@article{araya-ortega_exploring_2024,

title = {Exploring Genomic Differences between a Pair of Vitis vinifera Clones Using WGS Data: A Preliminary Study},

author = {Daniela Araya-Ortega and Felipe Gainza-Cortés and Gonzalo Riadi},

url = {https://www.mdpi.com/2311-7524/10/10/1026},

doi = {10.3390/horticulturae10101026},

issn = {2311-7524},

year  = {2024},

date = {2024-09-01},

urldate = {2025-01-02},

journal = {Horticulturae},

volume = {10},

number = {10},

pages = {1026},

abstract = {The differentiation of clones within grape cultivars, specifically Vitis vinifera, has significant potential for the wine industry. This differentiation involves associating morphological features or a genetic signature with a particular cultivar clone, which is a challenging task. It has been difficult to experimentally find genetic signatures that differentiate a pair of clones, despite evidence suggesting that genomic differences exist. Are there genetic or genomic differences in a pair of clones? If so, where are the variations in the genome? Are there variations in protein coding genes? We addressed these questions by performing a bioinformatic analysis to identify genetic differences between certified clones of the same cultivar. Utilising genome sequencing data from tissue samples, we identified genomic positions differing between the clones and their cultivar reference genome, meeting the filtering criteria. Applying this approach to the Carménère and Merlot clones resulted in 5718 and 5218 variations, respectively, that differentiated the clones. Visual validation of 50 variations per cultivar revealed that 12% of these variations were located in the Merlot genes, while 32% were found in the Carménère genes. We estimated between 600 and 1000 variations per cultivar that could be validated by visual inspection. Despite the presence of these variations within genes, none was found to have a disruptive effect on protein function. By comparing our results with those of previous studies, we discuss issues pertaining to clone differentiation. In conclusion, there are genomic variations in pairs of clones that allow for their differentiation, though the variations are not directly related to the phenotype.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{uribe_evolution_2024,

title = {Evolution of ion channels in cetaceans: a natural experiment in the tree of life},

author = {Cristóbal Loyola Uribe and Mariana F. Nery and Kattina Zavala and Gonzalo A. Mardones and Gonzalo Riadi and Juan C. Opazo},

url = {https://www.nature.com/articles/s41598-024-66082-1},

doi = {10.1038/s41598-024-66082-1},

issn = {2045-2322},

year  = {2024},

date = {2024-07-01},

urldate = {2024-07-01},

journal = {Scientific Reports},

volume = {14},

number = {1},

pages = {17024},

abstract = {Abstract 

 Cetaceans represent a natural experiment within the tree of life in which a lineage changed from terrestrial to aquatic habitats. This shift involved phenotypic modifications, representing an opportunity to explore the genetic bases of phenotypic diversity. Among the different molecular systems that maintain cellular homeostasis, ion channels are crucial for the proper physiological functioning of all living species. This study aims to explore the evolution of ion channels during the evolutionary history of cetaceans. To do so, we created a bioinformatic pipeline to annotate the repertoire of ion channels in the genome of the species included in our sampling. Our main results show that cetaceans have, on average, fewer protein-coding genes and a higher percentage of annotated ion channels than non-cetacean mammals. Signals of positive selection were detected in ion channels related to the heart, locomotion, visual and neurological phenotypes. Interestingly, we predict that the NaV1.5 ion channel of most toothed whales (odontocetes) is sensitive to tetrodotoxin, similar to NaV1.7, given the presence of tyrosine instead of cysteine, in a specific position of the ion channel. Finally, the gene turnover rate of the cetacean crown group is more than three times faster than that of non-cetacean mammals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Olivares2023,

title = {ETHANOL MODIFIES ALTERNATIVE SPLICING REGULATION IN DEVELOPING NEURONS},

author = {Montserrat Olivares and Camilo Fuentes-Beals and María Andrés and Gonzalo Riadi and Carlos Oliva and Fernando Faunes and Paola Haeger},

doi = {10.1016/j.ibneur.2023.08.139},

issn = {2667-2421},

year  = {2023},

date = {2023-10-01},

urldate = {2023-10-00},

journal = {IBRO Neuroscience Reports},

volume = {15},

pages = {S123--S124},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fuentes-Beals2023,

title = {Bioinformatic analysis predicts that ethanol exposure during early development causes alternative splicing alterations of genes involved in RNA post-transcriptional regulation},

author = {Camilo Fuentes-Beals and Montserrat Olivares-Costa and María Estela Andrés and Paola A. Haeger and Gonzalo Riadi and Carlos Oliva and Fernando Faunes},

editor = {Shrikanth Gadad},

doi = {10.1371/journal.pone.0284357},

issn = {1932-6203},

year  = {2023},

date = {2023-04-13},

journal = {PLoS ONE},

volume = {18},

number = {4},

publisher = {Public Library of Science (PLoS)},

abstract = {Prenatal ethanol exposure is associated with neurodevelopmental defects and long-lasting cognitive deficits, which are grouped as fetal alcohol spectrum disorders (FASD). The molecular mechanisms underlying FASD are incompletely characterized. Alternative splicing, including the insertion of microexons (exons of less than 30 nucleotides in length), is highly prevalent in the nervous system. However, whether ethanol exposure can have acute or chronic deleterious effects in this process is poorly understood. In this work, we used the bioinformatic tools VAST-TOOLS, rMATS, MAJIQ, and MicroExonator to predict alternative splicing events affected by ethanol from available RNA sequencing data. Experimental protocols of ethanol exposure included human cortical tissue development, human embryoid body differentiation, and mouse development. We found common genes with predicted differential alternative splicing using distinct bioinformatic tools in different experimental designs. Notably, Gene Ontology and KEGG analysis revealed that the alternative splicing of genes related to RNA processing and protein synthesis was commonly affected in the different ethanol exposure schemes. In addition, the inclusion of microexons was also affected by ethanol. This bioinformatic analysis provides a reliable list of candidate genes whose splicing is affected by ethanol during nervous system development. Furthermore, our results suggest that ethanol particularly modifies the alternative splicing of genes related to post-transcriptional regulation, which probably affects neuronal proteome complexity and brain function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{herrada_lymph_2022,

title = {Lymph Leakage Promotes Immunosuppression by Enhancing Anti-Inflammatory Macrophage Polarization},

author = {Andrés A. Herrada and Alexandra Olate-Briones and Rodrigo Lazo-Amador and Chaohong Liu and Bairon Hernández-Rojas and Gonzalo Riadi and Noelia Escobedo},

url = {https://www.frontiersin.org/articles/10.3389/fimmu.2022.841641/full},

doi = {10.3389/fimmu.2022.841641},

issn = {1664-3224},

year  = {2022},

date = {2022-05-01},

urldate = {2024-12-14},

journal = {Frontiers in Immunology},

volume = {13},

pages = {841641},

abstract = {Lymphatic vasculature is a network of capillaries and vessels capable of draining extracellular fluid back to blood circulation and to facilitate immune cell migration. Although the role of the lymphatic vasculature as coordinator of fluid homeostasis has been extensively studied, the consequences of abnormal lymphatic vasculature function and impaired lymph drainage have been mostly unexplored. Here, by using the 

 Prox1 

 +/– 

 mice with defective lymphatic vasculature and lymphatic leakage, we provide evidence showing that lymph leakage induces an immunosuppressive environment by promoting anti-inflammatory M2 macrophage polarization in different inflammatory conditions. In fact, by using a mouse model of tail lymphedema where lymphatic vessels are thermal ablated leading to lymph accumulation, an increasing number of anti-inflammatory M2 macrophages are found in the lymphedematous tissue. Moreover, RNA-seq analysis from different human tumors shows that reduced lymphatic signature, a hallmark of lymphatic dysfunction, is associated with increased M2 and reduced M1 macrophage signatures, impacting the survival of the patients. In summary, we show that lymphatic vascular leakage promotes an immunosuppressive environment by enhancing anti-inflammatory macrophage differentiation, with relevance in clinical conditions such as inflammatory bowel diseases or cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fuentes-Beals2022,

title = {Hidden Markov Modeling with HMMTeacher},

author = {Camilo Fuentes-Beals and Alejandro Valdés-Jiménez and Gonzalo Riadi},

editor = {Patricia M. Palagi},

doi = {10.1371/journal.pcbi.1009703},

issn = {1553-7358},

year  = {2022},

date = {2022-02-10},

journal = {PLoS Comput Biol},

volume = {18},

number = {2},

publisher = {Public Library of Science (PLoS)},

abstract = {Is it possible to learn and create a first Hidden Markov Model (HMM) without programming skills or understanding the algorithms in detail? In this concise tutorial, we present the HMM through the 2 general questions it was initially developed to answer and describe its elements. The HMM elements include variables, hidden and observed parameters, the vector of initial probabilities, and the transition and emission probability matrices. Then, we suggest a set of ordered steps, for modeling the variables and illustrate them with a simple exercise of modeling and predicting transmembrane segments in a protein sequence. Finally, we show how to interpret the results of the algorithms for this particular problem. To guide the process of information input and explicit solution of the basic HMM algorithms that answer the HMM questions posed, we developed an educational webserver called HMMTeacher. Additional solved HMM modeling exercises can be found in the user’s manual and answers to frequently asked questions. HMMTeacher is available at https://hmmteacher.mobilomics.org, mirrored at https://hmmteacher1.mobilomics.org. A repository with the code of the tool and the webpage is available at https://gitlab.com/kmilo.f/hmmteacher.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lozoya_brain-specific_2021,

title = {A brain-specific textitpgc1 α fusion transcript affects gene expression and behavioural outcomes in mice},

author = {Oswaldo A Lozoya and Fuhua Xu and Dagoberto Grenet and Tianyuan Wang and Korey D Stevanovic and Jesse D Cushman and Thomas B Hagler and Artiom Gruzdev and Patricia Jensen and Bairon Hernandez and Gonzalo Riadi and Sheryl S Moy and Janine H Santos and Richard P Woychik},

url = {https://www.life-science-alliance.org/lookup/doi/10.26508/lsa.202101122},

doi = {10.26508/lsa.202101122},

issn = {2575-1077},

year  = {2021},

date = {2021-12-01},

urldate = {2024-12-14},

journal = {Life Science Alliance},

volume = {4},

number = {12},

pages = {e202101122},

abstract = {PGC1α is a transcriptional coactivator in peripheral tissues, but its function in the brain remains poorly understood. Various brain-specific 

 Pgc1 

 α isoforms have been reported in mice and humans, including two fusion transcripts (FTs) with non-coding repetitive sequences, but their function is unknown. The FTs initiate at a simple sequence repeat locus ∼570 Kb upstream from the reference promoter; one also includes a portion of a short interspersed nuclear element (SINE). Using publicly available genomics data, here we show that the SINE FT is the predominant form of 

 Pgc1 

 α in neurons. Furthermore, mutation of the SINE in mice leads to altered behavioural phenotypes and significant up-regulation of genes in the female, but not male, cerebellum. Surprisingly, these genes are largely involved in neurotransmission, having poor association with the classical mitochondrial or antioxidant programs. These data expand our knowledge on the role of 

 Pgc1 

 α in neuronal physiology and suggest that different isoforms may have distinct functions. They also highlight the need for further studies before modulating levels of 

 Pgc1 

 α in the brain for therapeutic purposes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}