Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms

Background: High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms. Methodology/Principal Findings: This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples. Conclusions/Significance: These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography

Polycystic kidney disease with hyperinsulinemic hypoglycemia caused by a promoter mutation in PMM2

Hyperinsulinemic hypoglycemia (HI) and congenital polycystic kidney disease (PKD) are rare, genetically heterogeneous disorders. The co-occurrence of these disorders (HIPKD) in 17 children from 11 unrelated families suggested an unrecognized genetic disorder. Whole-genome linkage analysis in five informative families identified a single significant locus on chromosome 16p13.2 (logarithm of odds score 6.5). Sequencing of the coding regions of all linked genes failed to identify biallelic mutations. Instead, we found in all patients a promoter mutation (c.-167G>T) in the phosphomannomutase 2 gene (PMM2), either homozygous or in trans with PMM2 coding mutations. PMM2 encodes a key enzyme in N-glycosylation. Abnormal glycosylation has been associated with PKD, and we found that deglycosylation in cultured pancreatic β cells altered insulin secretion. Recessive coding mutations in PMM2 cause congenital disorder of glycosylation type 1a (CDG1A), a devastating multisystem disorder with prominent neurologic involvement. Yet our patients did not exhibit the typical clinical or diagnostic features of CDG1A. In vitro, the PMM2 promoter mutation associated with decreased transcriptional activity in patient kidney cells and impaired binding of the transcription factor ZNF143. In silico analysis suggested an important role of ZNF143 for the formation of a chromatin loop including PMM2. We propose that the PMM2 promoter mutation alters tissue-specific chromatin loop formation, with consequent organ-specific deficiency of PMM2 leading to the restricted phenotype of HIPKD. Our findings extend the spectrum of genetic causes for both HI and PKD and provide insights into gene regulation and PMM2 pleiotropy

Population genetic structuring in a rare tropical plant:\ud Idiospermum australiense (Diels) S.T. Blake

Idiospermum australiense (Diels) S.T. Blake is considered to be one of the few remaining species of an ancient assemblage to have survived the attrition ofAustralian tropical rain forest during historically drier periods. This monotypic species is currently restricted to two very wet lowland rain forest locations in Australia’s wet tropical World Heritage Area that are thought to have provided refuge for humid-adapted taxa during the last glacial maximum. Two dominant (RAPD and ISSR) molecular marker sets were employed to investigate whether the genetic structure of Idiospermum could be attributed to its restriction to these quite disjunct localities. The results reveal that neither its restriction to purported\ud Pleistocene refugia nor the geographic distance between\ud populations could fully explain the distribution of variation in the Idiospermum data set, with evidence to suggest that potentially deeper time events have played a role in population structuring and the distribution of diversity. Although there is sufficient evidence in the data to suggest that gene dispersal is quite limited in the species, further investigation is still needed to yield more informative detail on additional factors, such as breeding and germination strategies and their potential influence over population structuring and diversity levels within each population and refugium

Economics, Marketing and Performances of U.S. Classical Music: journeyin’ together to de promise land

Since the beginning of the latest financial and real crisis in 2008, USA symphony orchestras and opera houses have revealed adaptation to the turmoil of scarce resources and a very keen competition (Jeannotte, Duxbury, 2015; Turbide, Laurin, Lapierre, Morissette, 2008). Adaptation has had multiple implications: implementation of websites and social media as innovative tools for audience exploration and development (Pierotti, Risaliti, Cestari, 2014; Ravanas, 2008); revenue diversification and performance measurement (Hong, 2014; Besana, 2012;); community engagement together with testing of new segments like tourists (Kemp, Poole, 2016; Guachalla, 2012; Woosnam, McElroy, Van Winkle, 2009; Poon, Lai, 2008). Marketing, and especially social media marketing, has had a crucial new role and enhanced “interactive online world in which participants with different interests, resources and power co-create value” (Kornum, Mühlbacher, 2013). Marketing and fundraising have extracted both willingness-to-pay and willingness-to-donate from audiences, while audiences have been spending more time than ever using social media, and the U.S. classical music has been striving to use social media and to reach, engage, catch and hold the millions of consumers who use it daily, tourists included (Parsons, 2011). Marketing has called for e-commerce of audiences; fundraising has called for s-commerce of philanthropists. After analysing the new marketing scenario and pointing out social media marketing strategies of U.S. classical music, this paper investigates 100 symphony orchestras and 100 opera houses according to their revenues, expenses and gains (or losses) in 2015. Thanks to cluster analysis, three groups will emerge with different performances and prevailing fundraising

Targeting of Slc25a21 Is Associated with Orofacial Defects and Otitis Media Due to Disrupted Expression of a Neighbouring Gene

<div><p>Homozygosity for <i>Slc25a21^{tm1a(KOMP)Wtsi}</i> results in mice exhibiting orofacial abnormalities, alterations in carpal and rugae structures, hearing impairment and inflammation in the middle ear. In humans it has been hypothesised that the 2-oxoadipate mitochondrial carrier coded by <i>SLC25A21</i> may be involved in the disease 2-oxoadipate acidaemia. Unexpectedly, no 2-oxoadipate acidaemia-like symptoms were observed in animals homozygous for <i>Slc25a21^{tm1a(KOMP)Wtsi}</i> despite confirmation that this allele reduces <i>Slc25a21</i> expression by 71.3%. To study the complete knockout, an allelic series was generated using the <i>loxP</i> and <i>FRT</i> sites typical of a Knockout Mouse Project allele. After removal of the critical exon and neomycin selection cassette, <i>Slc25a21</i> knockout mice homozygous for the <i>Slc25a21^{tm1b(KOMP)Wtsi}</i> and <i>Slc25a21^{tm1d(KOMP)Wtsi}</i> alleles were phenotypically indistinguishable from wild-type. This led us to explore the genomic environment of <i>Slc25a21</i> and to discover that expression of <i>Pax9</i>, located 3′ of the target gene, was reduced in homozygous <i>Slc25a21^{tm1a(KOMP)Wtsi}</i> mice. We hypothesize that the presence of the selection cassette is the cause of the down regulation of <i>Pax9</i> observed. The phenotypes we observed in homozygous <i>Slc25a21^{tm1a(KOMP)Wtsi}</i> mice were broadly consistent with a hypomorphic <i>Pax9</i> allele with the exception of otitis media and hearing impairment which may be a novel consequence of <i>Pax9</i> down regulation. We explore the ramifications associated with this particular targeted mutation and emphasise the need to interpret phenotypes taking into consideration all potential underlying genetic mechanisms.</p></div