any changes. From May 2020 to June 2021, during the “lockdown” period of the COVID-19 pandemic, acrocarpous and pleurocarpous mosses were collected from five types of site in Aberdeen, United Kingdom, and the concentration of PAHs measured to track changes in PAHs as travel-related activities changed. The predominant types of PAHs found on mosses were of the four- and five-ring varieties, with the four-ring variety of PAH (medium molecular weight) becoming more dominant as the lockdown was lifted. However, for most sites, the concentration of PAHs was evidently perturbed by the transient lifting, reimposing, and then lifting of lockdown conditions, which either directly limited travel or changed people’s motivations to travel by car. Molecular diagnostic ratios or molecular marker parameters used to infer the source of PAHs varied little and were nearly always consistent with PAHs deriving from combustion in vehicle engines. Thus, even when travel was limited, PAHs were still derived from vehicle usage, although the overall concentrations on mosses were much lower. On average, the lowest PAH concentrations were found on mosses collected from a recreational park located the furthest from traffic. The highest PAH concentrations were observed on mosses collected from residential car parks during periods when the lockdown had been lifted. However, mosses from the same residential car parks had very low PAH concentrations during periods of travel restrictions, strongly suggesting that, for mosses, local factors and patterns of vehicle usage strongly determine their exposure to PAHs. Therefore, mosses within urban environments can be used for monthly monitoring of PAHs as they are able to detect changes induced by human behaviour.

Assessing the applicability of nuclear 18S and ITS2-28S rRNA genes for diagnostics of Bactrocera dorsalis (Diptera: Tephritidae) in the Philippines

Fruit flies belonging to the Bactrocera dorsalis species complex pose a significant threat to mangoes and other crops in the Philippines and worldwide. Identifying cryptic species within this complex is challenging, particularly when relying solely on morphological analysis. In this study, we sequenced two fragments of the nuclear 18S and ITS2-28S rRNA genes from specimens of Bactrocera dorsalis Hendel collected in the Philippines to assess their applicability for species diagnostics. Subsequent sequencing and analysis revealed that the 18S and 28S rRNA gene fragments matched B. dorsalis sequences in NCBI but also displayed high similarity with other Bactrocera and insect species. On the other hand, sequences of the ITS2 segment showed hits specific to B. dorsalis. Further analysis of the 18S rRNA gene in fruit flies collected from various sources and host plants in the country suggests conserved sequences among Bactrocera samples, irrespective of collection site and host plant species. In conclusion, our findings suggest that, among the tested nuclear DNA fragments, only the ITS2 demonstrates sufficient species-level nucleotide variation for effective use as a molecular diagnostic marker for B. dorsalis identification.

Bulk serum extracellular vesicles from stressed mice show a distinct proteome and induce behavioral and molecular changes in naive mice.

Chronic stress can trigger several pathologies including mood disorders for which no clear diagnostic molecular markers have been established yet. Attractive biomarker sources are extracellular vesicles (EVs). Evs are released by cells in health and disease and contain genetic material, proteins and lipids characteristic of the cell state. Here we show that Evs recovered from the blood of animals exposed to a repeated interrupted stress protocol (RIS) have a different protein profile compared to those obtained from control animals. Proteomic analysis indicated that proteins differentially present in bulk serum Evs from stressed animals were implicated in metabolic and inflammatory pathways and several of them were previously related to psychiatric disorders. Interestingly, these serum Evs carry brain-enriched proteins including the stress-responsive neuronal protein M6a. Then, we used an in-utero electroporation strategy to selectively overexpress M6a-GFP in brain neurons and found that M6a-GFP could also be detected in bulk serum Evs suggesting a neuronal origin. Finally, to determine if these Evs could have functional consequences, we administered Evs from control and RIS animals intranasally to naïve mice. Animals receiving stress EVs showed changes in behavior and brain M6a levels similar to those observed in physically stressed animals. Such changes could therefore be attributed, or at least in part, to EV protein transfer. Altogether these findings show that EVs may participate in stress signaling and propose proteins carried by EVs as a valuable source of biomarkers for stress-induced diseases.