A2ML1 and otitis media : novel variants, differential expression, and relevant pathways

A genetic basis for otitis media is established, however, the role of rare variants in disease etiology is largely unknown. Previously a duplication variant within A2ML1 was identified as a significant risk factor for otitis media in an indigenous Filipino population and in US children. In this report exome and Sanger sequencing was performed using DNA samples from the indigenous Filipino population, Filipino cochlear implantees, US probands, Finnish, and Pakistani families with otitis media. Sixteen novel, damaging A2ML1 variants identified in otitis media patients were rare or low-frequency in population-matched controls. In the indigenous population, both gingivitis and A2ML1 variants including the known duplication variant and the novel splice variant c.4061 + 1 G>C were independently associated with otitis media. Sequencing of salivary RNA samples from indigenous Filipinos demonstrated lower A2ML1 expression according to the carriage of A2ML1 variants. Sequencing of additional salivary RNA samples from US patients with otitis media revealed differentially expressed genes that are highly correlated with A2ML1 expression levels. In particular, RND3 is upregulated in both A2ML1 variant carriers and high-A2ML1 expressors. These findings support a role for A2ML1 in keratinocyte differentiation within the middle ear as part of otitis media pathology and the potential application of ROCK inhibition in otitis media.Peer reviewe

Draft Genome Sequences of Elizabethkingia anophelis Strains R26T and Ag1 from the Midgut of the Malaria Mosquito Anopheles gambiae

Elizabethkingia anophelis is a species in the family Flavobacteriaceae. It is a dominant resident in the mosquito gut and also a human pathogen. We present the draft genome sequences of two strains of E. anophelis, R26T and Ag1, which were isolated from the midgut of the malaria mosquito Anopheles gambiae

Insights from the Genome Annotation of <i>Elizabethkingia anophelis</i> from the Malaria Vector <i>Anopheles gambiae</i>

<div><p><i>Elizabethkingia anophelis</i> is a dominant bacterial species in the gut ecosystem of the malaria vector mosquito <i>Anopheles gambiae</i>. We recently sequenced the genomes of two strains of <i>E. anophelis</i>, R26^T and Ag1, isolated from different strains of <i>A. gambiae</i>. The two bacterial strains are identical with a few exceptions. Phylogenetically, <i>Elizabethkingia</i> is closer to <i>Chryseobacterium</i> and <i>Riemerella</i> than to <i>Flavobacterium.</i> In line with other Bacteroidetes known to utilize various polymers in their ecological niches, the <i>E. anophelis</i> genome contains numerous TonB dependent transporters with various substrate specificities. In addition, several genes belonging to the polysaccharide utilization system and the glycoside hydrolase family were identified that could potentially be of benefit for the mosquito carbohydrate metabolism. In agreement with previous reports of broad antibiotic resistance in <i>E. anophelis</i>, a large number of genes encoding efflux pumps and β-lactamases are present in the genome. The component genes of resistance-nodulation-division type efflux pumps were found to be syntenic and conserved in different taxa of Bacteroidetes. The bacterium also displays hemolytic activity and encodes several hemolysins that may participate in the digestion of erythrocytes in the mosquito gut. At the same time, the OxyR regulon and antioxidant genes could provide defense against the oxidative stress that is associated with blood digestion. The genome annotation and comparative genomic analysis revealed functional characteristics associated with the symbiotic relationship with the mosquito host.</p></div

Summary of the functional subcategories of resistance genes.

<p>Average identity reflects the mean identity of genes within the subcategory compared to R26^T. <i>E. m</i>., <i>Elizabethkingia meningoseptica</i>; <i>C. g.</i>, <i>Chryseobacterium gleum</i>; <i>F. b., Flavobacterium branchiophilum</i>.</p

Subsystem category distribution statistics for the genome of <i>E. Anophelis</i> as annotated by RAST.

<p>The pie chart represents relative abundance of each subsystem category and numbers depict subsystem feature counts.</p

The similarity of comparable CDS between R26^T and related genomes in the family Flavobacteriaceae.

<p>Numbers within parenthesis reflect the percentage of total comparable CDS.</p

Graphic view of a locus where three component genes of an RND efflux pump are located syntenically in four taxa of Bacteroidetes.

<p>Gene name was given on the top of each box. Locus ID of each gene is given in the boxes. OMP, outer membrane protein; RND: HAE1, Hydrophobe/amphiphile efflux-1; MFP, membrane fusion protein; HP: hypothetic protein. The scale bar represents 1 kb in length.</p

Graphic view of a syntenic gene cluster that is conserved in five taxa of Bacteroidetes.

<p>The genes encoding the components of TonB dependent transporters are ExbB, ExbD and TonB. Locus ID of each gene is given in the boxes, with taxon prefix (e.g. D505_ for <i>E.a.</i>) in the ExbB box for each species. The box with * in <i>D. fermentans</i> represents a predicted gene encoding a hypothetic protein. The scale bar represents 1 kb in length. Phylogenetically, <i>E. anophelis</i> and <i>F. johnsoniae</i> belong to the class Flavobacteria, <i>Dyadobacter fermentans</i> belongs to the class Cytophagia, <i>Arcticibacter svalbardensis</i> is in the class Sphingobacteriia, and <i>Bacteroides thetaiotaomicron</i> is located in the class Bacteroidia.</p

Isoprenoid synthesis pathway in four bacterial species.

<p>The color code represents the enzymes that are present in the species.</p