Host specificity of coral-associated fauna and its relevance for coral reef biodiversity.

Coral-associated fauna predominantly consists of invertebrates and constitutes an important component of coral reef biodiversity. The symbionts depend on their hosts for food, shelter and substrate. They may act as parasites by feeding on their hosts, by overgowing their polyps, or by excavating their skeletons. Because some of these species partly reside inside their hosts, they may be cryptic and can easily be overlooked in biodiversity surveys. Since no quantitative overview is available about these inter-specific relationships, this present study adresses variation in host ranges and specificity across four large coral-associated taxa and between the Atlantic and Indo-Pacific oceans. These taxa are: coral barnacles (Pyrgomatidae, n = 95), coral gall crabs (Cryptochiridae, n = 54), tubeworms (Serpulidae, n = 31), and date mussels (Lithophaginae, n = 23). A total of 335 host coral species was recorded. An index of host specificity (STD) was calculated per symbiont species, based on distinctness in taxonomic host range levels (species, genus, family, etc.). Mean indices were statistically compared among the four associated taxa and the two oceanic coral reef regions. Barnacles were the most host-specific, tubeworms the least. Indo-Pacific associates were approximately 10 times richer in species and two times more host-specific than their Atlantic counterparts. Coral families varied in the number of associates, with some hosting none. This variation could be linked to host traits (coral growth form, maximum host size) and is most probably also a result of the evolutionary history of the interspecific relationships.

Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue.

The long-read RNA sequencing developed by Oxford Nanopore Technologies provides a direct quantification of transcript isoforms, thereby making it possible to present alternative splicing (AS) profiles as arrays of single splice variants with different abundances. Additionally, AS profiles can be presented as arrays of genes characterized by the degree of alternative splicing (the DAS-the number of detected splice variants per gene). Here, we successfully utilized the DAS to reveal biological pathways influenced by the alterations in AS in human liver tissue and the hepatocyte-derived malignant cell lines HepG2 and Huh7, thus employing the mathematical algorithm of gene set enrichment analysis. Furthermore, analysis of the AS profiles as abundances of single splice variants by using the graded tissue specificity index τ provided the selection of the groups of genes expressing particular splice variants specifically in liver tissue, HepG2 cells, and Huh7 cells. The majority of these splice variants were translated into proteins products and appeal to be in focus regarding further insights into the mechanisms underlying cell malignization. The used metrics are intrinsically suitable for transcriptome-wide AS profiling using long-read sequencing.

Construction of Immune Infiltration-Related LncRNA Signatures Based on Machine Learning for the Prognosis in Colon Cancer.

Colon cancer is one of the malignant tumors with high morbidity, lethality, and prevalence across global human health. Molecular biomarkers play key roles in its prognosis. In particular, immune-related lncRNAs (IRL) have attracted enormous interest in diagnosis and treatment, but less is known about their potential functions. We aimed to investigate dysfunctional IRL and construct a risk model for improving the outcomes of patients. Nineteen immune cell types were collected for identifying house-keeping lncRNAs (HKLncRNA). GSE39582 and TCGA-COAD were treated as the discovery and validation datasets, respectively. Four machine learning algorithms (LASSO, Random Forest, Boruta, and Xgboost) and a Gaussian mixture model were utilized to mine the optimal combination of lncRNAs. Univariate and multivariate Cox regression was utilized to construct the risk score model. We distinguished the functional difference in an immune perspective between low- and high-risk cohorts calculated by this scoring system. Finally, we provided a nomogram. By leveraging the microarray, sequencing, and clinical data for immune cells and colon cancer patients, we identified the 221 HKLncRNAs with a low cell type-specificity index. Eighty-seven lncRNAs were up-regulated in the immune compared to cancer cells. Twelve lncRNAs were beneficial in improving performance. A risk score model with three lncRNAs (CYB561D2, LINC00638, and DANCR) was proposed with robust ROC performance on an independent dataset. According to immune-related analysis, the risk score is strongly associated with the tumor immune microenvironment. Our results emphasized IRL has the potential to be a powerful and effective therapy for enhancing the prognostic of colon cancer.

Discovery of tumor immune infiltration-related snoRNAs for predicting tumor immune microenvironment status and prognosis in lung adenocarcinoma.

Lung adenocarcinoma (LUAD) has a high mortality rate and is difficult to diagnose and treat in its early stage. Previous studies have demonstrated that small nucleolar RNAs (snoRNAs) play a critical role in tumor immune infiltration and the development of a variety of solid tumors. However, there have been no studies on the correlation between tumor-infiltrating immune-related snoRNAs (TIISRs) and LUAD. In this study, we filtered six immune-related snoRNAs based on the tissue specificity index (TSI) and expression profile of all snoRNAs between all LUAD cell lines from the Cancer Cell Line Encyclopedia and 21 types of immune cells from the Gene Expression Omnibus database. Further, we performed real-time quantitative polymerase chain reaction (RT-qPCR) to validate the expression status of these snoRNAs on peripheral blood mononuclear cells (PBMCs) and lung cancer cell lines. Next, we developed a TIISR signature based on the expression profiles of snoRNAs from 479 LUAD patients filtered by the random survival forest algorithm. We then analyzed the value of this TIISR signature (TIISR risk score) for assessing tumor immune infiltration, immune checkpoint inhibitor (ICI) treatment response, and the prognosis of LUAD between groups with high and low TIISR risk score. Further, we found that the TIISR risk score groups showed significant differences in biological characteristics and that the risk score could be used to assess the level of tumor immune cell infiltration, thereby predicting prognosis and responsiveness to immunotherapy in LUAD patients.

Evaluation of Treatment Integrity: The Treatment Specificity Index.

OBJECTIVE: To differentiate between treatments in a randomized controlled trial (RCT), therapies need to display not only high purity but also high specificity. The aim of this study was to demonstrate the benefits of calculating a treatment specificity index for the evaluation of treatment differentiation. METHOD: Based on an RCT of relapse prevention in depression, comparing a cognitive with a psychoeducational treatment, the specificity and the purity index were calculated. RESULTS: As indicated by the specificity index, both conditions differed in their levels of implemented specific and common interventions. A significant relationship was found between symptom change before a therapy session and treatment specificity. CONCLUSIONS: The specificity index is an appropriate method for enhancing the internal validity of RCTs in evaluating treatment integrity.

Los remedios del monte: vigencia del conocimiento fitoterapéutico local en Los Juríes Santiago del Estero, Argentina / The remedies from the “monte”: currency of local phytotherapeutic knowledge in Los JuríesSantiago del Estero, Argentina

The objective of this work was to analyze the currency of traditional medicine in the rural population of Los Juríes, Santiago del Estero, Argentina. Five field works have been performed to the study area, where ethnobotany walk and semistructured interviews were used for gathering data. Thirty nine plant species mentioned as medicinal have been recorded. Digestive illnesses were the most conspicuous ones, with 27 percent of mentions of use over the total of the named illnesses. An ad hoc designed index has been used to determine the specificity in the use of medicinal plants, which major value was presented by poleo (Lippia turbinata) and chañar (Geoffroea decorticans). The number of recorded plants was minor in comparison with similar works carried out in neighbouring areas, nevertheless the currency of the knowledge and use of phythotherapy was confirmed.

El objetivo de este trabajo consistió́ en analizar la vigencia de la medicina tradicional entre la población rural de Los Juríes, Santiago del Estero, Argentina. Se realizaron 5 viajes de campaña a la zona de estudio, donde fueron utilizadas caminatas etnobotánicas y entrevistas semiestructuradas para la recolección de los datos. Se registraron 39 especies de plantas mencionadas como medicinales. Las afecciones del sistema digestivo fueron las más conspicuas, correspondiéndose con el 27 por ciento de las menciones totales de uso por dolencia nombrada. Se aplicó́ un índice diseñado ad hoc a fin de evaluar la especificidad en el uso medicinal de las plantas, cuyo valor máximo fue alcanzado por el poleo (Lippia turbinata) y el chañar (Geoffroea decorticans). El número de plantas registradas fue menor que los mencionados en trabajos similares en áreas vecinas, sin embargo se confirmó́ la vigencia del conocimiento y uso de la fitoterapéutica.

Evaluation of cytotoxiciy and tumor-specificity of licorice flavonoids based on chemical structure.

BACKGROUND: The mechanism of cytotoxicity induction by flavonoids has been studied by many investigators, but their tumor specificity is not clear. To address this point, 10 licorice flavonoids were subjected to quantitative structure-activity relationship (QASR) analysis with cytotoxicity assay with four human oral carcinoma and three normal cell lines. MATERIALS AND METHODS: Cytotoxicity was determined by the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide method. Physico-chemical, structural, and quantum-chemical parameters were calculated based on the conformations optimized by the LowModeMD method. RESULTS: Licurazid and isoliquiritigenin had the highest cytotoxicity against tumor cells, and liquiritin, isoliquiritin and licurazid had the highest tumor specificity, suggesting an antitumor potential for licurazid. Chalcones had slightly higher cytotoxicity and tumor specificity than flavanones. The number of sugar units in the molecule was somewhat negatively-correlated with cytotoxicity, but not with tumor specificity. Parameters that reflect the three-dimensional structure, molecular volume and number of phenolic OH groups were significantly correlated with cytotoxicity, but not with tumor specificity. On the other hand, solvation energy was significantly correlated with tumor specificity, but not with cytotoxicity. CONCLUSION: These physicochemical descriptors may be useful to estimate cytotoxicity or tumor specificity of structurally-related compounds to these licorice flavonoids.