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Celebrating the life of Stuart Warren.

Graphical abstract, Highlights • Identification of soft drug S1PR agonists. • Development of a process for the evaluation of topical esterase soft drugs. • Study skin and plasma esterase SAR., The oral S1PR1 agonist ponesimod demonstrated substantial efficacy in a phase II clinical trial of psoriasis. Unfortunately, systemic side effects were observed, which included lymphopenia and transient bradycardia. We sought to develop a topical soft-drug S1PR1 agonist with an improved therapeutic index. By modifying ponesimod, we discovered an ester series of S1PR agonists. To increase metabolic instability in plasma we synthesised esters described as specific substrates for paraoxonase and butyrylcholinesterases, esterases present in human plasma.

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients., Single-cell gene expression analysis is challenging. This work describes a new droplet-based single cell RNA-seq platform capable of processing tens of thousands of cells across 8 independent samples in minutes, and demonstrates cellular subtypes and host–donor chimerism in transplant patients.

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.

As video-based sensor networks continue to scale and become more ubiquitous, it is becoming increasingly important to focus systems research on techniques that support content-based decisions in real-time towards the edge of the network. While some prior work has focused on high-level image and video quality’s effect on computer vision (e.g., object recognition). We are unaware of any work that focuses on the low-level details of why. This paper explores the impact of compression on underlying computer vision techniques. Specifically, this paper focuses on understanding the fundamental impact of compression on SIFT feature detection and matching. We show how reduced resolution or frame quality can negatively impact feature detection and tracking.

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of up to tens of thousands of single cells per sample. Cell encapsulation in droplets takes place in ∼6 minutes, with ∼50% cell capture efficiency, up to 8 samples at a time. The speed and efficiency allow the processing of precious samples while minimizing stress to cells. To demonstrate the system′s technical performance and its applications, we collected transcriptome data from ∼¼ million single cells across 29 samples. First, we validate the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. Then, we profile 68k peripheral blood mononuclear cells (PBMCs) to demonstrate the system′s ability to characterize large immune populations. Finally, we use sequence variation in the transcriptome data to determine host and donor chimerism at single cell resolution in bone marrow mononuclear cells (BMMCs) of transplant patients. This analysis enables characterization of the complex interplay between donor and host cells and monitoring of treatment response. This high-throughput system is robust and enables characterization of diverse biological systems with single cell mRNA analysis.

Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.

Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ~2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100,000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.

The design of a new class of chiral [2]catenanes is reported. The self-assembly of [2]catenanes comprising one or two 3,3′-bitolyl spacers in the π-electron-deficient component, and bis-p-phenylene-34-crown-10 (BPP 34 C 10) as the π-electron-rich component, is described. The X-ray crystal structures, together with solution-state dynamic 1H NMR spectroscopic studies, show that the degree of order characterizing the molecular structures is substantially different from that of the “parent” [2]-catenane, comprising cyclobis(paraquat-p-phenylene) and BPP34C 10. When appropriately substituted in their ortho positions, bitolyl compounds can support axial chirality: the self-assembly of axially chiral [2]catenanes, comprising one or two 3,3′-disubstituted-2,2′-dihydroxy-1,1′-binaphthyl spacers, has been achieved in good yields, showing that the introduction of the bulky, axially chiral spacer and the consequent distortion of the cavity of the π-electron-deficient component still permits good molecular recognition between the components leading to efficient catenane production. X-ray crystallography suggests that this recognition is driven by hydrogen bonding and π-π stacking interactions between the complementary subunits. The hydroxyl groups on the chiral spacer were further functionalized as benzoyl esters in a [2]catenane as well as in the tetracationic cyclophanes; that is, chemistry can be done on these catenanes. The chiral tetracationic cyclophanes exhibit good enantiomeric differentiation toward the D- and L-enantiomers of aromatic amino acids in water and their N-acetylated derivatives in organic solvents.

Aqueous mixtures of photosensitive and inert surfactants have been prepared; photoreactions and changes in aggregation after irradiation have been characterized. The photosensitive component was a stilbene-containing gemini photosurfactant (E-SGP), and the inert surfactants were either DTAB (dodecyltrimethylammonium bromide) or one of two different gemini surfactants, 12-4-12 or 16-4-16 (butanediyl-1,4-bis(dodecyldimethylammonium bromide) or butanediyl-1,4-bis(hexadecyldimethylammonium bromide)). Small-angle neutron scattering (SANS) studies revealed that in general the initial nonirradiated mixed systems form vesicle-type aggregates (100-200 angstroms radius), in equilibrium with some smaller charged spheroidal or ellipsoidal micelles (approximately 20 angstroms radius). In all cases, UV irradiation resulted in disruption of these vesicles and the formation of charged micelles. 1H NMR showed that the main photoproduct is the cis, anti, cis dimer of E-SGP (ZEZ-DiSGP); hence, photochemically induced changes in the reactive SGP drive significant changes in the preferred aggregation structure. These results demonstrate the utility of photoactive surfactants in mixtures with inert analogues.

In this paper we describe two groups of atropisomeric phosphinous acids—bis-[( N , N -diisopropyl-1-naphthamide)-2-]phosphinous acids ( 2 to 4 ) and their 8-methoxy- substituted relations ( 8 to 10 ). The first group of acids interconvert at room temperature and the second group do not. The interconversion and properties are illustrated by two dimensional TLC and some NMR spectra. The peri substituent turns out to be important.

An asymmetric synthesis of C3-symmetric phosphane 1 has been achieved. Two of the α-methylbenzyl groups were introduced as nucleophiles (using an α-methylbenzyl Grignard reagent), and asymmetry was introduced by resolution using (R)-α-methylbenzylamine. The final α-methylbenzyl group was introduced as an electrophile (α-methylbenzyl iodide) in a modestly selective reaction. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

A new photosurfactant has been synthesized, and its photoreactions in water, interfacial properties, and changes in aggregation have been characterized. The compound is a stilbene-containing gemini photosurfactant (SGP), which is of interest because the headgroup spacer is a stilbene chromophore, and it may be prepared initially in the trans (E-SGP) form. Molecular simulations show that UV-induced reactions cause significant changes in molecular conformation and especially the relative orientation of hydrophobic chains. 1H nuclear magnetic resonance, UV−vis absorption, and liquid chromatography−mass spectroscopy results are consistent with photodimerization in aqueous solutions. Irradiation causes significant changes in surface tension (maximum Δγ = −12 mN m-1) and wettability (Δθ = −15° on hydrophobic glass). Furthermore, small-angle neutron scattering shows the initial E-SGP form is present as large vesicle-like aggregates whereas the UV-induced dimer gives small 20 A spherical charged micelles. These r...

Studies to discover novel, potent and selective oxytocin antagonists are reported. Combinatorial libraries designed to find novel replacements of fragments of oxytocin antagonist L-371,257, identified pyrimidine, thiazole, indole and benzofuran as potential alternatives to the benzoic acid moiety of L-371,257. Additional investigations identified indole and benzofuran derivatives with potent oxytocin antagonist activity.

Several phosphepine oxides were synthesised in optically pure form. Sharpless asymmetric dihydroxylation was used to introduce the chiral centres in all cases. Ring closure was achieved using either PhPCl2 or PrPCl2 together with a double nucleophile generated by either a double ortho-lithiation or double bromine–lithium exchange. The X-ray crystal structures of three phosphepine oxides illustrate their different conformations. The NMR spectra of several phosphepine oxides are described as is the chemistry which is shown to differ from that of acyclic phosphine oxides.

Phosphine oxides may be chemoselectively reduced to phosphines in excellent yield in the presence of several other functional groups using alane. An aqueous workup is not required.

Novel thiepines were synthesised using a Sharpless asymmetric dihydroxylation reaction to introduce the two chiral centres and with ring closure achieved by using sulfur diimidazole in conjunction with either a double ortho -lithiation or a double bromine/lithium exchange.

As part of a program on the use of chiral aziridines in asymmetric synthesis and catalysis, the enantiopure (N,P) ligand 1, consisting of a C-2-symmetric chiral aziridine and a triarylphosphine uni ...

Racemic dihydroxylation of alkenes is efficiently accomplished with catalytic osmium (added as OsCl3), stoichiometric K3Fe(CN)6 and quinuclidine under conditions similar to those of the Sharpless asymmetric hydroxylation.

The preparation of the title compounds is greatly improved by combining seven steps (three lithiations, three substitutions and an oxidation) into a one-pot procedure. The hydrolysis of the related phosphonium salts, the lithiation of the P-propyl phosphepine oxides and their reaction with electrophiles are described.