Bayesian latent variable models for median regression on multiple outcomes

Often a response of interest cannot be measured directly and it is necessary to rely on multiple surrogates, which can be assumed to be conditionally independent given the latent response and observed covariates. Latent response models typically assume that residual densities are Gaussian. This article proposes a Bayesian median regression modeling approach, which avoids parametric assumptions about residual densities by relying on an approximation based on quantiles. To accommodate within-subject dependency, the quantile response categories of the surrogate outcomes are related to underlying normal variables, which depend on a latent normal response. This underlying Gaussian covariance structure simplifies interpretation and model fitting, without restricting the marginal densities of the surrogate outcomes. A Markov chain Monte Carlo algorithm is proposed for posterior computation, and the methods are applied to single-cell electrophoresis (comet assay) data from a genetic toxicology study.     

Electrophysiological characterization of olfactory cell types in the antennae and palps of the housefly

A set of odours was presented to the housefly Musca domestica and the electrophysiological responses of single olfactory receptor cells in the antennae and palps were recorded. The olfactory cells in the antennae of the housefly showed a large variability of response profiles, but multidimensional cluster analysis suggested a moderate clustering in olfactory response types. Receptor cells with similar or with different odour response profiles can reside in one and the same sensillum. No fixed spatial distribution of olfactory response types over the antennal of palpal surface was found. The odours of 1-octen-3-ol, amyl acetate, 3-methylphenol, 2-pentanone and R(+)limonene elicited the largest responses in antennal cells. Most odours elicited responses in cells of only a few of the clusters, but 1-octen-3-ol was detected by cells of almost all clusters of the antenna. Surprisingly, rather low responses were found to acetic acid, skatole, indole and muscalure, odours that are known to attract flies. Response profiles of palpal cells differed considerably from those of antennal cells. Palpal cells mostly responded to 3-methylphenol and 2-pentanone. In the palps, the clusters of cells responding to 3-methylphenol and 2-pentanone are clearly separated from the other olfactory cells.     

Human C-kit+CD45− cardiac stem cells are heterogeneous and display both cardiac and endothelial commitment by single-cell qPCR analysis

C-kit expressing cardiac stem cells have been described as multipotent. We have previously identified human cardiac C-kit+CD45− cells, but only found evidence of endothelial commitment. A small cardiac committed subpopulation within the C-kit+CD45− population might however be present. To investigate this at single-cell level, right and left atrial biopsies were dissociated and analyzed by FACS. Only right atrial biopsies contained a clearly distinguishable C-kit+CD45− population, which was single-cell sorted for qPCR. A minor portion of the sorted cells (1.1%) expressed early cardiac gene NKX2.5 while most of the cells (81%) expressed late endothelial gene VWF. VWF− cells were analyzed for a wider panel of genes. One group of these cells expressed endothelial genes (FLK-1, CD31) while another group expressed late cardiac genes (TNNT2, ACTC1). In conclusion, human C-kit+CD45− cells were predominantly localized to the right atrium. While most of these cells expressed endothelial genes, a minor portion expressed cardiac genes.     

Single-cell proteomic analysis of glucosinolate-rich S-cells in Arabidopsis thaliana

Single-cell analysis is essential for understanding the processes of cell differentiation and metabolic specialisation in rare cell types. The amount of single proteins in single cells can be as low as one copy per cell and is for most proteins in the attomole range or below; usually considered as insufficient for proteomic analysis. The development of modern mass spectrometers possessing increased sensitivity and mass accuracy in combination with nano-LC–MS/MS now enables the analysis of single-cell contents. In Arabidopsis thaliana, we have successfully identified nine unique proteins in a single-cell sample and 56 proteins from a pool of 15 single-cell samples from glucosinolate-rich S-cells by nanoLC–MS/MS proteomic analysis, thus establishing the proof-of-concept for true single-cell proteomic analysis. Dehydrin (ERD14_ARATH), two myrosinases (BGL37_ARATH and BGL38_ARATH), annexin (ANXD1_ARATH), vegetative storage proteins (VSP1_ARATH and VSP2_ARATH) and four proteins belonging to the S-adenosyl-l-methionine cycle (METE_ARATH, SAHH1_ARATH, METK4_ARATH and METK1/3_ARATH) with associated adenosine kinase (ADK1_ARATH), were amongst the proteins identified in these single-S-cell samples. Comparison of the functional groups of proteins identified in S-cells with epidermal/cortical cells and whole tissue provided a unique insight into the metabolism of S-cells. We conclude that S-cells are metabolically active and contain the machinery for de novo biosynthesis of methionine, a precursor for the most abundant glucosinolate glucoraphanine in these cells. Moreover, since abundant TGG2 and TGG1 peptides were consistently found in single-S-cell samples, previously shown to have high amounts of glucosinolates, we suggest that both myrosinases and glucosinolates can be localised in the same cells, but in separate subcellular compartments. The complex membrane structure of S-cells was reflected by the presence of a number of proteins involved in membrane maintenance and cellular organisation.     

Development of single-cell PCR methods for the Raphidophyceae

Many Raphidophytes are important algal bloom-forming species. Morphology-based identification of these species is often ambiguous, however, as many species are very similar in shape and size. To accurately detect the presence of these species in pre-bloom conditions, single-cell PCR is probably the most rapid and convenient method. However, direct single-cell PCRs with conserved primers are apparently not effective, probably due to the impermeability of the cell wall. We report here an effective detergent-based pre-PCR cell lysis method, which turned out to be a critical step for effective single-cell PCR of the Raphidophytes. Two PCR-based methods, nested SC-PCR and SC-RAPD, were evaluated. The nested SC-PCR involves two consecutive PCRs, the first of which is performed with the D1 and D2 primers (external primers) resulting in an amplification of a partial LSU rRNA gene. The second amplification is performed with primers targeting the LSU domain and specifically annealing to Chattonella ovata and Chattonella marina only. The SC-RAPD performed with the established random primers, RP1–RP4, produced unique haplotypes that could be exploited to differentiate the two Chattonella species. The assay was demonstrated to be sensitive, with the lowest detection limit of a single Raphidophyceae cell. The method developed is a valuable tool for the study of intra-specific variations of the Raphidophytes and represents a platform for further development of species-specific SC-RAPD for all members of the Raphidophyceae.     

Homology of olfactory receptor neuron response characteristics inferred from hybrids between Asian and European corn borer moths (Lepidoptera: Crambidae)

First generation hybrid males from crosses between the Asian corn borer (ACB), Ostrinia furnacalis, and the “univoltine Z-strain” European corn borer (ECB), Ostrinia nubilalis, were examined with respect to behavioral and physiological responses to ACB and ECB pheromones. The hybrid males often flew to the pheromone of ECB Z-strain, but very rarely to the ACB pheromone. We mapped the tuning profiles of each ORN of the F₁ hybrids with respect to the relevant pheromone components and a common behavioral antagonist by employing differential cross-adaptation and varying doses of the ligands. In the trichoid sensilla of F₁ hybrid males, the three co-compartmentalized ORNs produced spikes that were very difficult to distinguish by size, unlike the parental populations. Comparing the responses to ACB and ECB components at different doses reveals overlapping profiles similar to males of both parental types, but more responsiveness to the ECB pheromone components. We were unable to detect any differences in the ORN tuning profiles when comparing males with different behavioral phenotypes. While the two ECB pheromone races have similar ORN tuning properties that are different from those in ACB, the spike-amplitude patterns of ECB E-strain and ACB have greater homology when compared to ECB Z-strain.     

Looking beyond the post-genomic era

A report on BioMed Central’s fourth annual Beyond the Genome conference held at the University of California, San Francisco Mission Bay Conference Center, USA, 1–3 October 2013.     

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans

1. Download high-res image (291KB)
2. Download full-size image