Bayesian latent variable models for mixed discrete outcomes

In studies of complex health conditions, mixtures of discrete outcomes (event time, count, binary, ordered categorical) are commonly collected. For example, studies of skin tumorigenesis record latency time prior to the first tumor, increases in the number of tumors at each week, and the occurrence of internal tumors at the time of death. Motivated by this application, we propose a general underlying Poisson variable framework for mixed discrete outcomes, accommodating dependency through an additive gamma frailty model for the Poisson means. The model has log-linear, complementary log-log, and proportional hazards forms for count, binary and discrete event time outcomes, respectively. Simple closed form expressions can be derived for the marginal expectations, variances, and correlations. Following a Bayesian approach to inference, conditionally-conjugate prior distributions are chosen that facilitate posterior computation via an MCMC algorithm. The methods are illustrated using data from a Tg.AC mouse bioassay study.     

Locally Addressable Electrochemical Patterning Technique (LAEPT) applied to poly(L-lysine)-graft-poly(ethylene glycol) adlayers on titanium and silicon oxide surfaces

The protein-resistant polycationic graft polymer, poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG), was uniformly adsorbed onto a homogenous titanium surface and subsequently subjected to a direct current (dc) voltage. Under the influence of an ascending cathodic and anodic potential, there was a steady and gradual loss of PLL-g-PEG from the conductive titanium surface while no desorption was observed on the insulating silicon oxide substrates. We have implemented this difference in the electrochemical response of PLL-g-PEG on conductive titanium and insulating silicon oxide regions as a biosensing platform for the controlled surface functionalization of the titanium areas while maintaining a protein-resistant background on the silicon oxide regions. A silicon-based substrate was micropatterned into alternating stripes of conductive titanium and insulating silicon oxide with subsequent PLL-g-PEG adsorption onto its surfaces. The surface modified substrate was then subjected to +1800 mV (referenced to the silver electrode). It was observed that the potentiostatic action removed the PLL-g-PEG from the titanium stripes without inducing any polyelectrolyte loss from the silicon oxide regions. Time-of-flight secondary ions mass spectroscopy and fluorescence microscopy qualitatively confirmed the PLL-g-PEG retention on the silicon oxide stripes and its absence on the titanium region. This method, known as "Locally Addressable Electrochemical Patterning Technique" (LAEPT), offers great prospects for biomedical and biosensing applications. In an attempt to elucidate the desorption mechanism of PLL-g-PEG in the presence of an electric field on titanium surface, we have conducted electrochemical impedance spectroscopy experiments on bare titanium substrates. The results showed that electrochemical transformations occurred within the titanium oxide layer; its impedance and polarization resistance were found to decrease steadily upon both cathodic and anodic polarization resulting in the polyelectrolyte desorption from the titanium surface.     

Computational identification of microRNA targets

Recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of microRNA genes. Many of these microRNAs are thought to regulate the translational expression of other genes by binding to partially complementary sites in messenger RNAs. Phenotypic and expression analysis suggests an important role of microRNAs during development. Therefore, it is of fundamental importance to identify microRNA targets. However, no experimental or computational high-throughput method for target site identification in animals has been published yet. Our main result is a new computational method that is designed to identify microRNA target sites. This method recovers with high specificity known microRNA target sites that have previously been defined experimentally. Based on these results, we present a simple model for the mechanism of microRNA target site recognition. Our model incorporates both kinetic and thermodynamic components of target recognition. When we applied our method to a set of 74 Drosophila melanogaster microRNAs, searching 3'UTR sequences of a predefined set of fly mRNAs for target sites which were evolutionary conserved between D. melanogaster and Drosophila pseudoobscura, we found that many key developmental body patterning genes such as hairy and fushi-tarazu are likely to be translationally regulated by microRNAs.     

Gene expression suggests decoupled dorsal and ventral segmentation in the millipede Glomeris marginata (Myriapoda: Diplopoda)

Diplopods (millipedes) are known for their irregular body segmentation. Most importantly, the number of dorsal segmental cuticular plates (tergites) does not match the number of ventral structures (e.g., sternites). Controversial theories exist to explain the origin of this so-called diplosegmentation. We have studied the embryology of a representative diplopod, Glomeris marginata, and have analyzed the segmentation genes engrailed (en), hedgehog (hh), cubitus-interruptus (ci), and wingless (wg). We show that dorsal segments can be distinguished from ventral segments. They differ not only in number and developmental history, but also in gene expression patterns. engrailed, hedgehog, and cubitus-interruptus are expressed in both ventral and dorsal segments, but at different intrasegmental locations, whereas wingless is expressed only in the ventral segments, but not in the dorsal segments. Ventrally, the patterns are similar to what has been described from Drosophila and other arthropods, consistent with a conserved role of these genes in establishing parasegment boundaries. On the dorsal side, however, the gene expression patterns are different and inconsistent with a role in boundary formation between segments, but they suggest that these genes might function to establish the tergite borders. Our data suggest a profound and rather complete decoupling of dorsal and ventral segmentation leading to the dorsoventral discrepancies in the number of segmental elements. Based on gene expression, we propose a model that may resolve the hitherto controversial issue of the correlation between dorsal tergites and ventral leg pairs in basal diplopods (e.g., Glomeris) and is suggestive also for derived, ring-forming diplopods (e.g., Juliformia).     

Roles of erbB4, rhombomere-specific, and rhombomere-independent cues in maintaining neural crest-free zones in the embryonic head

Within the developing vertebrate head, the migration of neural tube-derived neural crest cells (NCCs) through the cranial mesenchyme is patterned into three streams, with mesenchyme adjacent to rhombomeres (r)3 and r5 maintained NCC-free. The receptor tyrosine kinase erbB4 is expressed within r3 and r5 and is required to maintain the r3-adjacent NCC-free zone in mouse embryos. In this study, we demonstrate that the extent of r3 involvement in patterning mouse NCC migration is restricted to the same dorsolateral region regulated by erbB4. In chick embryos, we show that erbB4 signaling similarly maintains the r3-adjacent NCC-free zone. However, although r5 expresses erbB4, this is insufficient to maintain the r3-adjacent NCC-free zone in grafting experiments where r5 replaced r3, indicating that erbB4 requires additional factors at the A-P level of r3 to pattern NCC migration. Furthermore, we show that the r5-adjacent NCC-free zone is maintained independently of r5, but requires surface ectoderm. Finally, we demonstrate that avian cranial surface ectoderm is patterned molecularly, with dorsolateral surface ectoderm at the levels of r2/3 and r7 expressing the sulfatase QSulf1 in quail, or the orthologue CSulf1 in chick. Aberrant NCC migration into r3-adjacent mesenchyme correlated with more focused QSulf1 expression in r2/3 surface ectoderm.     

Sonic hedgehog exerts distinct, stage-specific effects on tongue and taste papilla development

Taste papillae are ectodermal specializations that serve to house and distribute the taste buds and their renewing cell populations in specific locations on the tongue. We previously showed that Sonic hedgehog (Shh) has a major role in regulating the number and spatial pattern of fungiform taste papillae on embryonic rat tongue, during a specific period of papilla formation from the prepapilla placode. Now we have immunolocalized the Shh protein and the Patched receptor protein (Ptc), and have tested potential roles for Shh in formation of the tongue, emergence of papilla placodes, development of papilla number and size, and maintenance of papillae after morphogenesis is advanced. Cultures of entire embryonic mandible or tongues from gestational days 12 to 18 [gestational or embryonic days (E)12-E18] were used, in which tongues and papillae develop with native spatial, temporal, and molecular characteristics. The Shh signaling pathway was disrupted with addition of cyclopamine, jervine, or the 5E1 blocking antibody. Shh and Ptc proteins are diffuse in prelingual tissue and early tongue swellings, and are progressively restricted to papilla placodes and then to regions of developing papillae. Ptc encircles the dense Shh immunoproduct in papillae at various stages. When the Shh signal is disrupted in cultures of E12 mandible, tongue formation is completely prevented. At later stages of tongue culture initiation, Shh signal disruption alters development of tongue shape (E13) and results in a repatterned fungiform papilla distribution that does not respect normally papilla-free tongue regions (E13-E14). Only a few hours of Shh signal disruption can irreversibly alter number and location of fungiform papillae on anterior tongue and elicit papilla formation on the intermolar eminence. However, once papillae are well formed (E16-E18), Shh apparently does not have a clear role in papilla maintenance, nor does the tongue retain competency to add fungiform papillae in atypical locations. Our data not only provide evidence for inductive and morphogenetic roles for Shh in tongue and fungiform papilla formation, but also suggest that Shh functions to maintain the interpapilla space and papilla-free lingual regions. We propose a model for Shh function at high concentration to form and maintain papillae and, at low concentration, to activate between-papilla genes that maintain a papilla-free epithelium.     

Testing for marginal independence between two categorical variables with multiple responses

Questions that ask respondents to "choose all that apply" from a set of items occur frequently in surveys. Categorical variables that summarize this type of survey data are called both pick any/c variables and multiple-response categorical variables. It is often of interest to test for independence between two categorical variables. When both categorical variables can have multiple responses, traditional Pearson chi-square tests for independence should not be used because of the within-subject dependence among responses. An intuitively constructed version of the Pearson statistic is proposed to perform the test using bootstrap procedures to approximate its sampling distribution. First- and second-order adjustments to the proposed statistic are given in order to use a chi-square distribution approximation. A Bonferroni adjustment is proposed to perform the test when the joint set of responses for individual subjects is unavailable. Simulations show that the bootstrap procedures hold the correct size more consistently than the other procedures.     

一种农杆菌介导的赤霉菌CCRC3.572的转化方法

目的:建立农杆菌Ti质粒介导的转化赤霉菌的新方法。方法:以农杆菌Ti质粒pCAMBIA0390为基础,构建带有潮霉素抗性基因表达盒的双元载体,并用农杆菌介导的方法转化赤霉菌。结果:构建了双元载体pCAMBIA0390-hph(PgpdA),并获得了具有潮霉素抗性的赤霉菌转化子。结论:农杆菌介导的方法适于赤霉菌的转化,为赤霉菌的遗传研究提供了一种新的手段。     

The anterior visceral endoderm-turning heads

The Anterior Visceral Endoderm is an extraembryonic tissue that plays a pivotal role during embryogenesis, being responsible for the proper orientation of the anterior-posterior axis of the embryo and for appropriate pattering of adjacent embryonic tissue. In this review I discuss the formation and migration of the AVE, and attempt to place some recent findings in the context of a working model.