Search results for "Genome"
showing 10 items of 1913 documents
Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers
2023
Acknowledgements: The authors thank G. Marciani and O. Jöris for comments on archaeology; C. Jeong, M. Spyrou and K. Prüfer for comments on genetics; M. O’Reilly for graphical support for Fig. 5 and Extended Data Fig. 9; the entire IT and laboratory teams at the Department of Archaeogenetics of MPI-SHH for technical assistance; M. Meyer and S. Nagel for support with single-stranded library preparation; K. Post, P. van Es, J. Glimmerveen, M. Medendorp, M. Sier, S. Dikstra, M. Dikstra, R. van Eerden, D. Duineveld and A. Hoekman for providing access to human specimens from the North Sea (The Netherlands); M. D. Garralda and A. Estalrrich for providing access to human specimens from La Riera (S…
Ancient human genomes suggest three ancestral populations for present-day Europeans
2014
We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1,2,3,4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these popula…
Genome Stability in Embryonic Stem Cells
2011
Paola Rebuzzini1, Maurizio Zuccotti2*, Carlo Alberto Redi1,3 and Silvia Garagna1,4,5* 1Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia Animale, Universita degli Studi di Pavia, Via Ferrata 9, 27100 Pavia, 2Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, Universita degli Studi di Parma, Via Volturno 39, 43100 Parma 3Fondazione I.R.C.C.S. Policlinico San Matteo, Piazzale Golgi, 19, 27100 Pavia 4Centro di Ricerca Interdipartimentale di Ingegneria Tissutale, Universita degli Studi di Pavia, Via Ferrata 1, 27100 Pavia 5Centro di Eccellenza in Biologia Applicata, Universita degli Studi di Pavia, Via Ferrata 9, 27100 Pavia Italy
Evolutionary conservation and function of the human embryonic stem cell specific miR-302/367 cluster
2015
miRNA clusters define a group of related miRNAs closely localized in the genome with an evolution that remains poorly understood. The miR-302/367 cluster represents a single polycistronic transcript that produces five precursor miRNAs. The cluster is highly expressed and essential for maintenance of human embryonic stem cells. We found the cluster to be highly conserved and present in most mammals. In primates, seed sequence and miRNA structure are conserved, but inter-precursor sequences are evolving. Insertions of new miRNAs, deletions of individual miRNAs, and a cluster duplication observed in different species suggest an actively evolving cluster. Core transcriptional machinery consisti…
The Complex Regulatory Role of Cytomegalovirus Nuclear Egress Protein pUL50 in the Production of Infectious Virus
2021
The regulation of the nucleocytoplasmic release of herpesviral capsids is defined by the process of nuclear egress. Due to their large size, nuclear capsids are unable to traverse via nuclear pores, so that herpesviruses evolved to develop a vesicular transport pathway mediating their transition through both leaflets of the nuclear membrane. This process involves regulatory proteins, which support the local distortion of the nuclear envelope. For human cytomegalovirus (HCMV), the nuclear egress complex (NEC) is determined by the pUL50-pUL53 core that initiates multicomponent assembly with NEC-associated proteins and capsids. Hereby, pUL50 serves as a multi-interacting determinant that recru…
Genomics Meets Cancer Immunotherapy
2014
High-throughput cancer genomics and bioinformatics are revolutionizing our ability to profile tumor samples. With next-generation sequencing (NGS) and high-performance computing (HPC) platforms, we have developed the infrastructures to determine and characterize tumor genomes and transcriptomes within days. Now, we are integrating these platforms into both cancer immunology and patient therapy decision-making. Here, we briefly describe the technology platforms and highlight several emerging applications: profiling of tumor mutations and gene expression; determination of HLA type and tumor expression, enabling prediction of immunogenic tumor mutations; and identification of viruses present i…
Parallelized short read assembly of large genomes using de Bruijn graphs
2011
Abstract Background Next-generation sequencing technologies have given rise to the explosive increase in DNA sequencing throughput, and have promoted the recent development of de novo short read assemblers. However, existing assemblers require high execution times and a large amount of compute resources to assemble large genomes from quantities of short reads. Results We present PASHA, a parallelized short read assembler using de Bruijn graphs, which takes advantage of hybrid computing architectures consisting of both shared-memory multi-core CPUs and distributed-memory compute clusters to gain efficiency and scalability. Evaluation using three small-scale real paired-end datasets shows tha…
An Unexplained Congenital Disorder of Glycosylation-II in a Child with Neurohepatic Involvement, Hypercholesterolemia and Hypoceruloplasminemia
2017
We report on a 12-year-old adopted boy with psychomotor disability, absence seizures, and normal brain MRI. He showed increased (but initially, at 5 months, normal) serum cholesterol, increased alkaline phosphatases, transiently increased transaminases and hypoceruloplasminemia with normal serum and urinary copper. Blood levels of immunoglobulins, haptoglobin, antithrombin, and factor XI were normal. A type 2 serum transferrin isoelectrofocusing and hypoglycosylation of apoCIII pointed to a combined N- and O-glycosylation defect. Neither CDG panel analysis with 79 CDG-related genes, nor whole exome sequencing revealed the cause of this CDG. Whole genome sequencing was not performed since th…
Estrogen-Induced Mutations and Its Role in the Development of Tumorigenesis
2006
Using RAPD-PCR fingerprinting, the detection of mutations induced by estrogen (E) exposure was studied in nonmalignant- and malignant cells. Cells exposed to 17α-and 17β-estradiol, diethylstilbestrol, bisphenol A, and α-zearalanol induced mutations in different regions of the genome. They consisted of insertion/deletion as a result of point or length mutations and quantitative changes as a result of hypoploidy or polyploidy. We also detected several mutated loci in tumor-free tissues, adjacent to tumors, and DES-induced tumors. The data suggest that these mutations occurred in early stages of stilbene E-induced renal carcinogenesis, and that they may be induced as a result of stilbene E tre…
Closely Related Archaeal Haloarcula hispanica Icosahedral Viruses HHIV-2 and SH1 Have Nonhomologous Genes Encoding Host Recognition Functions
2012
Studies on viral capsid architectures and coat protein folds have revealed the evolutionary lineages of viruses branching to all three domains of life. A widespread group of icosahedral tailless viruses, the PRD1-adenovirus lineage, was the first to be established. A double -barrel fold for a single major capsid protein is characteristic of these viruses. Similar viruses carrying genes coding for two major capsid proteins with a more complex structure, such as Thermus phage P23-77 and haloarchaeal virus SH1, have been isolated. Here, we studied the host range, life cycle, biochemical composition, and genomic sequence of a new isolate, Haloarcula hispanica icosahedral virus 2 (HHIV-2), which…