Beyond directed evolution: Darwinian selection as a tool for synthetic biology

Synthetic biology is an engineering approach that seeks to design and construct new biological parts, devices and systems, as well as to re-design existing components. However, rationally designed synthetic circuits may not work as expected due to the context-dependence of biological parts. Darwinian selection, the main mechanism through which evolution works, is a major force in creating biodiversity and may be a powerful tool for synthetic biology. This article reviews selection-based techniques and proposes strict Darwinian selection as an alternative approach for the identification and characterization of parts. Additionally, a strategy for fine-tuning of relatively complex circuits by coupling them to a master standard circuit is discussed.     

Anthropological Genetics: Inferring the History of Our Species Through the Analysis of DNA

The genetic material, deoxyribonucleic acid (DNA), contains information about the evolutionary history of life. Both the relationships amongst organisms and the times of their divergence can be inferred from DNA sequences. Anthropological geneticists use DNA sequences to infer the evolutionary history of humans and their primate relatives. We review the basic methodology used to infer these relationships. We then review the anthropological genetic evidence for modern human origins. We conclude that modern humans evolved recently in Africa and then left to colonize the rest of the world within the last 50,000 years, largely replacing the other human groups that they encountered. Modern humans likely exchanged genes with Neanderthals prior to or early during their expansion out of Africa.     

Phospholipid transfer protein (PLTP) mRNA expression is stimulated by developing embryos in the oviduct

In mammal, fertilization and early preimplantation embryo development occurs in the oviduct. Evidence is accumulating that the oviductal epithelia secrete various biomolecules to the lumen during the secretory phase of the estrus cycle to enhance embryo development. This secretory activity of the oviduct is under the regulation of steroid hormones. Observations also suggested that the gametes and embryos modulate the physiology and gene-expressing pattern of the oviduct. However, the underlying molecular changes remain elusive. We hypothesize that the developing embryos interact with the surrounding environment and affect the gene expression patterns of the oviduct, thereby modulating the oviductal secretory activity conducive to the preimplantation embryo development. To test this hypothesis, suppression subtractive hybridization (SSH) was used to compare the gene expressions in mouse oviduct containing transferred in vitro cultured preimplantation embryos with that of oviduct containing oocytes during the preimplantation period. We reported here the identification and characterization of phospholipids transfer protein (PLTP), which is highly expressed in the embryo-containing oviduct and localized at the oviductal epithelium by in situ hybridization. PLTP contains signal peptide putative for secretory function. More importantly, PLTP mRNA increases in the oviductal epithelia of pregnant, but not pseudo-pregnant mice when assayed by real-time PCR. Taken together, our data suggested that PLTP may play important role(s) during in vivo preimplantation embryo development. This molecule would be a target to delineate the mechanisms and the roles of oviductal secretory proteins on early embryonic development.     

Synergistic epistasis of the deleterious effects of transposable elements

The replicative nature and generally deleterious effects of transposable elements (TEs) raise an outstanding question about how TE copy number is stably contained in host populations. Classic theoretical analyses predict that, when the decline in fitness due to each additional TE insertion is greater than linear, or when there is synergistic epistasis, selection against TEs can result in a stable equilibrium of TE copy number. While several mechanisms are predicted to yield synergistic deleterious effects of TEs, we lack empirical investigations of the presence of such epistatic interactions. Purifying selection with synergistic epistasis generates repulsion linkage between deleterious alleles. We investigated this population genetic signal in the likely ancestral Drosophila melanogaster population and found evidence supporting the presence of synergistic epistasis among TE insertions, especially TEs expected to exert large fitness impacts. Even though synergistic epistasis of TEs has been predicted to arise through ectopic recombination and TE-mediated epigenetic silencing mechanisms, we only found mixed support for the associated predictions. We observed signals of synergistic epistasis for a large number of TE families, which is consistent with the expectation that such epistatic interaction mainly happens among copies of the same family. Curiously, significant repulsion linkage was also found among TE insertions from different families, suggesting the possibility that synergism of TEs’ deleterious fitness effects could arise above the family level and through mechanisms similar to those of simple mutations. Our findings set the stage for investigating the prevalence and importance of epistatic interactions in the evolutionary dynamics of TEs.     

Effect of silicon-doped calcium phosphate cement on angiogenesis based on controlled macrophage polarization

Vascularization is an important early indicator of osteogenesis involving biomaterials.Bone repair and new bone formation are associated with extensive neovascu...     

Comparative proteome analysis using amine-reactive isobaric tagging reagents coupled with 2D LC/MS/MS in 3T3-L1 adipocytes following hypoxia or normoxia

Hypoxia during the expansion of adipocytes is known to contribute both to the secretion of multiple inflammation-related adipokines as well as to obesity. We therefore investigated the nature of protein changes occurring in adipocytes during hypoxia by observation of the intracellular proteins that are expressed in 3T3-L1 adipocytes. Lysates were utilized for quantitative proteome analysis using isobaric tags for relative and absolute quantitation (iTRAQ) combined with peptide separation by multi-dimensional liquid chromatography. Antioxidants and elongation factors, as well as glycolytic enzymes were increased in hypoxic adipocytes. These changes were supported by similar changes suggested by real-time PCR. The proteins showing changes are all potential targets for revering the mechanism behind the phenomenon of induction of obese adipocytes by hypoxia. This study can therefore aid in defining the proteomic changes that occur in adipocytes in response to oxygen stress, and can further characterize adipocyte metabolism and adaptation to low oxygen conditions.     

Long-term use of high-efficiency vacuum cleaners and residential airborne fungal-spore exposure

Exposure to fungal allergens is an important contributor to allergic respiratory disease, but information on the efficacy of residential fungal allergen-avoidance in allergic-disease management is lacking. Using vacuum cleaners with high-efficiency exhaust filtration is one method recommended for reducing residential allergen exposure levels, but their use to reduce fungal-spore exposure levels has not been evaluated. To evaluate the effectiveness of high-efficiency vacuuming to control airborne fungal-spore levels, fungal bioaerosols were repeatedly assessed over the course of 10 months in homes randomly assigned to groups using either conventionally filtered (control) or high-efficiency-filtered vacuum cleaners for routine vacuum cleaning. Air samples were analyzed for three fungal-spore categories representing taxa with predominantly outdoor sources and one representing taxa that commonly have indoor sources. In a two-way analysis of variance, sampling period had a significant effect on mean levels of all fungal-spore categories. Vacuum cleaner type had a marginally significant effect on the indoor spore category, with one high-efficiency vacuum group mean (of three) significantly lower than one control mean. No effect was observed of vacuum cleaner type on outdoor spore categories. Including home-environment variables in analysis of covariance models strengthened the effect of the vacuum-type treatment on the indoor spore category, with no effect on the three outdoor spore categories. Decreased indoor spore levels vs. controls were only observed in high-efficiency vacuum groups during the last sampling period, at the end of the heating season. The results suggest that using a vacuum with high-efficiency filtered exhaust could have some modest effectiveness in controlling airborne fungal-spore exposure in homes when infiltration of outdoor air is very limited.