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The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp genome data with nuclear DNA information offers a more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives. The resulting nuclear DNA trees were consistent with existing nuclear evolutionary relationships derived from high-throughput sequencing, but diverged from cp genome-based trees. To elucidate the underlying complex evolutionary processes causing these discordances, we implemented an integrative workflow that utilized multiple alignments of each gene generated by Read2Tree, in conjunction with other phylogenomic methods. Our analysis revealed that incomplete lineage sorting predominantly drives these discordances, while introgression and ancient introgression also contribute to topological discrepancies within certain clades. This study underscores the cost-effectiveness of using the same raw sequencing data for both cp and nuclear DNA analyses in understanding plant evolutionary relationships.

Oral squamous cell carcinoma (OSCC) is a serious public health problem in various Asian countries, including Sri Lanka, and a combination of cultural practices, lifestyle factors, and genetic predispositions influences the incidence of these cancers. The examination of the connection between exposure to heavy metals and the probability of developing oral potentially malignant disorders (OPMD) and OSCC has been limited in its scope, and the overall consequences of such exposure remain largely unknown. This study aims to clarify the link between serum levels of heavy metals and the risk of OSCC and OPMD. The concentrations of seven heavy metals—namely, arsenic (As), cadmium (Cd), chromium (Cr), cobalt (Co), copper (Cu), lead (Pb), and zinc (Zn)—were analyzed in serum samples from 60 cases and 15 controls in the Sri Lankan cohort. The Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) was used for the analysis. Subsequently, the data underwent statistical evaluation via the Kruskal–Wallis H test, using the Statistical Package for Social Sciences (SPSS) version 28 software, with a confidence interval set at 95%. A p-value less than 0.05 was considered statistically significant. The cohort consisted of 48 men and 27 women, with 15 patients each diagnosed with OSCC, OSF, OLK, and OLP, and 15 healthy controls. The study used the Kruskal–Wallis Test to compare metal concentrations across groups, finding significant differences for all metals except As and Pb. Significant associations were observed between age, past medical history, drug history, gender, smoking, alcohol consumption, and betel chewing. The Spearman Correlation test showed significant correlations between the concentrations of Cr, Co, Cu, As, and Zn and the presence of cancer/precancer conditions. The study’s findings suggest that heavy metal contamination may be linked to the development of OSCC and precancerous conditions. When comparing OSCC and OPMD cases with controls, the serum concentrations of As and Pb did not differ significantly. However, Cd, Cr, Co, Cu, and Zn exhibited significantly higher concentrations among cases compared to controls ( p  <  0.05 ). This study observed significant variations in the levels of these five heavy metals among cancerous (OSCC), premalignant (OPMD), and healthy tissues, suggesting a potential role in the progression of malignancies. These findings underscore the importance of environmental pollution in this specific context.

The research examined the salivary concentrations of various biomarkers, such as OAZ1 , SAT , S100P , IL-1β , and IL-8 aiming to detect early-stage oral squamous cell carcinoma (OSCC). These biomarkers show potential as indicators for detecting both pre-cancerous and cancerous states within the oral cavity. Analyzing these specific molecules in saliva could help clinicians enhance diagnostic accuracy and refine early detection methods for OSCC. The research encompassed a cohort of nine OSCC patients, ten with oral submucous fibrosis (OSF), eleven individuals with oral lichen planus (OLP), and ten healthy controls. The study focused on assessing the expression levels of key biomarkers— IL-1β , IL-8 , SAT , S100P , and OAZ1 mRNA—in extracellular RNA extracted from saliva samples. This evaluation was conducted using real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) with sequence-specific primers. Additionally, receiver operating characteristic curve (ROC) curve analysis was employed to gauge the efficacy of these biomarkers in detecting OSCC. Based on the results we observe, when these five biomarkers are used together, they give a 90% predictive probability for patients with OLP, an 80% predictive probability for OSF, and an impressive 100% predictive probability for patients with OSCC (AUC = 1.000, p  = 0.000). This study demonstrates the efficacy of salivary transcriptome diagnostics in detecting OSCC. This novel clinical technique has the potential to be a powerful, efficient, and reliable tool for early detection of cancer. Salivary transcriptomes can be further analyzed to evaluate their effectiveness in other important illness contexts and for regular health monitoring.

Background Identification of disease-associated spectral alterations of oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMD) is critical to improving patient outcomes. Protein structural changes in serum can be investigated using a minimally invasive, potential adjunctive analytical method. This preliminary, exploratory study aimed to explore the ability of attenuated total reflection–Fourier transform infrared (ATR-FTIR) spectroscopy to characterize disease-associated serum protein structural alterations in OSCC and OPMDs relative to healthy controls (HCs). Methods A laboratory-based analytical study was conducted using 110 serum samples from clinically and histopathologically confirmed cases: OSCC ( n  = 22), oral leukoplakia (OLK) ( n  = 22), oral lichen planus (OLP) ( n  = 22), oral submucous fibrosis (OSF) ( n  = 22), and HCs ( n  = 22). Spectral data were obtained with a FTIR over the 400–4000 cm⁻¹ range. Protein secondary structure alterations were analyzed using spectral deconvolution and Gaussian curve fitting. The relevance of specific wavenumbers was evaluated, and sensitivity and specificity were calculated to describe their ability to differentiate diseased groups from HCs in an exploratory manner. Results Alterations in the Amide I region were evident in serum samples from OSCC and OLK compared with controls, although no direct statistical comparison between disease groups was performed. Ten wavenumbers (1372, 1381, 1390, 1398, 1412, 1421, 1609, 1635, 1665, and 1683 cm⁻¹) showed statistically significant disease-associated differences between diseased groups and healthy controls. Among the evaluated spectral features, the wavenumber 1390 cm⁻¹ showed the highest sensitivity and specificity values for distinguishing OSCC from HCs (77.3% sensitivity, 86.4% specificity) and OLK from HCs (86.4% sensitivity, 77.3% specificity). Conclusions ATR-FTIR spectroscopy revealed distinct protein structural alterations in serum samples from patients with OSCC and OPMD when compared with healthy individuals. Specific spectral features, particularly at 1381 cm⁻¹ and 1683 cm⁻¹, demonstrated consistent disease-associated alterations compared with HCs, indicating their potential utility as minimally invasive serum-based spectral markers in exploratory studies of oral cancer and OPMD.

Background Oral cancers, which include tumors of the oral cavity, salivary glands, and pharynx, are becoming increasingly prevalent worldwide. Squamous cell carcinoma accounts for over 90% of malignant oral lesions, with oral squamous cell carcinoma (OSCC) being notably common in the Indian subcontinent and other regions of Asia. This is especially true in South-Central Asia, including Sri Lanka, where it is particularly prevalent among men. This study aims to evaluate the levels of Vascular Endothelial Growth Factor-A (VEGF-A) and Cytokeratin-19 (CK-19) mRNAs in whole blood as a potential method for the early detection of OSCC. Methods The study included 40 patients (each from OSCC, Oral Submucous Fibrosis (OSF), Oral Leukoplakia (OLK), Oral Lichen Planus (OLP), and 10 healthy controls. The expression levels of VEGF-A and CK-19 mRNAs were measured from extracellular RNA extracted from whole blood samples using real-time reverse transcription polymerase chain reaction (RT-PCR) with sequence-specific primers. Receiver operating characteristic (ROC) curve analysis was used to evaluate the effectiveness of these biomarkers in detecting OSCC. Results The results demonstrated a significant increase in blood transcripts of the candidate mRNAs CK-19 and VEGF-A in patients with OSCC, OSF, OLK, and OLP. The Wilcoxon signed-rank test revealed a p -value of 0.002 for each specific comparison between diseased patients and healthy controls (i.e., OSCC vs. HC, OSF vs. HC, OLP vs. HC, OLK vs. HC) for both CK-19 and VEGF-A. When these two biomarkers were used together, they provided a 60% predictive probability for patients with OSCC ( p  = 0.023). Conclusion This study highlights the efficacy of blood mRNA transcriptome diagnostics in detecting OSCC. This innovative clinical approach has the potential to be a robust, efficient, and reliable tool for early cancer detection. Blood-based transcriptomes could be further explored for their effectiveness in various health contexts and for routine health monitoring.

The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp genome data with nuclear DNA information offers a more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives. The resulting nuclear DNA trees were consistent with existing nuclear evolutionary relationships derived from high-throughput sequencing, but diverged from cp genome-based trees. To elucidate the underlying complex evolutionary processes causing these discordances, we implemented an integrative workflow that utilized multiple alignments of each gene generated by Read2Tree, in conjunction with other phylogenomic methods. Our analysis revealed that incomplete lineage sorting predominantly drives these discordances, while introgression and ancient introgression also contribute to topological discrepancies within certain clades. This study underscores the cost-effectiveness of using the same raw sequencing data for both cp and nuclear DNA analyses in understanding plant evolutionary relationships.Competing Interest StatementThe authors have declared no competing interest.Footnotes* Revisions in the Peer Review Process of Scientific Journal

Soil salinity is one of the inherent problems in coastal soils. Increased soil salinity in coastal soils results in low bacterial diversity. However the salt tolerant bacteria have the ability to survive in saline soils because of their unique salt tolerant mechanisms. The current study was focused on identifying salinity tolerant bacteria in the West coast of Sri Lanka. Four soil samples each were collected from three locations namely Negombo lagoon, Balapitiya coastal area and Beruwala coastal area. From 12 soil samples 20 bacterial isolates were obtained namely NE01 to NE09 (Negombo lagoon), BA01 to BA07 (Balapitiya coastal area) and BE01 to BE04 (Beruwala coastal area). The isolates were characterized based on bacterial colony morphology, Grams stain and biochemical tests namely catalase test, modified oxidase test, hemolytic reaction on blood agar and growth on MacConkey agar. All the bacterial isolates were screened for salt tolerance at different concentrations of NaCl ranging from 3 dS/m to 18 dS/m. All 20 bacterial isolates were found to be salt tolerant upto the highest NaCl concentration tested (18 dS/m). The salinity tolerance behavior of selected five isolates were observed by enumerating the number of colony forming units per milliliter (CFU/mL) with increasing salinity. Molecular identification of these five isolates were carried out by sequencing the 16S rRNA gene. It is recommended to screen the identified salt tolerant bacterial isolates for their plant growth promoting rhizobacterial (PGPR) activities such as phosphate solubilization, indole acetic acid and ammonia production. The findings reveal a potential of using these isolates through biotechnological applications with the aim of increasing the productivity of saline affected soils of Sri Lanka. Key words: 16S rRNA, Balapitiya, Beruwala, Negombo, Salt tolerance, Soil salinity