Evaluating the capacity of human gut microorganisms to colonize the zebrafish larvae (Danio rerio)

Indexación: Scopus.In this study we evaluated if zebrafish larvae can be colonized by human gut microorganisms. We tested two strategies: (1) through transplantation of a human fecal microbiota and (2) by successively transplanting aerotolerant anaerobic microorganisms, similar to the colonization in the human intestine during early life. We used conventionally raised zebrafish larvae harboring their own aerobic microbiota to improve the colonization of anaerobic microorganisms. The results showed with the fecal transplant, that some members of the human gut microbiota were transferred to larvae. Bacillus, Roseburia, Prevotella, Oscillospira, one unclassified genus of the family Ruminococcaceae and Enterobacteriaceae were detected in 3 days post fertilization (dpf) larvae; however only Bacillus persisted to 7 dpf. Successive inoculation of Lactobacillus, Bifidobacterium and Clostridioides did not improve their colonization, compared to individual inoculation of each bacterial species. Interestingly, the sporulating bacteria Bacillus clausii and Clostridioides difficile were the most persistent microorganisms. Their endospores persisted at least 5 days after inoculating 3 dpf larvae. However, when 5 dpf larvae were inoculated, the proportion of vegetative cells in larvae increased, revealing proliferation of the inoculated bacteria and better colonization of the host. In conclusion, these results suggest that it is feasible to colonize zebrafish larvae with some human bacteria, such as C. difficile and Bacillus and open an interesting area to study interactions between these microorganisms and the host. © 2018 Valenzuela, Caruffo, Herrera, Medina, Coronado, Feijóo, Muñoz, Garrido, Troncoso, Figueroa, Toro, Reyes-Jara, Magne and Navarrete.https://www.frontiersin.org/articles/10.3389/fmicb.2018.01032/ful

Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment

The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical–chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex

Aquatic mammal fossils in Latin America – a review of records, advances and challenges in research in the last 30 years

Records of aquatic mammal fossils (e.g. cetaceans, pinnipeds, sirenians, mustelids, and desmostylians) from Latin America (Mexico to Tierra del Fuego, including Antartica) span since the mid-1800s. Aquatic mammal fossils received little attention from the scientific community, with most of the first studies conducted by Northern Hemisphere researchers. Over the last 30 years, paleontological research in Latin America has increased considerably, with descriptions of several new species and revisions of published original records. The Latin American fossil record of marine mammals spans from the Eocene to the Pleistocene, with formations and specimens of global significance. All three main groups of cetaceans are represented in the continent (Archaeoceti, Mysticeti, and Odontoceti). Pinnipedia are represented by the families Otariidae and Phocidae, with records starting in the Middle Miocene. Both living families of Sirenia (Trichechidae and Dugongidae) are recorded. While less common, but still relevant, records of desmostylians and mustelids are known from Oligocene and Miocene deposits. This review provides a summary of the aquatic mammals known to date, with a special focus on the advances and developments of the last 30 years, since Cozzuol’s (1996) review of the South American fossil record. An up-to-date complete list of species based on the literature and unpublished data is also provided. The study also provides future directions for paleontological research in Latin America, and discusses the challenges and opportunities in the field, including the emergence of a strong new generation of Latin American researchers, many of whom are women. Keywords: Cetacea, Pinnipedia, Sirenia, Southern Hemispher

Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology.

Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care

Pathological variants in TOP3A cause distinct disorders of mitochondrial and nuclear genome stability

Topoisomerase 3α (TOP3A) is an enzyme that removes torsional strain and interlinks between DNA molecules. TOP3A localises to both the nucleus and mitochondria, with the two isoforms playing specialised roles in DNA recombination and replication respectively. Pathogenic variants in TOP3A can cause a disorder similar to Bloom syndrome, which results from bi-allelic pathogenic variants in BLM, encoding a nuclear-binding partner of TOP3A. In this work, we describe 11 individuals from 9 families with an adult-onset mitochondrial disease resulting from bi-allelic TOP3A gene variants. The majority of patients have a consistent clinical phenotype characterised by bilateral ptosis, ophthalmoplegia, myopathy and axonal sensory-motor neuropathy. We present a comprehensive characterisation of the effect of TOP3A variants, from individuals with mitochondrial disease and Bloom-like syndrome, upon mtDNA maintenance and different aspects of enzyme function. Based on these results, we suggest a model whereby the overall severity of the TOP3A catalytic defect determines the clinical outcome, with milder variants causing adult-onset mitochondrial disease and more severe variants causing a Bloom-like syndrome with mitochondrial dysfunction in childhood

Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases

Altres ajuts: Generalitat de Catalunya, Departament de Salut; Generalitat de Catalunya, Departament d'Empresa i Coneixement i CERCA Program; Ministerio de Ciencia e Innovación; Instituto Nacional de Bioinformática; ELIXIR Implementation Studies (CNAG-CRG); Centro de Investigaciones Biomédicas en Red de Enfermedades Raras; Centro de Excelencia Severo Ochoa; European Regional Development Fund (FEDER).Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%)

Unexpected decadal density-dependent shifts in California sea lion size, morphology, and foraging niche. Valenzuela-Toro et al.

Original morphological and carbon and nitrogen stable isotope measurements of California sea lions (Data S1-S4). Population counts and estimations of California sea lions on the west coast of the United States from the literature (Data S5-S8; S10-S19). Records of Pacific sardine and northern anchovy catches from the eastern North Pacific from the literature (Data S9).Original R code used for analyses and data visualization (zip file

Unexpected decadal density-dependent shifts in California sea lion size, morphology, and foraging niche. Valenzuela-Toro et al.

Original morphological and carbon and nitrogen stable isotope measurements of California sea lions (Data S1-S4). Population counts and estimations of California sea lions on the west coast of the United States from the literature (Data S5-S8; S10-S19). Records of Pacific sardine and northern anchovy catches from the eastern North Pacific from the literature (Data S9).Original R code used for analyses and data visualization (zip file)THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Pioneers of a Century of Anatomical Teaching in the City of Concepción, Chile

Reviewing a century of history, the development of anatomical activities in the city of Concepcion, in the south of Chile, did not occur without difficulties. The present work gathered the historical background related with the beginnings and development of Anatomy teaching at the Universidad de Concepcion. Research was carried out including the review of historical books, magazines, digital archives and institutional records such as files or photographic archives. The foundation of the university, the beginnings of anatomical activities in 1919 and the contribution of its highlighted pioneers, show the difficulties of teaching this discipline in Chile. From a historical perspective, having knowledge during this century of teaching, the physical resources used in cadaveric dissection, the detail of teaching methodologies applied, and the anatomical resources available, contribute the anatomy's development knowledge in Chile