BackgroundAn emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively.ResultsThe assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes.ConclusionAs the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users.

Plants use both cell surface-resident pattern recognition receptors (PRRs) and intracellular nucleotide binding leucine-rich repeat (NLR) receptors to detect various pathogens. Plant PRRs typically recognize conserved pathogen-associated molecular patterns (PAMPs) to provide broad-spectrum resistance. By contrast, plant NLRs generally detect pathogen strain-specific effectors and confer race-specific resistance. Here, we demonstrate that the tomato () NLR Sw-5b confers broad-spectrum resistance against American-type tospoviruses by recognizing a conserved 21-amino acid peptide region within viral movement protein NSm (NSm). Sw-5b NB-ARC-LRR domains directly associate with NSm in vitro and in planta. Domain swap, site-directed mutagenesis and structure modeling analyses identified four polymorphic sites in the Sw-5b LRR domain that are critical for the recognition of NSm Furthermore, recognition of NSm by Sw-5b likely disturbs the residues adjacent to R927 in the LRR domain to weaken the intramolecular interaction between LRR and NB-ARC domains, thus translating recognition of NSm into activation of Sw-5b. Natural variation analysis of Sw-5b homologs from wild tomato species of South America revealed that the four polymorphic sites in the Sw-5b LRR domain were positively selected during evolution and are all necessary to confer resistance to tospovirus. The results described here provide a new example of a plant NLR mediating broad-spectrum resistance through recognition of a small conserved PAMP-like region within the pathogen effector.

Systemic gene transfer provides new opportunities for the analysis of gene function and gene regulation in vivo, as well as for human gene therapy. We used the chloramphenicol acetyltransferase reporter gene to examine several parameters important for the development of efficient, cationic liposome-mediated, intravenous (IV) gene transfer in mice. We then demonstrated that this approach can produce high level expression of biologically important genes. Specifically, we assessed the relationship of expression vector design to the level of systemic gene expression produced, and compared transfection levels produced by intravenously injecting DNA alone versus DNA⅐liposome complexes. We found that both the position of the heterologous intron, and the promoter element used in the expression plasmid, significantly affected the level of systemic gene expression produced. Although intravenous injection of plasmid DNA alone transfected every tissue analyzed, liposome-mediated delivery was much more efficient. We also established that repeated IV injection of DNA⅐liposome complexes produced high level systemic transfection. The second injection of DNA⅐liposome complexes produced levels of gene expression at least as high as those following a single IV injection. Thus, unlike some viral vectors, a neutralizing host-immune response does not limit re-expression, following reinjection of DNA⅐liposome complexes.Finally, we showed that the expression vectors which produced the highest levels of chloramphenicol acetyltransferase reporter gene expression could also produce high level expression of two colony stimulating factor genes in mice. Specifically, IV injection of liposomes complexed to expression vectors into which we had inserted either the murine granulocyte-macrophagecolony stimulating factor cDNA or the human granulocyte-CSF cDNA, produced circulating levels of the corresponding colony stimulating factor gene product comparable to levels which have been shown previously to be both biologically and therapeutically significant.

ABSTRACT:Caco-2 cell lysate, and intestinal and liver microsomes derived from female humans and rats were used to compare and contrast the metabolism and disposition of raloxifene. In Caco-2 cell lysate, raloxifene 6-␤-glucuronide (M1) was the main metabolite, although raloxifene 4-␤-glucuronide (M2) was formed in comparable abundance (58% versus 42%). In rat liver and intestinal microsomes, M1 represented about 76 to 86% of glucuronidated metabolites. In contrast, raloxifene 4-␤-glucuronide (M2) was the predominant metabolite in expressed UGT1A10 (96%) and human intestinal (92%) microsomes. Intrinsic clearance for M2 (CL int, M2 ) in human intestinal microsomes was 33-to 72-fold higher than in rat microsomes, whereas intrinsic clearance for M1 (CL int, M1 ) was 3-to 4-fold lower. Taken together, total intrinsic clearance (CL int, M1 ؉ CL int, M2 ) in human intestinal microsomes was 3-to 6-fold higher than that in rat intestinal microsomes, but was similar in liver microsomes. In addition, intrinsic clearance in small intestinal microsomes was 2-to ϳ5-fold higher than that in hepatic microsomes, regardless of species. To account for the difference in species-and disposition model-dependent intestinal metabolism, we probed the presence of various UGT1A isoforms in Caco-2 cells using real-time reverse transcriptase-polymerase chain reaction and, as expected, detected no UGT1A10. In conclusion, the lack of UGT1A10 may explain why Caco-2 cell and rat intestinal microsomes metabolized raloxifene differently from human intestinal microsomes. The presence of human intestinal UGT1A10 and the higher overall intrinsic clearance value in the human intestine as the result of UGT1A10 expression could explain why raloxifene has much lower bioavailability in humans (2%) than in rats (39%).