Water Buffalo Genome Science Comes of Age

The water buffalo is vital to the lives of small farmers and to the economy of many countries worldwide. Not only are they draught animals, but they are also a source of meat, horns, skin and particularly the rich and precious milk that may be converted to creams, butter, yogurt and many cheeses. Genome analysis of water buffalo has advanced significantly in recent years. This review focuses on currently available genome resources in water buffalo in terms of cytogenetic characterization, whole genome mapping and next generation sequencing. No doubt, these resources indicate that genome science comes of age in the species and will provide knowledge and technologies to help optimize production potential, reproduction efficiency, product quality, nutritional value and resistance to diseases. As water buffalo and domestic cattle, both members of the Bovidae family, are closely related, the vast amount of cattle genetic/genomic resources might serve as shortcuts for the buffalo community to further advance genome science and biotechnologies in the species

Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the african continent

The disease caused by the apicomplexan protozoan parasite Theileria parva, known as East Coast fever or Corridor disease, is one of the most serious cattle diseases in Eastern, Central, and Southern Africa. We performed whole-genome sequencing of nine T. parva strains, including one of the vaccine strains (Kiambu 5), field isolates from Zambia, Uganda, Tanzania, or Rwanda, and two buffalo-derived strains. Comparison with the reference Muguga genome sequence revealed 34 814–121 545 single nucleotide polymorphisms (SNPs) that were more abundant in buffalo-derived strains. High-resolution phylogenetic trees were constructed with selected informative SNPs that allowed the investigation of possible complex recombination events among ancestors of the extant strains. We further analysed the dN/dS ratio (non-synonymous substitutions per non-synonymous site divided by synonymous substitutions per synonymous site) for 4011 coding genes to estimate potential selective pressure. Genes under possible positive selection were identified that may, in turn, assist in the identification of immunogenic proteins or vaccine candidates. This study elucidated the phylogeny of T. parva strains based on genome-wide SNPs analysis with prediction of possible past recombination events, providing insight into the migration, diversification, and evolution of this parasite species in the African continent

Sequencing technologies and genome sequencing

The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research

Whole genome single nucleotide polymorphism (SNP) transfer from cattle to water buffalo

Single nucleotide polymorphisms (SNPs) represent the most abundant form of genetic variation serving as valuable tools for linking genes to normal physiological changes, diseases, and responses to pathogens, chemicals, drugs, vaccines and adaption to environmental changes. In recent years, the cattle research community has discovered a large number of SNPs in the genome of the species. These publicly available SNPs have led to the development of a high-density SNP genotyping microarray with 54,001 bovine SNPs, most of which have been mapped to the current bovine genome assembly Btau_4.0; we annotated the SNPs on a whole genome level. We classified these SNPs into intergenic (between-gene) and intragenic (within-gene) categories and found that most genes do not have an intragenic SNP. In contrast, all intergenic regions have at least 1 SNP and there are many more intergenic SNPs than intragenic SNPs. Kernel density plots also identified SNP-poor and SNP-rich regions on each bovine chromosome. In contrast to cattle, SNP resources in water buffalo are decidedly lacking; the community has however, started to work on genome sequencing, mapping and phylogenetic investigation of the species. Due to the similarities between cattle and water buffalo, we investigated the cross-species transferability of the 52,255 SNPs on the BovineSNP50 Genotyping BeadChip placed in Btau_4.0. Among them, only ~10% had no calls and of the called SNPs, only 3,067 remained polymorphic in water buffalo. Of the transferable SNPs, 37.2% were intragenic and 62.8% intergenic. We also targeted 20 genes associated with muscle growth and development and found that 15 genes had a total of 69 SNPs on the BovineSNP50 BeadChip; among them, 56 were genotyped on ≥9 water buffalo samples. Overall, our present annotation and characterization of the BovineSNP50 BeadChip will help users design their experiments and explain their results. Our work may also provide some useful suggestions on updating the bovine SNP array in the near future. Furthermore, the results of this research make it possible to identify potential economically important genes in water buffalo, set groundwork for future water buffalo research, and develop genomic technologies for advancing water buffalo genome science and applications

Il Ciclo Combinato della centrale Enel di La Casella. Analisi tecnica del funzionamento in esercizio flessibile e proposta di interventi migliorativi

Con l’avvento del mercato dell’energia si è accresciuta la competizione tra i produttori di energia per far fronte alla variabilità nella domanda e nell’offerta sul mercato. Visti i competitivi costi di esercizio che caratterizzano i cicli combinati, questi si trovano sempre più frequentemente ad operare in condizioni di funzionamento altamente variabili coprendo non solo fasce di “carico base” ma anche fasce di “carico intermedio”. In questa ottica risultano più appetibili sul mercato impianti a ciclo combinato adatti ad operare in regime flessibile, caratterizzato dal susseguirsi di avviamenti, fermate e frequenti e rapide variazioni di carico, in un campo di esercizio il più possibile ampio, per rispondere alle logiche della borsa elettrica e mantenere l’impianto attivo solo quando sono positivi i margini di guadagno. Questa tesi, elaborata per il conseguimento della Laurea in Ingegneria Meccanica, propone delle soluzioni di adeguamento degli impianti a ciclo combinato per rispondere alle esigenze di flessibilità operativa, in particolare per migliorare la riduzione delle prestazioni ai carichi parziali e velocizzare le manovre di avviamento da freddo dell’impianto