Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

BACKGROUND: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.The authors would like to thank Alain Vignal and Thomas Faraut of INRA Toulouse (France) for access to the duck chromosome assembly data. This research was funded in part by PL-Grid Infrastructure (DML), Biotechnology and Biological Sciences Research Council BB/K008161 (DML, DKG), BB/K008226/1 (DML), BB/J010170/1 (DML, MF) and a knowledge transfer partnership award (DKG and Cytocell Ltd). The authors are grateful to Malcolm Ferguson-Smith’s lab (Cambridge, UK) for producing the flow-sorted chicken microchromosome paints. We also thank Cytocell Ltd (Cambridge, UK) for technical support in FISH technologies.This article was originally published in BMC Genomics 2014, 15:1060 doi:10.1186/1471-2164-15-106

Acquired resistance to oxaliplatin is not directly associated with increased resistance to DNA damage in SK-N-ASrOXALI4000, a newly established oxaliplatin-resistant sub-line of the neuroblastoma cell line SK-N-AS

The formation of acquired drug resistance is a major reason for the failure of anti-cancer therapies after initial response. Here, we introduce a novel model of acquired oxaliplatin resistance, a sub-line of the non-MYCN-amplified neuroblastoma cell line SK-N-AS that was adapted to growth in the presence of 4000 ng/mL oxaliplatin (SK-N-ASrOXALI4000). SK-N-ASrOXALI4000 cells displayed enhanced chromosomal aberrations compared to SK-N-AS, as indicated by 24-chromosome fluorescence in situ hybridisation. Moreover, SK-N-ASrOXALI4000 cells were resistant not only to oxaliplatin but also to the two other commonly used anti-cancer platinum agents cisplatin and carboplatin. SK-N-ASrOXALI4000 cells exhibited a stable resistance phenotype that was not affected by culturing the cells for 10 weeks in the absence of oxaliplatin. Interestingly, SK-N-ASrOXALI4000 cells showed no cross resistance to gemcitabine and increased sensitivity to doxorubicin and UVC radiation, alternative treatments that like platinum drugs target DNA integrity. Notably, UVC-induced DNA damage is thought to be predominantly repaired by nucleotide excision repair and nucleotide excision repair has been described as the main oxaliplatin-induced DNA damage repair system. SK-N-ASrOXALI4000 cells were also more sensitive to lysis by influenza A virus, a candidate for oncolytic therapy, than SK-N-AS cells. In conclusion, we introduce a novel oxaliplatin resistance model. The oxaliplatin resistance mechanisms in SK-N-ASrOXALI4000 cells appear to be complex and not to directly depend on enhanced DNA repair capacity. Models of oxaliplatin resistance are of particular relevance since research on platinum drugs has so far predominantly focused on cisplatin and carboplatin

Identification of host factors which restrict African swine fever virus replication

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Identification of host factors which restrict African swine fever virus replication

African swine fever (ASF) is a fatal haemorrhagic disease of domestic pigs. The etiological agent of ASF is African swine fever virus (ASFV), a large DNA virus and only member of the Asfarviridae family. The virus replicates in macrophages and infection has previously been suggested to correlate with expression of cell surface markers, including CD163, which is a characteristic marker of intermediate and late stages of macrophage differentiation. ASFV cell tropism and host factors which modulate infection have not previously been studied extensively in macrophages. Macrophages retain a plasticity of function in vivo and in vitro and alter their phenotype in response to various stimuli. This allows them to respond to a variety of situations. The impact of priming macrophages by different stimuli on ASFV infection rates was investigated. The results provide information relevant to identifying cellular factors which modulate infection in vitro and in vivo. To characterise the impact of macrophage activation on ASFV replication, adherent porcine bone marrow cells were stimulated to form regulatory, classically or alternatively activated macrophages using media supplemented with IL10, IFN? or IL4 respectively. Cell surface marker expression was assessed using FACS analysis to confirm the predicted macrophage phenotypes were induced. The percentage of macrophages infected was shown to vary significantly, dependent upon virus isolate, treatment and duration of infection. Differences were also observed in production of infectious progeny virus and cell survival following infection of macrophages in different activation states. The results indicate that the activation state of macrophages is important for ASFV infection and that treatment with IL4 to stimulate alternative activation may increase persistence of ASFV infection. Infection of differentially activated cells with porcine reproductive and respiratory syndrome virus (PRRSV) was also investigated to allow comparison to ASFV infection. Interestingly, despite similar cell tropisms of ASFV and PRRSV, PRRSV infection of alternatively activated macrophages was severely inhibited unlike ASFV infection. The requirement of the cell surface marker CD163 for ASFV infection was investigated as it is a marker of alternatively activated macrophages and has also been suggested to be a receptor for ASFV. However, ASFV infection rate did not correlate with its presence on the cell surface and the data indicated that ASFV infection rates were not increased in cells stably transformed to express CD163