30 research outputs found

    From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)

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    Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA

    Smooth-muscle myosin mutations in hereditary non-polyposis colorectal cancer syndrome

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    We examined adenomas and cancers from hereditary non-polyposis colorectal cancer (HNPCC) syndrome patients for the presence of frameshift mutations in the smooth-muscle myosin gene, MYH11. Our results show that mutations in MYH11 occur more frequently in cancers than adenomas (P=0.008) and are dependent on microsatellite instability (MSI+)

    Correction: Exome Sequencing in an Admixed Isolated Population IndicatesNFXL1 Variants Confer a Risk for Specific Language Impairment

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    Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10–4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model

    Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

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    Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

    Genetics of chloroquine-resistant malaria: a haplotypic view

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    Molting while breeding? Lessons from New World Tyrannus Flycatchers

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    Songbirds must annually undergo two energetically demanding but important activities: breeding and feather molt. Due to the high energetic investment that each demands, these two events are generally not carried out simultaneously. However, substantial variation in the level of annual reproductive investment among populations may result in variation in molt-breeding overlap between them. With the goal of understanding whether different songbird populations overlap molt and breeding, and, if so, to determine directions for research on the potential tradeoffs involved, we describe the relationship between clutch size, molt, and energetic condition within a genus of New World Flycatchers (Tyrannus). Of 219 Flycatchers sampled, only one individual molted flight feathers while breeding, suggesting that molting flight feathers and breeding simultaneously is too energetically expensive at any clutch size. However, some Flycatchers molted body feathers during the breeding season. When we tested for an effect of clutch size, sex and energetic condition on body molt intensity during the breeding season, only clutch size and sex had significant effects, with a negative effect of clutch size on body molt intensity in males but not in females. Based on these results, we develop a set of hypotheses to guide future studies on the potential tradeoffs between investment in reproduction and molt.Fil: Jahn, Alex E.. Universidade Estadual Paulista; BrasilFil: Bejarano, Vanesa. Universidade Estadual Paulista; BrasilFil: Benavides Guzmán, Marcela. Universidade Estadual Paulista; BrasilFil: Brown, Leone M.. University of Georgia; Estados UnidosFil: Carvalho Provinciato, Ivan C.. Universidade Estadual Paulista; BrasilFil: Cereghetti, Joaquín. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Cueto, Víctor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Centro de Investigación Esquel de Montaña y Estepa Patagóica. Universidad Nacional de la Patagonia "San Juan Bosco". Facultad de Ciencias Naturales - Sede Esquel. Centro de Investigación Esquel de Montaña y Estepa Patagónica; ArgentinaFil: Giraldo, José I.. Aves Internacionales-Colombia; ColombiaFil: Gómez Bahamón, Valentina. Universidad de los Andes; ColombiaFil: Husak, Michael S.. Cameron University; Estados UnidosFil: LePage, Heather K.. Oklahoma State University; Estados UnidosFil: MacPherson, Maggie. Tulane University; Estados UnidosFil: Marini, Miguel Ângelo. Universidade do Brasília; BrasilFil: Pizo, Marco Aurelio. Universidade Estadual Paulista; BrasilFil: Quickle, Aaron. Cameron University; Estados UnidosFil: Roeder, Diane V.. Cameron University; Estados UnidosFil: Sarasola, José Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; Argentina. Universidad Nacional de La Pampa; ArgentinaFil: Tuero, Diego Tomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentin
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