Zebrafish mdk2, a novel secreted midkine, participates in posterior neurogenesis

Patterning the neural plate in vertebrates depends on complex interactions between a variety of secreted growth factors. Here we describe a novel secreted factor in zebrafish, named mdk2, related to the midkine family of heparin-binding growth factors that is involved in posterior neural development. mdk2 is expressed shortly after the onset of gastrulation in the presumptive neural plate cells of the epiblast, and this expression is enhanced by exogenous retinoic acid. Ectopic expression of mdk2 enhances neural crest cell fates at the lateral edges of the caudal neural plate, concomitant with a repression of anterior structures and mesendodermal and ectodermal markers. Reciprocally, ectopic expression of a dominant negative mdk2 results in severe deficiencies of structures posterior to the midbrain-hindbrain boundary, with negligible effects on anterior structures. In these embryos, the expression of hindbrain and neural crest markers is strongly reduced, and the formation of posterior primary moto- and sensory neurons is blocked. Analyses in mutant zebrafish embryos shows that expression of mdk2 is independent of FGF8 and nodal-related-1 signaling, but is under negative control of BMP signaling. These data support the hypothesis that mdk2 participates in posterior neural development in zebrafish.     

Structure-activity relationships of apio nucleosides as potential antiviral agents

Several types of novel apio nucleosides were synthesized starting from 1,3-dihydroxyacetone and evaluated for antiviral activity. Among compounds tested, amino substituted apio dideoxynucleosides exhibited anti-HBV activity, while thioapio dideoxynucleosides were found to be active against HIV-1. Apio dideoxydidehydro nucleosides showed moderate to potent anti-HCMV activity, but their bioisosteric thioapio dideoxydidehydro nucleosides did not exhibit any significant antiviral activity.     

Cloning of a dextransucrase gene (fmcmds) from a constitutive dextransucrase hyper-producing Leuconostoc mesenteroides B-512FMCM developed using VUV

Dextransucrase (FMCMDS) from Leuconostoc mesenteroides B-512FMCM, a dextransucrase constitutive and hyper-producing strain, catalyzes the synthesis of dextran from sucrose. The coding region for fmcmds was isolated and sequenced. It consisted of an open reading frame (ORF) of 4699 bp, coding for a 1527 amino acid protein with a molecular mass of 170 kDa. However, it showed a dextransucrase activity band at 180 kDa in SDS-PAGE. Only one nucleotide changed in the promoter site and two amino acid residues were changed in the structural gene from that of the parent L. mesenteroides NRRL B-512F dsrS; an inducible dextransucrase gene of low productivity.     

A statistical model for describing and simulating microbial community profiles

Many methods have been developed for statistical analysis of microbial community profiles, but due to the complex nature of typical microbiome measurements (e.g. sparsity, zero-inflation, non-independence, and compositionality) and of the associated underlying biology, it is difficult to compare or evaluate such methods within a single systematic framework. To address this challenge, we developed SparseDOSSA (Sparse Data Observations for the Simulation of Synthetic Abundances): a statistical model of microbial ecological population structure, which can be used to parameterize real-world microbial community profiles and to simulate new, realistic profiles of known structure for methods evaluation. Specifically, SparseDOSSA’s model captures marginal microbial feature abundances as a zero-inflated log-normal distribution, with additional model components for absolute cell counts and the sequence read generation process, microbe-microbe, and microbe-environment interactions. Together, these allow fully known covariance structure between synthetic features (i.e. “taxa”) or between features and “phenotypes” to be simulated for method benchmarking. Here, we demonstrate SparseDOSSA’s performance for 1) accurately modeling human-associated microbial population profiles; 2) generating synthetic communities with controlled population and ecological structures; 3) spiking-in true positive synthetic associations to benchmark analysis methods; and 4) recapitulating an end-to-end mouse microbiome feeding experiment. Together, these represent the most common analysis types in assessment of real microbial community environmental and epidemiological statistics, thus demonstrating SparseDOSSA’s utility as a general-purpose aid for modeling communities and evaluating quantitative methods. An open-source implementation is available at http://huttenhower.sph.harvard.edu/sparsedossa2.     

Establishment of the site of involution at novel locations on the amphibian embryo

Anuran (Rana) and urodele (Ambystoma) amphibian eggs were subjected to prolonged unnatural orientations in relation to gravity. In some cases eggs were rotated 90°, while in other instances eggs were rotated 180° (complete inversion). Alterations in the pigmentation pattern, cleavage pattern, and site of involution were observed. Despite these unnatural orientations to gravity, the morphogenesis of axial structures was frequently normal. Reorganization of the egg cytoplasm apparently takes place after the unnatural orientation. Rather than being localized in a fixed position in the egg (e.g., the egg cortex), the determinants for the pattern of early embryogenesis are probably located in that portion of the cytoplasm (e.g., “internal” cytoplasm) that orients to gravity.