Cationic Cyclization Involving a Remote Allene Function in the Trifluoroethanolysis of Hepta-5,6-dienyl Toluene-p-sulphonate

The remote allene function participates efficiently in the trifluoroethanolysis of hepta-5,6-dienyl toluene-p-sulphonate, leading to the cyclized 2-methylenecyclohexyl cation

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia

Rapid creation and quantitative monitoring of high coverage shRNA libraries.

Short hairpin RNA libraries are limited by low efficacy of many shRNAs and by off-target effects, which give rise to false negatives and false positives, respectively. Here we present a strategy for rapidly creating expanded shRNA pools (approximately 30 shRNAs per gene) that are analyzed by deep sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of true hits

Structural and stereogenic properties of spiro- and ansa-substituted 1,3-propanedioxy derivatives of a spermine-bridged cyclotriphosphazene

Reaction of 1,3-propanediol with the achiral spermine-bridged cyclophosphazene 1 at various molar ratios in THF gives a number of spiro-and ansa-derivatives that exhibit different stereogenic properties, viz. racemic, meso or achiral forms. As expected, spiro forms are preferred (giving mono-, di-, tri- and tetra-substitution), although significant amounts of mono- and di-substituted ansa derivatives also occur. A number of new structures have been characterized by NMR spectroscopy and X-ray crystallography in this work; mono-spiro 2, di-mono-ansa 6 and di-spiro/mono-ansa 8. The mono-ansa compound 3 was observed in solution by NMR spectroscopy but no evidence was found for the monospiro/monoansa 5, a necessary precursor of compound 8. The tri-spiro derivative 7 has been isolated and characterized by 31P NMR spectroscopy, whereas the structures of the di-monospiro 4 (meso) and tetra-spiro 9 have been characterized previously. The stereogenic properties of many of the products have been confirmed by X-ray crystallography and/or by 31P NMR spectroscopy on addition of the chiral solvating agent, (S)-(+)-2,2,2-trifluoro-1-(9-anthryl)ethanol. Although the starting compound 1 is achiral, it is found that unsymmetrically-substituted derivatives with 1,3-propanediol give racemic mixtures for the mono-spiro 2 and tri-spiro 7 derivatives, whereas symmetrically-substituted derivatives such as di-mono-ansa 6 and di-spiro/mono-ansa 8 are meso. It is found that care must taken in interpreting the 'splitting' of 31P NMR signals on addition of CSA in terms of 'chirality' of molecules, because some meso compounds give false positive results due to changes from A2X-like to A2B or ABX spin systems

The art and science of searching MEDLINE to answer clinical questions. Finding the right number of articles

The current medical environment makes information retrieval a matter of practical importance for clinicians. Many avenues present themselves to the clinician, but here we focus on MEDLINE by summarizing the current state of the art and providing an innovative approach for skill enhancement. Because new search engines appear rapidly, we focus on generic principles that can be easily adapted to various systems, even those not yet available. We propose an idealized classification system for the results of a MEDLINE search. Type A searches produce a few articles of high quality that are directly focused on the immediate question. Type B searches yield a large number of articles, some more relevant than others. Type C searches produce few or no articles, and those that are located are not germane. Providing that relevant, high-quality articles do exist, type B and C searches may often be improved with attention to search technique. Problems stem from poor recall and poor precision. The most daunting task lies in achieving the balance between too few and too many articles. By providing a theoretical framework and several practical examples, we prepare the searcher to overcome the following barriers: a) failure to begin with a well-built question; b) failure to use the Medical Subject Headings; c) failure to leverage the relationship between recall and precision; and d) failure to apply proper limits to the search. Thought and practice will increase the utility and enjoyment of searching MEDLINE