Multicenter, Prospective Clinical Evaluation of Respiratory Samples from Subjects at Risk for Pneumocystis jirovecii Infection by Use of a Commercial Real-Time PCR Assay ᰔ †

Pneumocystis jirovecii pneumonia (PCP) is a common opportunistic infection. Microscopic diagnosis, including diagnosis using the Merifluor-Pneumocystis direct fluorescent antigen (MP-DFA) test, has limitations. Real-time PCR may assist in diagnosis, but no commercially validated real-time PCR assay has been available to date. MycAssay Pneumocystis is a commercial assay that targets the P. jirovecii mitochondrial large subunit (analytical detection limit, <3.5 copies/l of sample). A multicenter trial recruited 110 subjects: 54 with transplants (40 with lung transplants), 32 with nonmalignant conditions, 13 with leukemia, and 11 with solid tumors; 9 were HIV positive. A total of 110 respiratory samples (92% of which were bronchoalveolar lavage [BAL] specimens) were analyzed by PCR. Performance was characterized relative to investigator-determined clinical diagnosis of PCP (including local diagnostic tests), and PCR results were compared with MP-DFA test results for 83 subjects. Thirteen of 14 subjects with PCP and 9/96 without PCP (including 5 undergoing BAL surveillance after lung transplantation) had positive PCR results; sensitivity, specificity, and positive and negative predictive values (PPV and NPV, respectively) were 93%, 91%, 59%, and 99%, respectively. Fourteen of 83 subjects for whom PCR and MP-DFA test results were available had PCP; PCR sensitivity, specificity, PPV, and NPV were 93%, 90%, 65%, and 98%, respectively, and MP-DFA test sensitivity, specificity, PPV, and NPV were 93%, 100%, 100%, and 98%. Of the 9 PCR-positive subjects without PCP, 1 later developed PCP. The PCR diagnostic assay compares well with clinical diagnosis using nonmolecular methods. Additional positive results compared with the MP-DFA test may reflect low-level infection or colonization

A single point-mutation within the melanophilin gene causes the <it>lavender </it>plumage colour dilution phenotype in the chicken

Abstract Background The lavender phenotype in the chicken causes the dilution of both black (eumelanin) and red/brown (phaeomelanin) pigments. Defects in three genes involved in intracellular melanosomal transport, previously described in mammals, give rise to similar diluted pigmentation phenotypes as those seen in lavender chickens. Results We have used a candidate-gene approach based on an expectation of homology with mammals to isolate a gene involved in pigmentation in chicken. Comparative sequence analysis of candidate genes in the chicken identified a strong association between a mutation in the MLPH gene and the diluted pigmentation phenotype. This mutation results in the amino acid change R35W, at a site also associated with similar phenotypes in mice, humans and cats. Conclusion This is the first time that an avian species with a mutation in the MLPH gene has been reported.</p

Characterization of Japanese Quail yellow as a Genomic Deletion Upstream of the Avian Homolog of the Mammalian ASIP (agouti) Gene

ASIP is an important pigmentation gene responsible for dorsoventral and hair-cycle-specific melanin-based color patterning in mammals. We report some of the first evidence that the avian ASIP gene has a role in pigmentation. We have characterized the genetic basis of the homozygous lethal Japanese quail yellow mutation as a >90-kb deletion upstream of ASIP. This deletion encompasses almost the entire coding sequence of two upstream loci, RALY and EIF2B, and places ASIP expression under control of the RALY promoter, leading to the presence of a novel transcript. ASIP mRNA expression was upregulated in many tissues in yellow compared to wild type but was not universal, and consistent differences were not observed among skins of yellow and wild-type quail. In a microarray analysis on developing feather buds, the locus with the largest downregulation in yellow quail was SLC24A5, implying that it is regulated by ASIP. Finally, we document the presence of ventral skin-specific isoforms of ASIP mRNA in both wild-type quails and chickens. Overall, there are remarkable similarities between yellow in quail and lethal yellow in mouse, which involve a deletion in a similar genomic position. The presence of ventral-specific ASIP expression in birds shows that this feature is conserved across vertebrates

A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken-2

<p><b>Copyright information:</b></p><p>Taken from "A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken"</p><p>http://www.biomedcentral.com/1471-2156/9/7</p><p>BMC Genetics 2008;9():7-7.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2253553.</p><p></p>, and respective amino acids are shown above the first base pair in a codon for the homozygous sequences. (B) ClustalW alignment of the wild type (WT) and mutated (LN, GS3 and LAV, respectively) amino acid sequences from mouse [6], human [13], and chicken

A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken-6

<p><b>Copyright information:</b></p><p>Taken from "A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken"</p><p>http://www.biomedcentral.com/1471-2156/9/7</p><p>BMC Genetics 2008;9():7-7.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2253553.</p><p></p>x) spleen, and skin at ages (a) E14, (b) E17 and (c) 10 weeks. Size is indicated on the right

A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken-0

<p><b>Copyright information:</b></p><p>Taken from "A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken"</p><p>http://www.biomedcentral.com/1471-2156/9/7</p><p>BMC Genetics 2008;9():7-7.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2253553.</p><p></p>orms

A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken-5

<p><b>Copyright information:</b></p><p>Taken from "A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken"</p><p>http://www.biomedcentral.com/1471-2156/9/7</p><p>BMC Genetics 2008;9():7-7.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2253553.</p><p></p>orms

A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken-4

<p><b>Copyright information:</b></p><p>Taken from "A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken"</p><p>http://www.biomedcentral.com/1471-2156/9/7</p><p>BMC Genetics 2008;9():7-7.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2253553.</p><p></p>ozygous dams, A) 5368, 5372 and B) 5363, 5385, is consistent with the phenotype. Males are denoted by squares, and females by circles. () and wild-type () haplotypes are indicated as solid black and solid white symbols, respectively

A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken-1

<p><b>Copyright information:</b></p><p>Taken from "A single point-mutation within the melanophilin gene causes the plumage colour dilution phenotype in the chicken"</p><p>http://www.biomedcentral.com/1471-2156/9/7</p><p>BMC Genetics 2008;9():7-7.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2253553.</p><p></p>x) spleen, and skin at ages (a) E14, (b) E17 and (c) 10 weeks. Size is indicated on the right