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.     

The Effect of Lateral Root Outgrowth on the Structure and Permeability of the Onion Root Exodermis

Lateral root development in onion is accompanied by a variety of anatomical and permeability changes in some cells of the adventitious root. The endodermal Casparian band of the parent root is disrupted early in the development of the lateral but later extends so as to be continuous with the developing Casparian band of the new root. The lateral root emerges through a longitudinal split in the adventitious root exodermis and epidermis. Following this, the cell walls and intercellular air spaces adjacent to the lateral become incrusted with suberin and a small amount of lignin, forming a collar of modified tissue around the lateral. Subsequent radial expansion of the lateral distorts the adjacent cells of the adventitious root and forces a tight association between it and the lateral. The apoplastic permeability of lateral/parent root junctions was tested using Cellufluor, an apoplastic fluorescent dye which binds to cellulose. Prior to lateral root emergence, no dye enters the parent root cortex due to the Casparian band of the exodermis. Immediately after emergence, dye often penetrates through the break in the exodermal Casparian band and diffuses into the first cortical cell layer. However, when the collar of suberized cells develops (two days after lateral root emergence), movement of the dye into an undisturbed adventitious root is usually prevented (i.e., in 77% of the cases examined). In contrast, only 17% of the root systems which were transplanted just prior to treatment excluded the dye. This indicates that the apoplastic seals around the laterals are sensitive to movement and we recommend that only undisturbed root systems be used for permeability studies.