Synthesis and cell-free cloning of DNA libraries using programmable microfluidics

Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cellfree cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development

Cell Lineage Analysis of the Mammalian Female Germline

Fundamental aspects of embryonic and post-natal development, including maintenance of the mammalian female germline, are largely unknown. Here we employ a retrospective, phylogenetic-based method for reconstructing cell lineage trees utilizing somatic mutations accumulated in microsatellites, to study female germline dynamics in mice. Reconstructed cell lineage trees can be used to estimate lineage relationships between different cell types, as well as cell depth (number of cell divisions since the zygote). We show that, in the reconstructed mouse cell lineage trees, oocytes form clusters that are separate from hematopoietic and mesenchymal stem cells, both in young and old mice, indicating that these populations belong to distinct lineages. Furthermore, while cumulus cells sampled from different ovarian follicles are distinctly clustered on the reconstructed trees, oocytes from the left and right ovaries are not, suggesting a mixing of their progenitor pools. We also observed an increase in oocyte depth with mouse age, which can be explained either by depth-guided selection of oocytes for ovulation or by post-natal renewal. Overall, our study sheds light on substantial novel aspects of female germline preservation and development

Accelerated increase in GV oocyte from large antral follicles depth following unilateral ovariectomy.

<p>a–c) Reconstructed lineage trees of oocytes from both ovaries of unilaterally ovariectomized mice. Blue circles are oocytes extracted from the ovary removed at a young age – 23 days (a) 29 days (b) and 26 days (c). Green circles are oocytes extracted from the contralateral ovary removed at an older age – 139 days (a) 161 days (b) and 150 days in which the ovulated oocytes were marked with blue dots (c). Horizontal lines are the average depths of young oocytes (blue) and old oocytes (green). d) Increase in depth with age following ovariectomy is accelerated relative to the increase observed for non-ovariectomized mice. Last two boxes include pooled data from the indicated mice. * p<0.05, ** p<0.01.</p

Oocyte depth increases with age.

<p>a–c) Reconstructed lineage trees of GV oocytes from large antral follilces in three mice demonstrate an increase in oocyte depth (Y axis) with age. The putative zygote is at depth 0. Median depth of oocytes is 13 divisions in M27, a 27 day old mouse (Mouse names represent their age in days) (a), 16 divisions in mouse M159 (b) and 19 in mouse M268 which contains 6 ovulated oocytes which were marked on the tree with blue dots (c). Horizontal red lines denote the median depth. All lineage trees were reconstructed using the maximum-likelihood neighbor joining method and rooted with the median identifier of all cells. d) Median depth of GV oocytes from large antral follicels increases with age. Each blue point is the median of the depths of all oocytes sampled from a single mouse. The Pearson correlation of median depth and age is 0.81 (p = 0.007). High inter-mouse variability can be seen. Errorbars are standard errors of the means. (e) Depth of pancreatic islet cells does not increase with age. Shown are the depths of pancreatic islet cells from M36, a 1-month old mouse and from M280, a 9-month old mouse.</p

Oocytes form a cluster distinct from bone marrow cells.

<p>Reconstructed cell lineage tree of mice in several ages, each showing that GV oocytes from large antral follicles (red) form a cluster that is distinct from cells of bone marrow origin (mesenchymal stem cells- yellow and lymphocytes-blue). Ovarian cumulus cells are in green. Shaded boxes denote subtrees that are statistically enriched for cells of a certain cell population, using a hyper-geometric enrichment test. Mouse names represent their age in days. Y axis is depth (number of divisions since the zygote). One cell in M278 was cropped for visual clarity.</p

Microsatellite mutations are replication dependent.

<p>a) Shown are two scenarios for microsatellite mutations – replication dependent mutations that occur during mitotic divisions at a cell stage with two chromosomal copies (left), and spontaneous, replication independent mutations occurring at the quiescent oocyte stage with four chromosomal copies (right). While replication dependent mutations would result in two alleles, spontaneous mutations would mostly result in more than two alleles. The bottom plots show representative capillary signals. b) The increase with age in fraction of alleles with spontaneous mutations is significantly smaller than the increase in fraction of alleles with replication dependent mutations. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002477#s2" target="_blank">Results</a> are for the three longitudinal experiments.</p