Programmatic change: lung disease research in the era of induced pluripotency

Human lung research has made remarkable progress over the last century largely through the use of animal models of disease. The challenge for the future is to translate these findings into human disease and bring about meaningful disease modification or even cure. The ability to generate transformative therapies in the future will require human tissue, currently scarce under the best of circumstances. Unfortunately, patient-derived somatic cells are often poorly characterized and have a limited life span in culture. Moreover, these cells are frequently obtained from patients with end-stage disease exposed to multiple drug therapies, leaving researchers with questions about whether their findings recapitulate disease-initiating processes or are simply the result of pharmacological intervention or subsequent host responses. The goal of studying early disease in multiple cell and tissue types has driven interest in the use of induced pluripotent stem cells (iPSCs) to model lung disease. These cells provide an alternative model for relevant lung research and hold promise in particular for studying the initiation of disease processes in genetic conditions such as heritable pulmonary arterial hypertension as well as other lung diseases. In this Perspective, we focus on potential iPSC use in pulmonary vascular disease research as a model for iPSC use in many types of advanced lung disease.     

Actinopolyspora righensis sp. nov., a novel halophilic actinomycete isolated from Saharan soil in Algeria

A novel halophilic actinomycete strain, H23^T, was isolated from a Saharan soil sample collected in Djamâa (Oued Righ region), El-Oued province, South Algeria. Strain H23^T was identified as a member of the genus Actinopolyspora by a polyphasic approach. Phylogenetic analysis showed that strain H23^T had 16S rRNA gene sequence similarities ranging from 97.8 % (Actinopolyspora xinjiangensis TRM 40136^T) to 94.8 % (Actinopolyspora mortivallis DSM 44261^T). The strain grew optimally at pH 6.0–7.0, 28–32 °C and in the presence of 15–25 % (w/v) NaCl. The substrate mycelium was well developed and fragmented with age. The aerial mycelium produced long, straight or flexuous spore chains with non-motile, smooth-surfaced and rod-shaped spores. Strain H23^T had MK-10 (H₄) and MK-9 (H₄) as the predominant menaquinones. The whole micro-organism hydrolysates mainly consisted of meso-diaminopimelic acid, galactose and arabinose. The diagnostic phospholipid detected was phosphatidylcholine. The major cellular fatty acids were anteiso-C_17:0 (37.4 %), iso-C_17:0 (14.8 %), iso-C_15:0 (14.2 %), and iso-C_16:0 (13.9 %). The genotypic and phenotypic data show that the strain represents a novel species of the genus Actinopolyspora, for which the name Actinopolyspora righensis sp. nov. is proposed, with the type strain H23^T (=DSM 45501^T = CCUG 63368^T = MTCC 11562^T).     

Evaluation of FT-IR spectroscopy as a tool to quantify bacteria in binary mixed cultures

Fourier-transform infrared (FT-IR) spectroscopy is known as a high-resolution method for the rapid identification of pure cultures of microorganisms. Here, we evaluated FT-IR as a method for the quantification of bacterial populations in binary mixed cultures consisting of Pseudomonas putida and Rhodococcus ruber. A calibration procedure based on Principal Component Regression was developed for estimating the ratio of the bacterial species. Data for method calibration were gained from pure cultures and artificially assembled communities of known ratios of the two member populations. Moreover, to account for physiological variability, FT-IR measurements were performed with organisms sampled at different growth phases. Measurements and data analyses were subsequently applied to growing mixed cultures revealing that growth of R. ruber was almost completely suppressed in co-culture with P. putida. Population ratios obtained by fatty acid analysis as an independent reference method were in high agreement with the FT-IR derived ratios.     

Gluten-specific T cells cross-react between HLA-DQ8 and the HLA-DQ2α/DQ8β transdimer

Because susceptibility to celiac disease is associated strongly with HLA-DQ2 (DQA1*05/DQB1*02) and weakly with HLA-DQ8 (DQA1*03/DQB1*03), a subset of patients carries both HLA-DQ2 and HLA-DQ8. As a result, these patients may express two types of mixed HLA-DQ2/8 transdimers (encoded by DQA1*05/DQB1*03 and DQA1*03/DQB1*02) in addition to HLA-DQ2 and HLA-DQ8. Using T cells from a celiac disease patient expressing HLA-DQ8trans (encoded by DQA*0501/DQB*0302), but neither HLA-DQ2 nor HLA-DQ8, we demonstrate that this transdimer is expressed on the cell surface and can present multiple gluten peptides to T cell clones isolated from the duodenum of this patient. Furthermore, T cell clones derived from this patient and HLA-DQ2/8 heterozygous celiac disease patients respond to gluten peptides presented by HLA-DQ8trans, as well as HLA-DQ8, in a similar fashion. Finally, one gluten peptide is recognized better when presented by HLA-DQ8trans, which correlates with preferential binding of this peptide to HLA-DQ8trans. These results implicate HLA-DQ8trans in celiac disease pathogenesis and demonstrate extensive T cell cross-reactivity between HLA-DQ8 and HLA-DQ8trans. Because type 1 diabetes is strongly associated with the presence of HLA-DQ8trans, our findings may bear relevance to this disease as well.     

Assimilation of Cellulose-Derived Carbon by Microeukaryotes in Oxic and Anoxic Slurries of an Aerated Soil

Soil microeukaryotes may trophically benefit from plant biopolymers. However, carbon transfer from cellulose into soil microeukaryotes has not been demonstrated so far. Microeukaryotes assimilating cellulose-derived carbon in oxic and anoxic soil slurries were therefore examined by rRNA-based stable-isotope probing. Bacteriovorous flagellates and ciliates and, likely, mixotrophic algae and saprotrophic fungi incorporated carbon from supplemental [U-¹³C]cellulose under oxic conditions. A previous study using the same soil suggested that cellulolytic Bacteria assimilated ¹³C of supplemental cellulose. Thus, it can be assumed that ciliates, cercozoa, and chrysophytes assimilated carbon by grazing upon and utilizing metabolic products of Bacteria that hydrolyzed cellulose in the soil slurries.     

Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp, Andricus coriarius

The oak gallwasp Andricus coriarius is distributed across the Western Palaearctic from Morocco to Iran. It belongs to a clade of host-alternating Andricus species that requires host oaks in two sections of Quercus subgenus Quercus to complete its lifecycle, a requirement that has restricted the historic distribution and dispersal of members of this clade. Here we present nuclear and mitochondrial sequence evidence from the entire geographic range of A. coriarius to investigate the genetic legacy of longitudinal range expansion. We show A. coriarius as currently understood to be para- or polyphyletic, with three evolutionarily independent (but partially sympatric) lineages that diverged c. 10 million years ago (mya). The similarities in gall structure that have justified recognition of single species to date thus represent either strong conservation of an ancestral state or striking convergence. All three lineages originated in areas to the east of Europe, underlining the significance of Turkey, Iran and the Levant as 'cradles' of gallwasp evolution. One of the three lineages gave rise to all European populations, and range expansion from a putative Eastern origin to the present distribution is predicted to have occurred around 1.6 mya.     

Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil

Using cultivation-independent methods the ciliate communities of a clay-rich soil with a 90-year record of pollution by polycyclic aromatic hydrocarbons (PAH) (4.5 g kg(-1) PAH) were compared with that of a nonpolluted soil collected in its vicinity and with similar properties. A ciliate-specific set of 18S rRNA gene targeting primers was designed and used to amplify DNA extracted from both soils (surface and 20 cm depth). Four clone libraries were generated with PCR products that covered an 18S rRNA gene fragment of up to 670 bp. Comparative sequence analysis of representative clones proved that the primer set was highly specific for ciliates. Calculation of similarity indices based on operational taxonomic units after amplified ribosomal DNA restriction analysis of the clones showed that the community from the nonpolluted surface soil was highly dissimilar to the other communities. The presence of several taxa, namely sequences affiliated to the orders Phyllopharyngia, Haptoria, Nassophorea, Peniculida and Scuticociliatia in samples from nonpolluted soil, points to the existence of various trophic functional groups. In contrast, the 18S rRNA gene diversity was much lower in the clone libraries from the polluted soil. More than 90% of these sequences belonged to the class Colpodea, a well-known clade of mainly bacterivorous and r-selected species, thus potentially also indicating a lower functional diversity.     

Bayesian estimation of concordance among gene trees

Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species.