Computational Methods for Sequencing and Analysis of Heterogeneous RNA Populations

Next-generation sequencing (NGS) and mass spectrometry technologies bring unprecedented throughput, scalability and speed, facilitating the studies of biological systems. These technologies allow to sequence and analyze heterogeneous RNA populations rather than single sequences. In particular, they provide the opportunity to implement massive viral surveillance and transcriptome quantification. However, in order to fully exploit the capabilities of NGS technology we need to develop computational methods able to analyze billions of reads for assembly and characterization of sampled RNA populations. In this work we present novel computational methods for cost- and time-effective analysis of sequencing data from viral and RNA samples. In particular, we describe: i) computational methods for transcriptome reconstruction and quantification; ii) method for mass spectrometry data analysis; iii) combinatorial pooling method; iv) computational methods for analysis of intra-host viral populations

Krausz dimension and its generalizations in special graph classes

A {\it krausz $(k,m)$-partition} of a graph $G$ is the partition of $G$ into cliques, such that any vertex belongs to at most $k$ cliques and any two cliques have at most $m$ vertices in common. The {\it $m$-krausz} dimension $kdim_m(G)$ of the graph $G$ is the minimum number $k$ such that $G$ has a krausz $(k,m)$-partition. 1-krausz dimension is known and studied krausz dimension of graph $kdim(G)$. In this paper we prove, that the problem $"kdim(G)\leq 3"$ is polynomially solvable for chordal graphs, thus partially solving the problem of P. Hlineny and J. Kratochvil. We show, that the problem of finding $m$-krausz dimension is NP-hard for every $m\geq 1$, even if restricted to (1,2)-colorable graphs, but the problem $"kdim_m(G)\leq k"$ is polynomially solvable for $(\infty,1)$-polar graphs for every fixed $k,m\geq 1$

Introducing Parallelism to First-Year CS Majors

We propose to strengthen the computer science (CS) curriculum by embedding parallel concepts in a required first-semester seminar taken by all incoming declared CS majors. We introduce students to parallel computing concepts through a series of unplugged activities so that students see parallel approaches as a natural form of solution to a task. We describe a pilot offering of the class and activities, with measurements and analysis of what students self-report and their performance on assessments

Mitochondrial genetic diversity, selection and recombination in a canine transmissible cancer.

Canine transmissible venereal tumour (CTVT) is a clonally transmissible cancer that originated approximately 11,000 years ago and affects dogs worldwide. Despite the clonal origin of the CTVT nuclear genome, CTVT mitochondrial genomes (mtDNAs) have been acquired by periodic capture from transient hosts. We sequenced 449 complete mtDNAs from a global population of CTVTs, and show that mtDNA horizontal transfer has occurred at least five times, delineating five tumour clades whose distributions track two millennia of dog global migration. Negative selection has operated to prevent accumulation of deleterious mutations in captured mtDNA, and recombination has caused occasional mtDNA re-assortment. These findings implicate functional mtDNA as a driver of CTVT global metastatic spread, further highlighting the important role of mtDNA in cancer evolution.Wellcome Trust Investigator Award, 102942/Z/13/A Elizabeth P Murchison Leverhulme Trust Philip Leverhulme Prize Elizabeth P Murchison Royal Society Research Grant, RG130615 Elizabeth P Murchiso

Somatic evolution and global expansion of an ancient transmissible cancer lineage

Made available in DSpace on 2019-10-06T15:53:36Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-08-02GPD Charitable TrustLeverhulme TrustThe canine transmissible venereal tumor (CTVT) is a cancer lineage that arose several millennia ago and survives by “metastasizing” between hosts through cell transfer. The somatic mutations in this cancer record its phylogeography and evolutionary history. We constructed a time-resolved phylogeny from 546 CTVT exomes and describe the lineage's worldwide expansion. Examining variation in mutational exposure, we identify a highly context-specific mutational process that operated early in the cancer's evolution but subsequently vanished, correlate ultraviolet-light mutagenesis with tumor latitude, and describe tumors with heritable hyperactivity of an endogenous mutational process. CTVT displays little evidence of ongoing positive selection, and negative selection is detectable only in essential genes. We illustrate how long-lived clonal organisms capture changing mutagenic environments, and reveal that neutral genetic drift is the dominant feature of long-term cancer evolution.Transmissible Cancer Group Department of Veterinary Medicine University of CambridgeAnimal Management in Rural and Remote Indigenous Communities (AMRRIC)World VetsAnimal Shelter Stichting Dierenbescherming SurinameSikkim Anti-Rabies and Animal Health Programme Department of Animal Husbandry Livestock Fisheries and Veterinary Services Government of SikkimRoyal (Dick) School of Veterinary Studies Roslin Institute University of Edinburgh Easter Bush CampusConserLab Animal Preventive Medicine Department Faculty of Animal and Veterinary Sciences University of ChileCorozal Veterinary Hospital University of PanamáSt. George's UniversityNakuru District Veterinary Scheme LtdAnimal Medical CentreInternational Animal Welfare Training Institute UC Davis School of Veterinary MedicineCentro Universitário de Rio Preto (UNIRP)Department of Clinical and Veterinary Surgery São Paulo State University (UNESP)Ladybrand Animal ClinicVeterinary Clinic Sr. Dog'sWorld Vets Latin America Veterinary Training CenterNational Veterinary Research InstituteAnimal ClinicIntermunicipal Stray Animals Care Centre (DIKEPAZ)Animal Protection Society of SamoaFaculty of Veterinary Science University of ZuliaVeterinary Clinic BIOCONTROLFaculty of Veterinary Medicine School of Health Sciences University of ThessalyVeterinary Clinic El Roble Animal Healthcare Network Faculty of Animal and Veterinary Sciences University of ChileOnevetGroup Hospital Veterinário BernaUniversidade Vila VelhaVeterinary Clinic ZoovetservisÉcole Inter-états des Sciences et Médecine Vétérinaires de DakarDepartment of Small Animal Medicine Faculty of Veterinary Medicine Utrecht UniversityVetexpert Veterinary GroupVeterinary Clinic Lopez QuintanaClinique Veterinaire de Grand Fond Saint Gilles les BainsDepartment of Veterinary Sciences University of MessinaFacultad de Medicina Veterinaria y Zootecnia Universidad Autónoma del Estado de MéxicoSchool of Veterinary Medicine Universidad de las AméricasCancer Development and Innate Immune Evasion Lab Champalimaud Center for the UnknownTouray and Meyer Vet ClinicHillside Animal HospitalKampala Veterinary SurgeryAsavet Veterinary CharitiesVets Beyond BordersFaculty of Veterinary Medicine Autonomous University of YucatanLaboratorio de Patología Veterinaria Universidad de CaldasInterdisciplinary Centre of Research in Animal Health (CIISA) Faculty of Veterinary Medicine University of LisbonFour Paws InternationalHelp in SufferingVeterinary Clinic Dr José RojasDepartment of Biotechnology Balochistan University of Information Technology Engineering and Management SciencesCorozal Veterinary ClinicVeterinary Clinic VetmasterState Hospital of Veterinary MedicineJomo Kenyatta University of Agriculture and TechnologyLaboratory of Biomedicine and Regenerative Medicine Department of Clinical Sciences Faculty of Animal and Veterinary Sciences University of ChileFaculty of Veterinary and Agricultural Sciences University of MelbourneAnimal Anti Cruelty LeagueClinical Sciences Department Faculty of Veterinary Medicine BucharestDepartment of Pathology Faculty of Veterinary Medicine Ankara UniversityFaculty of Veterinary Sciences National University of AsuncionLilongwe Society for Protection and Care of Animals (LSPCA)Wellcome Sanger InstituteDepartment of Cellular and Molecular Medicine University of California San DiegoDepartment of Clinical and Veterinary Surgery São Paulo State University (UNESP)Leverhulme Trust: 102942/Z/13/

Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer

Abstract: Autonomous replication and segregation of mitochondrial DNA (mtDNA) creates the potential for evolutionary conflict driven by emergence of haplotypes under positive selection for ‘selfish’ traits, such as replicative advantage. However, few cases of this phenomenon arising within natural populations have been described. Here, we survey the frequency of mtDNA horizontal transfer within the canine transmissible venereal tumour (CTVT), a contagious cancer clone that occasionally acquires mtDNA from its hosts. Remarkably, one canine mtDNA haplotype, A1d1a, has repeatedly and recently colonised CTVT cells, recurrently replacing incumbent CTVT haplotypes. An A1d1a control region polymorphism predicted to influence transcription is fixed in the products of an A1d1a recombination event and occurs somatically on other CTVT mtDNA backgrounds. We present a model whereby ‘selfish’ positive selection acting on a regulatory variant drives repeated fixation of A1d1a within CTVT cells

Gas to Liquids – Historical Development and Future Prospects

While GTL or ‘Gas to Liquids’ is frequently referred to in natural gas circles, apart from project-specific summaries produced by the sponsoring companies, there is little in the way of contemporary literature to set the context for GTL against the backdrop of today’s increasingly connected global gas situation. As with many technological advances, ‘necessity was the mother of invention’ for the Fischer Tropsch Gas to Liquid (FTGTL) process in Germany during World War II and in South Africa during the long period of OPEC and UN oil sanctions. This paper reviews the genesis of the technology in these countries and also subsequent related applications in Malaysia, New Zealand and Alaska. The major expansion in FTGTL production in Qatar can be seen as a strategic push to diversify market monetisation channels by this major gas resource holder. The Oryx project in particular provides sufficient cost and operating data from which the wider economic characteristics of FTGTL can be broadly assessed.</p

Gas to Liquids – Historical Development and Future Prospects: OIES paper: NG 80

While GTL or ‘Gas to Liquids’ is frequently referred to in natural gas circles, apart from project-specific summaries produced by the sponsoring companies, there is little in the way of contemporary literature to set the context for GTL against the backdrop of today’s increasingly connected global gas situation. As with many technological advances, ‘necessity was the mother of invention’ for the Fischer Tropsch Gas to Liquid (FTGTL) process in Germany during World War II and in South Africa during the long period of OPEC and UN oil sanctions. This paper reviews the genesis of the technology in these countries and also subsequent related applications in Malaysia, New Zealand and Alaska. The major expansion in FTGTL production in Qatar can be seen as a strategic push to diversify market monetisation channels by this major gas resource holder. The Oryx project in particular provides sufficient cost and operating data from which the wider economic characteristics of FTGTL can be broadly assessed.</p