Pinpointing cell identity in time and space

Copyright © 2020 Savulescu, Jacobs, Negishi, Davignon and Mhlanga. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Mammalian cells display a broad spectrum of phenotypes, morphologies, and functional niches within biological systems. Our understanding of mechanisms at the individual cellular level, and how cells function in concert to form tissues, organs and systems, has been greatly facilitated by centuries of extensive work to classify and characterize cell types. Classic histological approaches are now complemented with advanced single-cell sequencing and spatial transcriptomics for cell identity studies. Emerging data suggests that additional levels of information should be considered, including the subcellular spatial distribution of molecules such as RNA and protein, when classifying cells. In this Perspective piece we describe the importance of integrating cell transcriptional state with tissue and subcellular spatial and temporal information for thorough characterization of cell type and state. We refer to recent studies making use of single cell RNA-seq and/or image-based cell characterization, which highlight a need for such in-depth characterization of cell populations. We also describe the advances required in experimental, imaging and analytical methods to address these questions. This Perspective concludes by framing this argument in the context of projects such as the Human Cell Atlas, and related fields of cancer research and developmental biology.info:eu-repo/semantics/publishedVersio

First detection of [CII]158um at high redshift: vigorous star formation in the early universe

We report the detection of the 2P_3/2 -> 2P_1/2 fine-structure line of C+ at 157.74 micron in SDSSJ114816.64+525150.3 (hereafter J1148+5251), the most distant known quasar, at z=6.42, using the IRAM 30-meter telescope. This is the first detection of the [CII] line at high redshift, and also the first detection in a Hyperluminous Infrared Galaxy (L_FIR > 10^13 Lsun). The [CII] line is detected at a significance level of 8 sigma and has a luminosity of 4.4 x 10^9 Lsun. The L_[CII]/L_FIR ratio is 2 x 10^-4, about an order of magnitude smaller than observed in local normal galaxies and similar to the ratio observed in local Ultraluminous Infrared Galaxies. The [CII] line luminosity indicates that the host galaxy of this quasar is undergoing an intense burst of star formation with an estimated rate of ~3000 Msun/yr. The detection of C+ in SDSS J1148+5251 suggests a significant enrichment of metals at z ~ 6 (age of the universe ~870 Myr), although the data are consistent with a reduced carbon to oxygen ratio as expected from chemical evolutionary models of the early phases of galaxy formation.Comment: 5 pages, 2 figures, accepted by A&A Letter

[CI] and CO in the center of M 51

We present J=2-1, J=3-2, J=4-3 12CO maps as well as J=2-1, J=3-2 13CO and 492 GHz [CI] measurements of the central region in M51. The distribution of CO is strongly concentrated towards the spiral arms. The center itself is poor in, though not devoid of, CO emission. The observed line intensities require modelling with a multi-component molecular gas. A dense component must be present with n(H2) = 1000 cm-3 and kinetic temperature T(kin)= 100 K, combined with either a less dense (about 100 cm-3) component of the same temperature, or a more dense (n(H2) = 3000 cm-3) and much cooler (T(kin) = 10-30 K) component. Atomic carbon amounts are between 5 and 10 times those of CO. Much of the molecular gas mass is associated with the hot PDR phase. The center of M 51 has a face-on gas mass density of about 40+/-20 M(O) pc-2, and a well-established CO-to-H2 conversion ratio X four to five times lower than the standard Galactic value.Comment: Accepted for publication by A&

The Error and Repair Catastrophes: A Two-Dimensional Phase Diagram in the Quasispecies Model

This paper develops a two gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by $\sigma_{via}$, yields a viable organism with first order growth rate constant $k > 1$ if it is equal to some target ``master'' sequence $\sigma_{via, 0}$. The second gene, denoted by $\sigma_{rep}$, yields an organism capable of genetic repair if it is equal to some target ``master'' sequence $\sigma_{rep, 0}$. This model is analytically solvable in the limit of infinite sequence length, and gives an equilibrium distribution which depends on \mu \equiv L\eps , the product of sequence length and per base pair replication error probability, and \eps_r , the probability of repair failure per base pair. The equilibrium distribution is shown to exist in one of three possible ``phases.'' In the first phase, the population is localized about the viability and repairing master sequences. As \eps_r exceeds the fraction of deleterious mutations, the population undergoes a ``repair'' catastrophe, in which the equilibrium distribution is still localized about the viability master sequence, but is spread ergodically over the sequence subspace defined by the repair gene. Below the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds \ln k/\eps_r , while above the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds $\ln k/f_{del}$, where $f_{del}$ denotes the fraction of deleterious mutations.Comment: 14 pages, 3 figures. Submitted to Physical Review

Scope and Mechanistic Study of the Coupling Reaction of α,β-Unsaturated Carbonyl Compounds with Alkenes: Uncovering Electronic Effects on Alkene Insertion vs Oxidative Coupling Pathways

The cationic ruthenium-hydride complex [(C6H6)(PCy3)(CO)RuH]+BF4– (1) was found to be a highly effective catalyst for the intermolecular conjugate addition of simple alkenes to α,β-unsaturated carbonyl compounds to give (Z)-selective tetrasubstituted olefin products. The analogous coupling reaction of cinnamides with electron-deficient olefins led to the oxidative coupling of two olefinic C–H bonds in forming (E)-selective diene products. The intramolecular version of the coupling reaction efficiently produced indene and bicyclic fulvene derivatives. The empirical rate law for the coupling reaction of ethyl cinnamate with propene was determined as follows: rate = k[1]1[propene]0[cinnamate]−1. A negligible deuterium kinetic isotope effect (kH/kD = 1.1 ± 0.1) was measured from both (E)-C6H5CH═C(CH3)CONHCH3 and (E)-C6H5CD═C(CH3)CONHCH3 with styrene. In contrast, a significant normal isotope effect (kH/kD = 1.7 ± 0.1) was observed from the reaction of (E)-C6H5CH═C(CH3)CONHCH3 with styrene and styrene-d8. A pronounced carbon isotope effect was measured from the coupling reaction of (E)-C6H5CH═CHCO2Et with propene (13C(recovered)/13C(virgin) at Cβ = 1.019(6)), while a negligible carbon isotope effect (13C(recovered)/13C(virgin) at Cβ = 0.999(4)) was obtained from the reaction of (E)-C6H5CH═C(CH3)CONHCH3 with styrene. Hammett plots from the correlation of para-substituted p-X-C6H4CH═CHCO2Et (X = OCH3, CH3, H, F, Cl, CO2Me, CF3) with propene and from the treatment of (E)-C6H5CH═CHCO2Et with a series of para-substituted styrenes p-Y-C6H4CH═CH2 (Y = OCH3, CH3, H, F, Cl, CF3) gave the positive slopes for both cases (ρ = +1.1 ± 0.1 and +1.5 ± 0.1, respectively). Eyring analysis of the coupling reaction led to the thermodynamic parameters, ΔH⧧ = 20 ± 2 kcal mol–1 and ΔS⧧ = −42 ± 5 eu. Two separate mechanistic pathways for the coupling reaction have been proposed on the basis of these kinetic and spectroscopic studies

Association between electrocardiographic and echocardiographic markers of stage B heart failure and cardiovascular outcome

Aims: The detection of non-ischaemic (mainly hypertension, diabetes, and obesity) stage B heart failure (SBHF) may facilitate the recognition of those at risk of progression to overt HF and HF prevention. We sought the relationship of specific electrocardiographic (ECG) markers of SBHF to echocardiographic features of SBHF and their prognostic value for development of HF. The ECG markers were Cornell product (Cornell-P), P-wave terminal force in lead V1 (PTFV1), ST depression in lead V5 V6 (minSTmV5V6), and increased heart rate. Echocardiographic assessment of SBHF included left ventricular hypertrophy (LVH), impaired global longitudinal strain (GLS), and diastolic dysfunction (DD).Methods and Results: Asymptomatic subjects ≥65 years without prior cardiac history, but with HF risks, were recruited from the local community. At baseline, they underwent clinical assessment, 12-lead ECG, and comprehensive echocardiography. New HF was assessed clinically at mean follow-up of 14 ± 4 months, and echocardiography was repeated in subjects with HF. Of the 447 study subjects (age 71 ± 5, 47% men) with SBHF, 13% had LVH, 32% impaired GLS, and 65% ≥grade I DD (10% ≥grade II DD). Forty were lost to follow-up. Clinical HF developed in 47 of 407, of whom 20% had echocardiographic LVH, 51% abnormal GLS, and 76% DD at baseline. Baseline LVH and abnormal GLS (not grade I DD) were independently associated with outcomes (clinical HF and cardiovascular death). Cornell-P and heart rate (not minSTmV5V6 nor PTFV1) were independently associated with LVH, impaired GLS, and DD. Cornell-P and minSTV5V6 (not heart rate nor PTFV1) were independently associated with outcomes. More ECG abnormalities improved sensitivity, but ECG-markers were not independent of or incremental to echocardiographic markers to predict HF in SBHF.Conclusions: In this elderly study population, ECG markers showed low diagnostic sensitivity for non-ischaemic SBHF and low prognostic value for outcomes. Cornell-P and minSTmV5V6 had predictive value for outcomes in non-ischaemic SBHF independent of age, gender, and common comorbidities but were not incremental to echocardiography

Comparison of two-dimensional strain analysis using vendor-independent and vendor-specific software in adult and pediatric patients

Introduction: Two-dimensional strain analysis is a powerful analysis modality, however, clinical utilization has been limited by variability between different analysis systems and operators. We compared strain in adults and children using vendor-specific and vendor-independent software to evaluate variability.Methods: One hundred and ten subjects (50/110 pediatric, 80/110 normal left ventricular function) had echocardiograms with a General Electric ultrasound scanner between September 2010 and January 2012. Left ventricular longitudinal strain was derived with EchoPAC (General Electric, v10.8.1), a vendor-specific software, and Velocity Vector Imaging (Siemens, v3.5), which is vendor-independent. Three independent readers analyzed all the echocardiograms yielding 330 datasets.Results: Mean left ventricular global longitudinal Lagrangian strain was -18.1 ± SD 4.4% for EchoPAC and -15.3 ± SD 4.1% for Velocity Vector Imaging. Velocity Vector Imaging yielded lower absolute global longitudinal Lagrangian strain by mean 2.9 (±SD 2.7, p Conclusion: Velocity Vector Imaging produces lower left ventricular longitudinal strain values versus EchoPAC for the same echo images. Both systems have similar inter-observer variability, Velocity Vector Imaging slightly higher intra-observer variability. A statistically significant change in global longitudinal Lagrangian strain occurs with changes >3-5 strain points on repeat measurements. Strain values between the systems are not interchangeable