@article {68341,
	title = {Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling},
	journal = {bioRxiv},
	year = {2020},
	month = {07/2020},
	abstract = {<p>Acquiring both lineage and cell-type information during brain development could elucidate transcriptional programs underling neuronal diversification. This is now feasible with single-cell RNA-seq combined with CRISPR-based lineage tracing, which generates genetic barcodes with cumulative CRISPR edits. This technique has not yet been optimized to deliver high-resolution lineage reconstruction of protracted lineages. Drosophila neuronal lineages are an ideal model to consider, as multiple lineages have been morphologically mapped at single-cell resolution. Here we find the parameter ranges required to encode a representative neuronal lineage emanating from 100 stem cell divisions. We derive the optimum editing rate to be inversely proportional to lineage depth, enabling encoding to persist across lineage progression. Further, we experimentally determine the editing rates of a Cas9-deaminase in cycling neural stem cells, finding near ideal rates to map elongated Drosophila neuronal lineages. Moreover, we propose and evaluate strategies to separate recurring cell-types for lineage reconstruction. Finally, we present a simple method to combine multiple experiments, which permits dense reconstruction of protracted cell lineages despite suboptimum lineage encoding and sparse cell sampling.Competing Interest StatementThe authors have declared no competing interest.</p>
},
	doi = {10.1101/2020.07.27.223321},
	url = {https://www.biorxiv.org/content/early/2020/07/29/2020.07.27.223321},
	author = {Sugino, Ken and Miyares, Rosa L. and Espinosa-Medina, Isabel and Chen, Hui-Min and Potter, Christopher J and Lee, Tzumin}
}
@article {68447,
	title = {A transcriptional reporter of intracellular Ca(2+) in Drosophila.},
	journal = {Nat Neurosci},
	volume = {18},
	year = {2015},
	month = {06/2015},
	pages = {917-25},
	abstract = {<p>Intracellular Ca(2+) is a widely used neuronal activity indicator. Here we describe a transcriptional reporter of intracellular Ca(2+) (TRIC) in Drosophila that uses a binary expression system to report Ca(2+)-dependent interactions between calmodulin and its target peptide. We found that in vitro assays predicted in vivo properties of TRIC and that TRIC signals in sensory systems depend on neuronal activity. TRIC was able to quantitatively monitor neuronal responses that changed slowly, such as those of neuropeptide F-expressing neurons to sexual deprivation and neuroendocrine pars intercerebralis cells to food and arousal. Furthermore, TRIC-induced expression of a neuronal silencer in nutrient-activated cells enhanced stress resistance, providing a proof of principle that TRIC can be used for circuit manipulation. Thus, TRIC facilitates the monitoring and manipulation of neuronal activity, especially those reflecting slow changes in physiological states that are poorly captured by existing methods. TRIC{\textquoteright}s modular design should enable optimization and adaptation to other organisms.</p>
},
	keywords = {Animals, Calcium, Calcium Signaling, Cells, Cultured, Drosophila, Molecular Sequence Data, Mutagenesis, Neural Pathways, Olfactory Pathways, Optic Lobe, Nonmammalian, Stress, Psychological, Synaptic Transmission, Visual Pathways},
	issn = {1546-1726},
	doi = {10.1038/nn.4016},
	author = {Gao, Xiaojing J and Riabinina, Olena and Li, Jiefu and Potter, Christopher J and Clandinin, Thomas R and Luo, Liqun}
}
