Endophoma, a new didymellaceous endoconidial genus from bat-cave soil

A new endoconidial taxon, Endophoma elongata gen. et sp. nov., isolated from bat-cave soil, is reported from Alberta, Canada. It is morphologically unique in producing two forms of unilocular, endoconidial conidiomata (i.e. a superficially Phoma-like spherical, often ostiolate form and a cylindrical, non-ostiolate, often setose cleistopycnidial form). Locules of both forms are pseudoparenchymatous, filled with hyaline, thin-walled, endoconidial conidiogenous cells. Endoconidia are hyaline and unicellular. One- or two-celled chlamydospores are abundant in culture. Phylogenetic analysis of the LSU, ITS and β-tubulin regions indicates Endophoma is a member of the Didymellaceae and remote from all other endoconidial genera. Endoconidiogenesis has not been reported previously within the Didymellaceae, and Endophoma represents the first report of a coelomycetous, endoconidial genus in the Pleosporales.     

Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

Background

Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.

Results

Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.

Conclusions

Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users.     

Generation and maintenance of Dmbx1 gene-targeted mutant alleles

Dmbx1 encodes a paired-like homeodomain protein that is expressed in neural tissues at mouse embryonic and postnatal stages. We previously generated two Dmbx1 mutant alleles, Dmbx1 ⁻ and Dmbx1 ^z , by homologous recombination in mouse embryonic stem (ES) cells. In this article we report the generation of three novel Dmbx1 mutant alleles, Dmbx1 ^τZ , Dmbx1 ^τG , and Dmbx1 ^Cre , that carry the intronic insertion of tau (τ)-lacZ, τ-eGFP, and Cre reporter genes, respectively. Dmbx1 ^τZ and Dmbx1 ^τG recapitulated the Dmbx1 expression, and the reporter gene expression was detected in the diencephalon and mesencephalon during embryogenesis. The crossing of Dmbx1 ^Cre mice with Rosa26 reporter mice identified the Cre-mediated DNA excision in the postnatal midbrain, cerebellum, medulla oblongata, and spinal cord. To maintain the Dmbx1 mutant alleles without genotyping, we crossed Dmbx1 mutant mice with Inv4(1) ^Brd mice that possess the inversion between D4Mit117 and D4Mit281 on Chromosome 4, where Dmbx1 is located. The intercrossing of the non-agouti (a/a) albino (Tyr ^c-Brd /Tyr ^c-Brd ) Dmbx1 mutant mice carrying Inv4(1) ^Brd tagged with K14-Agouti and Tyrosinase coat-color markers resulted in the generation of dark brown Dmbx1 wild-type [Inv4(1) ^Brd /Inv4(1) ^Brd ], light brown Dmbx1 heterozygous [Dmbx1 ^tm /Inv4(1) ^Brd ], and albino Dmbx1 homozygous (Dmbx1 ^tm /Dmbx1 ^tm ) mutant mice. To our knowledge, this is the first demonstration of the proof-of-principle of the maintenance of viable gene-targeted alleles using coat-color-tagged nonlethal balancer chromosomes.     

Notch2 Signaling Maintains NSC Quiescence in the Murine Ventricular-Subventricular Zone

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Development of a chemically defined platform fed-batch culture media for monoclonal antibody-producing CHO cell lines with optimized choline content

A chemically defined platform basal medium and feed media were developed using a single Chinese hamster ovary (CHO) cell line that produces a monoclonal antibody (mAb). Cell line A, which showed a peak viable cell density of 5.9 × 10⁶ cells/mL and a final mAb titer of 0.5 g/L in batch culture, was selected for the platform media development. Stoichiometrically balanced feed media were developed using glucose as an indicator of cell metabolism to determine the feed rates of all other nutrients. A fed-batch culture of cell line A using the platform fed-batch medium yielded a 6.4 g/L mAb titer, which was 12-fold higher than that of the batch culture. To examine the applicability of the platform basal medium and feed media, three other cell lines (A16, B, and C) that produce mAbs were cultured using the platform fed-batch medium, and they yielded mAb titers of 8.4, 3.3, and 6.2 g/L, respectively. The peak viable cell densities of the three cell lines ranged from 1.3 × 10⁷ to 1.8 × 10⁷ cells/mL. These results show that the nutritionally balanced fed-batch medium and feeds worked well for other cell lines. During the medium development, we found that choline limitation caused a lower cell viability, a lower mAb titer, a higher mAb aggregate content, and a higher mannose-5 content. The optimal choline chloride to glucose ratio for the CHO cell fed-batch culture was determined. Our platform basal medium and feed media will shorten the medium-development time for mAb-producing cell lines.