The influence of a biomimetic pulmonary surfactant modification on the in vivo fate of nanoparticles in the lung.

Direct biomimetic modification of nanoparticles (NPs) with endogenous surfactants is helpful to improve the biocompatibility of NPs and avoid damage to the physiological function of the lung. Therefore, the objective of this study is to investigate the influence of biomimetic endogenous pulmonary surfactant phospholipid modification on the in vivo fate of NPs after lung delivery. Here, two neutral phospholipids (dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylamine (DPPE)) and two negatively charged phospholipids (dipalmitoylphosphatidylglycerol (DPPG), dipalmitoylphosphatidylserine (DPPS)) were selected to modify paclitaxel (PTX)-loaded PLGA NPs with different molar ratio.

Exploring the intrinsic micro-/nanoparticle size on their in vivo fate after lung delivery.

Micro-/nanocarriers due to their significant advantages are widely investigated in pulmonary drug delivery. However, different size carriers have varied drug release rate, concealing the effect of particle size on the fate of drugs in vivo. Therefore, by keeping drug release rate comparable, the objective of this study is to elucidate the influence of particle size itself on drug in vivo fate after intratracheal instillation to mice.

Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.

We present a new phylogenetic approach, selection on amino acids and codons (SelAC), whose substitution rates are based on a nested model linking protein expression to population genetics. Unlike simpler codon models that assume a single substitution matrix for all sites, our model more realistically represents the evolution of protein-coding DNA under the assumption of consistent, stabilizing selection using a cost-benefit approach. This cost-benefit approach allows us to generate a set of 20 optimal amino acid-specific matrix families using just a handful of parameters and naturally links the strength of stabilizing selection to protein synthesis levels, which we can estimate.

Ebolavirus comparative genomics.

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes.

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam.

Background: Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank.

Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance.

Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis.

Omega: an overlap-graph de novo assembler for metagenomics.

Motivation: Metagenomic sequencing allows reconstruction of microbial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed for assembling and scaffolding Illumina sequencing data of microbial communities.

Results: Omega found overlaps between reads using a prefix/suffix hash table.

Influence of root-exudates concentration on pyrene degradation and soil microbial characteristics in pyrene contaminated soil.

The effect of ryegrass (Lolium perenne L.) root-exudates concentration on pyrene degradation and the microbial ecological characteristics in the pyrene contaminated soil was investigated by simulating a gradually reducing concentration of root exudates with the distance away from root surface in the rhizosphere. Results showed that, after the root-exudates were added 15 d, the pyrene residue in contaminated soil responded nonlinearly in the soils with the same pyrene contaminated level as the added root-exudates concentration increased, which decreased first and increased latter with the increase of the added root-exudates concentration.

Spacial characteristics of pyrene degradation and soil microbial activity with the distance from the ryegrass (Lolium perenne L.) root surface in a multi-interlayer rhizobox.

To investigate rhizosphere effects on the biodegradation of pyrene with the distance away from root surface in the rhizosphere of ryegrass (Lolium perenne L.), a glasshouse experiment was conducted using a multi-interlayer rhizobox where ryegrass were grown in a soil spiked with pyrene. The largest and most rapid dissipation of pyrene in planted soil appeared at 2 mm zone from the root zone.

On the number of binary characters needed to recover a phylogeny using maximum parsimony.

We give an explicit construction to solve a conjecture of Mike Steel and David Penny that any phylogeny involving N taxa can be recovered unambiguously using on the order of log N binary characters and the method of maximum parsimony. Biologically, this means that homoplasy need not be a deterrent to parsimony methods. Some patterns of homoplasy are phylogenetically informative and can exponentially reduce the amount of data needed to resolve a phylogeny.