Article
Immunology
Guanghao Li, Yongheng Liu, Yanting Zhang, Yao Xu, Jin Zhang, Xianfu Wei, Zhongmin Zhang, Chao Zhang, Jinyan Feng, Qiang Li, Guowen Wang
Summary: This study explores the prognostic value of ferroptosis-related lncRNAs in HCC patients. A novel signature consisting of five ferroptosis-related lncRNAs is established and shown to have a high clinical application value in predicting overall survival. The findings suggest that this signature could serve as an efficient indicator for predicting prognosis and guiding treatment in HCC patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Weian Zhu, Jianjie Wu, Jiongduan Huang, Dongming Xiao, Fengao Li, Chenglun Wu, Xiaojuan Li, Hengda Zeng, Jiayu Zheng, Wenjie Lai, Xingqiao Wen
Summary: This study identifies macrophage-related marker genes and evaluates their impact on prostate cancer development using single-cell sequencing data analysis. A prognostic signature based on these marker genes is constructed and shown to have excellent predictive ability. Furthermore, the study explores the relationship between the prognostic signature and the tumor immune microenvironment, therapeutic response, and drug selection.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Weian Zhu, Jiongduan Huang, Jianjie Wu, Chenglun Wu, Fengxi Ye, Xiang Li, Wenjie Lai
Summary: This study constructed an inflammation-related prognostic signature (IRPS) using machine learning methods and validated its predictive ability for survival outcomes in prostate cancer patients. The IRPS was found to be significantly associated with tumor immunity, genomic heterogeneity, therapeutic response, and drug selection.
Review
Biodiversity Conservation
Noelia Perez-Pereira, Armando Caballero, Aurora Garcia-Dorado
Summary: Genetic rescue is viewed as a promising but underutilized conservation strategy, with limited empirical evidence to support its application. Inbreeding depression and genetic purging are key factors determining the success of rescue programs in the medium to long term. In some scenarios, hybrid vigor and purging can lead to sustained successful rescue, but in specific situations where the recipient population is too small to purge inbreeding load introduced by migrants, increased fitness inbreeding depression and extinction risk may occur.
CONSERVATION GENETICS
(2022)
Correction
Biodiversity Conservation
Noelia Perez-Pereira, Armando Caballero, Aurora Garcia-Dorado
CONSERVATION GENETICS
(2022)
Biographical-Item
Ecology
Armando Caballero, Jinliang Wang, Carlos Lopez-Fanjul
Article
Genetics & Heredity
Irene Novo, Enrique Santiago, Armando Caballero
Summary: The study explores the impact of selection and recombination rate heterogeneity on the estimation of historical Ne, indicating that NeLD mainly reflects demographic changes in population size across generations and is not affected by selection.
Article
Biodiversity Conservation
N. Perez-Pereira, E. Lopez-Cortegano, A. Garcia-Dorado, A. Caballero
Summary: The study found that the change in fitness due to deleterious recessive alleles in inbreeding can be predicted by estimating the inbreeding load and purging coefficient. These parameters can be estimated in pedigreed populations and accurately predict the change in fitness under different breeding systems. The fitness predictions can help inform conservation designs under different breeding scenarios.
ANIMAL CONSERVATION
(2023)
Article
Biodiversity Conservation
Noelia Perez-Pereira, Jinliang Wang, Humberto Quesada, Armando Caballero
Summary: This article investigates the influence of purging on the establishment of a minimum viable population (MVP) for long-term survival. Computer simulations were used to study extinction times and loss of genetic diversity for different effective population sizes. The results indicate that purging can reduce the MVP needed for a population to persist in the long term, especially for species with higher reproductive rates.
BIODIVERSITY AND CONSERVATION
(2022)
Correction
Biodiversity Conservation
Noelia Perez-Pereira, Jinliang Wang, Humberto Quesada, Armando Caballero
BIODIVERSITY AND CONSERVATION
(2023)
Article
Evolutionary Biology
Noelia Perez-Pereira, Humberto Quesada, Armando Caballero
Summary: This study evaluated the effectiveness of molecular markers in estimating inbreeding depression in fruit flies and found that genomic measures provided estimates of inbreeding depression that were comparable to those obtained from simple pedigree estimations with larger sample sizes, even under challenging scenarios.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Irene Novo, Noelia Perez-Pereira, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The availability of high-density markers allows the estimation of historical effective population size. Recent refinement methods have been shown to be accurate with simulation data and have been applied to real data of various species. An experimental design with Drosophila melanogaster was carried out to test the method, which showed generally good performance. The limitations of the method and its application were discussed.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Enrique Santiago, Armando Caballero, Carlos Kopke, Irene Novo
Summary: A new method is developed to estimate the contemporary effective population size (Ne) based on linkage disequilibrium (LD) in non-model species. It can be applied to different mating systems and variations in family size distribution. The method uses an artificial neural network to predict confidence intervals, providing more consistent estimates.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Agriculture, Dairy & Animal Science
Armando Caballero, Almudena Fernandez, Beatriz Villanueva, Miguel A. Toro
Summary: This study investigates the accuracy of estimators of inbreeding based on molecular markers in different mating systems and artificially selected populations. The results show that when the allele frequencies of the base population are known, all estimators based on marker allele frequencies provide accurate estimates of inbreeding coefficients and inbreeding depression. When the allele frequencies are unknown, F-LH1 is the most correlated estimator with the actual values, and F-YA2 provides the most accurate estimates of inbreeding depression.
GENETICS SELECTION EVOLUTION
(2022)