Search results for "genomics"
showing 10 items of 1255 documents
Type IV Laryngotracheoesophageal Cleft Associated with Type III Esophageal Atresia in 1p36 Deletions Containing the RERE Gene: Is There a Causal Role…
2018
The causes of embryological developmental anomalies leading to laryngotracheoesophageal clefts (LTECs) are not known, but are proposed to be multifactorial, including genetic and environmental factors. Haploinsufficiency of the RERE gene might contribute to different phenotypes seen in individuals with 1p36 deletions. We describe a neonate of an obese mother, diagnosed with type IV LTEC and type III esophageal atresia (EA), in which a 1p36 deletion including the RERE gene was detected. On the second day of life, a right thoracotomy and extrapleural esophagus atresia repair were attempted. One week later, a right cervical approach was performed to separate the cervical esophagus from the tra…
The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
2017
We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. ch…
OSAnalyzer: A Bioinformatics Tool for the Analysis of Gene Polymorphisms Enriched with Clinical Outcomes.
2016
Background: The identification of biomarkers for the estimation of cancer patients’ survival is a crucial problem in modern oncology. Recently, the Affymetrix DMET (Drug Metabolizing Enzymes and Transporters) microarray platform has offered the possibility to determine the ADME (absorption, distribution, metabolism, and excretion) gene variants of a patient and to correlate them with drug-dependent adverse events. Therefore, the analysis of survival distribution of patients starting from their profile obtained using DMET data may reveal important information to clinicians about possible correlations among drug response, survival rate, and gene variants. Methods: In order to provide support …
De Novo Genome Assembly of the Raccoon Dog (Nyctereutes Procyonoides)
2021
The raccoon dog, Nyctereutes procyonoides (NCBI Taxonomy ID: 34880, Figure 1a) belongs to the family Canidae, with foxes (genus Vulpes) being their closest relatives (Lindblad-Toh et al., 2005; Sun et al., 2019). Its original distribution in East Asia ranges from south-eastern Siberia to northern Vietnam and the Japanese islands. In the early 20th century, the raccoon dog was introduced into Western Russia for fur breeding and hunting purposes, which led to its widespread establishment in many European countries, Figure 1b. Together with the raccoon (Procyon lotor), it is now listed in Europe as an invasive species of Union concern (Regulation (EU) No. 1143/2014) and member states are requi…
Genome-wide scan of fat-tail sheep identifies signals of selection for fat deposition and adaptation
2018
Fat tail in sheep represents a valuable energy reserve for facing future climate changes. The identification of genes with a role in the fat-tail phenotype may contribute to understanding the physiology of fat deposition and the mechanisms of adaptation. Genotypic data obtained with the OvineSNP50K array in 13 thin-tail sheep breeds from Italy were used to identify selection signatures of fat tail through pairwise thin- versus fat-tail sheep breed comparisons, with the following fat-tail breeds of the Mediterranean area: two unique Italian fat-tail breeds (Barbaresca and Laticauda), a Barbary sheep breed from Libya, Ossimi breed from Egypt, Cyprus Fat-Tail and Chios from the Greek islands …
Bacteria classification using minimal absent words
2017
Bacteria classification has been deeply investigated with different tools for many purposes, such as early diagnosis, metagenomics, phylogenetics. Classification methods based on ribosomal DNA sequences are considered a reference in this area. We present a new classificatier for bacteria species based on a dissimilarity measure of purely combinatorial nature. This measure is based on the notion of Minimal Absent Words, a combinatorial definition that recently found applications in bioinformatics. We can therefore incorporate this measure into a probabilistic neural network in order to classify bacteria species. Our approach is motivated by the fact that there is a vast literature on the com…
Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-s…
2019
AbstractMetagenomic studies have revolutionized the study of novel phages. However these studies trade the depth of coverage for breadth. In this study we show that the targeted sequencing of a phage genomic region as small as 200-300 base pairs, can provide sufficient sequence diversity to serve as an individual-specific barcode or “Phageprint”. The targeted approach reveals a high-resolution view of phage communities that is not available through metagenomic datasets. By creating instructional videos and collection kits, we enabled citizen scientists to gather ∼700 oral samples spanning ∼100 individuals residing in different parts of the world. In examining phage communities at 6 differen…
DNA folds threaten genetic stability and can be leveraged for chemotherapy
2020
International audience; Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an…
Balancing of mitochondrial translation through METTL8-mediated m3C modification of mitochondrial tRNAs.
2021
Mitochondria contain a specific translation machinery for the synthesis of mitochondria-encoded respiratory chain components. Mitochondrial tRNAs (mt-tRNAs) are also generated from the mitochondrial DNA and, similar to their cytoplasmic counterparts, are post-transcriptionally modified. Here, we find that the RNA methyltransferase METTL8 is a mitochondrial protein that facilitates 3-methyl-cytidine (m3C) methylation at position C32 of the mt-tRNASer(UCN) and mt-tRNAThr. METTL8 knockout cells show a reduction in respiratory chain activity, whereas overexpression increases activity. In pancreatic cancer, METTL8 levels are high, which correlates with lower patient survival and an enhanced resp…
DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes
2019
Abstract Epigenomics is the study of modifications on the genetic material of a cell that do not depend on changes in the DNA sequence, since those latter involve specific proteins around which DNA wraps. The end result is that Epigenomic changes have a fundamental role in the proper working of each cell in Eukaryotic organisms. A particularly important part of Epigenomics concentrates on the study of chromatin, that is, a fiber composed of a DNA-protein complex and very characterizing of Eukaryotes. Understanding how chromatin is assembled and how it changes is fundamental for Biology. In more than thirty years of research in this area, Mathematics and Theoretical Computer Science have gai…