Moment-based analysis of biochemical networks in a heterogeneous population of communicating cells

Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic subpopulations. Here we discuss a moment-based approach to study how cell-cell communication affects noise in biochemical networks that arises from both intrinsic and extrinsic sources. We derive a system of approximate differential equations that captures lower-order moments of a population of cells, which communicate by secreting and sensing a diffusing molecule. Since the number of obtained equations grows combinatorially with number of considered cells, we employ a previously proposed model reduction technique, which exploits symmetries in the underlying moment dynamics. Importantly, the number of equations obtained in this way is independent of the number of considered cells such that the method scales to arbitrary population sizes. Based on this approach, we study how cell-cell communication affects population variability in several biochemical networks. Moreover, we analyze the accuracy and computational efficiency of the moment-based approximation by comparing it with moments obtained from stochastic simulations.Comment: 6 pages, 5 Figure

Building synthetic multicellular systems from the bottom-up

Biological cell populations, such as in tissues or microbial communities, are constantly subject to different sources of noise and variability. Despite this, multicellular systems are still able to function properly because cells coordinate with each other by communication. Using biological model systems to study this multiscalar process can be challenging because of their innate complexity. In this thesis, we address this challenge by building a synthetic multicellular system using bottom-up in vitro assembly approaches. Using this platform, we aim to study the effect of cell-to-cell communication to population variability in a minimal and simplified context. To achieve this, we require a synthetic cell population with (i) quantifiable gene expression dynamics, (ii) customizable population variability, and (iii) intercellular communication. Having these characteristics will allow us to test different initial configurations of population variability and monitor population gene expression dynamics with and without cell-to-cell communication. To generate these synthetic cell populations, reconstituted cell-free expression systems (CFES) are encapsulated into monodisperse-sized liposomes using double-emulsion microfluidics. Both transcription and translation levels are simultaneously monitored and quantified to develop models of cell-free gene expression dynamics and differentiate between bulk and encapsulated formats. Population variability was then incorporated by combining different batches of cells to create distinct subpopulations or by using a two-inlet double-emulsion microfluidic device to generate single populations with a large dispersion of encapsulated DNA template. Lastly, genetic circuits based on the quorum sensing system of Vibrio fischeri are used to implement diffusion-mediated intercellular signalling. Quorum sensing gene circuits in Escherichia coli extract-based CFES were tested in bulk and phase transfer-generated synthetic cells. Together with these experimental systems, corresponding models of synthetic cell populations that can account for population variability and secrete-and-sensing communication are developed using mixed-effects models and moment dynamics. Overall, this work leverages CFES and microfluidic technologies to reproducibly generate a simplified in vitro model of multicellular systems that can be easily monitored spatiotemporally to study multi-scalar processes.:Preface Chapter 1 Bottom-up multicellular systems Chapter 2 Building blocks: cell-free expression and liposomes Chapter 3 Gene expression dynamics in synthetic cell populations Chapter 4 Variability and communication in synthetic cell populations Chapter 5 Modeling variability & communication in synthetic cell populations Summary and outlook Appendices BibliographyBiologische Zellpopulationen, z.B. in Geweben oder mikrobiellen Gemeinschaften, sind ständig verschiedenen Quellen von Rauschen und Variabilität ausgesetzt. Trotzdem sind multizelluläre Systeme in der Lage, ordnungsgemäß zu funktionieren, weil sich die Zellen durch Kommunikation miteinander abstimmen. Die Verwendung biologischer Modellsysteme zur Untersuchung dieses multiskalaren Prozesses kann aufgrund ihrer angeborenen Komplexität eine Herausforderung darstellen. In dieser Arbeit gehen wir diese Herausforderung an, indem wir ein synthetisches multizelluläres System mit Hilfe von Bottom-up-in vitro-Assembly-Ansätzen aufbauen. Mit Hilfe dieser Plattform wollen wir die Auswirkungen der Kommunikation von Zelle zu Zelle auf die Populationsvariabilität in einem minimalen und vereinfachten Kontext untersuchen. Um dies zu erreichen, benötigen wir eine synthetische Zellpopulation mit (i) quantifizierbarer Genexpressionsdynamik, (ii) anpassbarer Populationsvariabilität und (iii) interzellulärer Kommunikation. Mit diesen Eigenschaften können wir verschiedene Ausgangskonfigurationen der Populationsvariabilität testen und die Genexpressionsdynamik der Population mit und ohne Zell-zu-Zell-Kommunikation beobachten. Um diese synthetischen Zellpopulationen zu erzeugen, werden rekonstituierte zellfreie Expressionssysteme (CFES) mit Hilfe der Doppelemulsions-Mikrofluidik in monodisperse Liposomen eingekapselt. Sowohl die Transkriptions- als auch die Translationsraten werden gleichzeitig überwacht und quantifiziert, um Modelle für die Dynamik der zellfreien Genexpression zu entwickeln und zwischen Bulk- und verkapselten Formaten zu unterscheiden. Die Variabilität der Populationen wurde dann durch die Kombination verschiedener Zellchargen zur Bildung unterschiedlicher Subpopulationen oder durch die Verwendung einer mikrofluidischen Doppelemulsionsvorrichtung mit zwei Einlässen zur Erzeugung einzelner Populationen mit einer großen Streuung der eingekapselten DNA-Vorlage einbezogen. Schließlich werden genetische Schaltkreise auf der Grundlage des Quorum-Sensing-Systems von Vibrio fischeri verwendet, um diffusionsvermittelte interzelluläre Signalübertragung zu implementieren. Quorum-Sensing-Genkreisläufe in CFES auf der Basis von Escherichia coli-Extrakten wurden in synthetischen Zellen getestet, die durch Bulk- und Phasentransfer erzeugt wurden. Zusammen mit diesen experimentellen Systemen wurden entsprechende Modelle synthetischer Zellpopulationen entwickelt, die die Populationsvariabilität und die Sekretions- und Sensing-Kommunikation mit Hilfe von Mixed-Effects-Modellen und Momentendynamik berücksichtigen können. Insgesamt nutzt diese Arbeit CFES- und Mikrofluidik-Technologien, um reproduzierbar ein vereinfachtes in vitro-Modell multizellulärer Systeme zu erzeugen, das leicht raum-zeitlich überwacht werden kann, um multiskalare Prozesse zu untersuchen.:Preface Chapter 1 Bottom-up multicellular systems Chapter 2 Building blocks: cell-free expression and liposomes Chapter 3 Gene expression dynamics in synthetic cell populations Chapter 4 Variability and communication in synthetic cell populations Chapter 5 Modeling variability & communication in synthetic cell populations Summary and outlook Appendices Bibliograph

Discovery of a Transiting Adolescent Sub-Neptune Exoplanet with K2

The role of stellar age in the measured properties and occurrence rates of exoplanets is not well understood. This is in part due to a paucity of known young planets and the uncertainties in age-dating for most exoplanet host stars. Exoplanets with well-constrained ages, particularly those which are young, are useful as benchmarks for studies aiming to constrain the evolutionary timescales relevant for planets. Such timescales may concern orbital migration, gravitational contraction, or atmospheric photo-evaporation, among other mechanisms. Here we report the discovery of an adolescent transiting sub-Neptune from K2 photometry of the low-mass star K2-284. From multiple age indicators we estimate the age of the star to be 120 Myr, with a 68% confidence interval of 100-760 Myr. The size of K2-284 b ($R_P$ = 2.8 $\pm$ 0.1 $R_\oplus$) combined with its youth make it an intriguing case study for photo-evaporation models, which predict enhanced atmospheric mass loss during early evolutionary stages.Comment: Accepted to AJ, 36 pages, 17 figures, 5 table

Determining the Structure of Higgs Couplings at the LHC

Higgs boson production via weak boson fusion at the CERN Large Hadron Collider has the capability to determine the dominant CP nature of a Higgs boson, via the tensor structure of its coupling to weak bosons. This information is contained in the azimuthal angle distribution of the two outgoing forward tagging jets. The technique is independent of both the Higgs boson mass and the observed decay channel.Comment: 5 pages, 4 figures, version accepted for publication in PR

IR and UV Galaxies at z=0.6 -- Evolution of Dust Attenuation and Stellar Mass as Revealed by SWIRE and GALEX

We study dust attenuation and stellar mass of $\rm z\sim 0.6$ star-forming galaxies using new SWIRE observations in IR and GALEX observations in UV. Two samples are selected from the SWIRE and GALEX source catalogs in the SWIRE/GALEX field ELAIS-N1-00 ($\Omega = 0.8$ deg$^2$). The UV selected sample has 600 galaxies with photometric redshift (hereafter photo-z) $0.5 \leq z \leq 0.7$ and NUV$\leq 23.5$ (corresponding to \rm L_{FUV} \geq 10^{9.6} L_\sun). The IR selected sample contains 430 galaxies with $f_{24\mu m} \geq 0.2$ mJy (\rm L_{dust} \geq 10^{10.8} L_\sun) in the same photo-z range. It is found that the mean $\rm L_{dust}/L_{FUV}$ ratios of the z=0.6 UV galaxies are consistent with that of their z=0 counterparts of the same $\rm L_{FUV}$. For IR galaxies, the mean $\rm L_{dust}/L_{FUV}$ ratios of the z=0.6 LIRGs (\rm L_{dust} \sim 10^{11} L_\sun) are about a factor of 2 lower than local LIRGs, whereas z=0.6 ULIRGs (\rm L_{dust} \sim 10^{12} L_\sun) have the same mean $\rm L_{dust}/L_{FUV}$ ratios as their local counterparts. This is consistent with the hypothesis that the dominant component of LIRG population has changed from large, gas rich spirals at z$>0.5$ to major-mergers at z=0. The stellar mass of z=0.6 UV galaxies of \rm L_{FUV} \leq 10^{10.2} L_\sun is about a factor 2 less than their local counterparts of the same luminosity, indicating growth of these galaxies. The mass of z=0.6 UV lunmous galaxies (UVLGs: \rm L_{FUV} > 10^{10.2} L_\sun) and IR selected galaxies, which are nearly exclusively LIRGs and ULIRGs, is the same as their local counterparts.Comment: 27 pages, 8 figures, to be published in the Astrophysical Journal Supplement series dedicated to GALEX result

The Influences of Reproductive Status and Acute Stress on the Levels of Phosphorylated Mu Opioid Receptor Immunoreactivity in Rat Hippocampus

Opioids play a critical role in hippocampally dependent behavior and plasticity. In the hippocampal formation, mu opioid receptors (MOR) are prominent in parvalbumin (PARV) containing interneurons. Previously we found that gonadal hormones modulate the trafficking of MORs in PARV interneurons. Although sex differences in response to stress are well documented, the point at which opioids, sex, and stress interact to influence hippocampal function remains elusive. Thus, we used quantitative immunocytochemistry in combination with light and electron microscopy for the phosphorylated MOR (pMOR) at the SER375 carboxy-terminal residue in male and female rats to assess these interactions. In both sexes, pMOR-immunoreactivity (ir) was prominent in axons and terminals and in a few neuronal somata and dendrites, some of which contained PARV in the mossy fiber pathway region of the dentate gyrus (DG) hilus and CA3 stratum lucidum. In unstressed rats, the levels of pMOR-ir in the DG or CA3 were not affected by sex or estrous cycle stage. However, immediately following 30 min of acute immobilization stress (AIS), males had higher levels of pMOR-ir whereas females at proestrus and estrus (high estrogen stages) had lower levels of pMOR-ir within the DG. In contrast, the number and types of neuronal profiles with pMOR-ir were not altered by AIS in either males or proestrus females. These data demonstrate that although gonadal steroids do not affect pMOR levels at resting conditions, they are differentially activated both pre and postsynaptic MORs following stress. These interactions may contribute to the reported sex differences in hippocampally dependent behaviors in stressed animals

The role of childhood social position in adult type 2 diabetes: Evidence from the English Longitudinal Study of Ageing

Copyright @ 2014 Pikhartova et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: Socioeconomic circumstances in childhood and early adulthood may influence the later onset of chronic disease, although such research is limited for type 2 diabetes and its risk factors at the different stages of life. The main aim of the present study is to examine the role of childhood social position and later inflammatory markers and health behaviours in developing type 2 diabetes at older ages using a pathway analytic approach. Methods. Data on childhood and adult life circumstances of 2,994 men and 4,021 women from English Longitudinal Study of Ageing (ELSA) were used to evaluate their association with diabetes at age 50 years and more. The cases of diabetes were based on having increased blood levels of glycated haemoglobin and/or self-reported medication for diabetes and/or being diagnosed with type 2 diabetes. Father's job when ELSA participants were aged 14 years was used as the measure of childhood social position. Current social characteristics, health behaviours and inflammatory biomarkers were used as potential mediators in the statistical analysis to assess direct and indirect effects of childhood circumstances on diabetes in later life. Results: 12.6 per cent of participants were classified as having diabetes. A disadvantaged social position in childhood, as measured by father's manual occupation, was associated at conventional levels of statistical significance with an increased risk of type 2 diabetes in adulthood, both directly and indirectly through inflammation, adulthood social position and a risk score constructed from adult health behaviours including tobacco smoking and limited physical activity. The direct effect of childhood social position was reduced by mediation analysis (standardised coefficient decreased from 0.089 to 0.043) but remained statistically significant (p = 0.035). All three indirect pathways made a statistically significantly contribution to the overall effect of childhood social position on adulthood type 2 diabetes. Conclusions: Childhood social position influences adult diabetes directly and indirectly through inflammatory markers, adulthood social position and adult health behaviours. © 2014Pikhartova et al.; licensee BioMed Central Ltd.Economic and Social Research Council-funded International Centre for Life Course Studies in Society and Health (RES-596-28-0001)

Role of Interleukin 17 in arthritis chronicity through survival of synoviocytes via regulation of synoviolin expression

Background: The use of TNF inhibitors has been a major progress in the treatment of chronic inflammation. However, not all patients respond. In addition, response will be often lost when treatment is stopped. These clinical aspects indicate that other cytokines might be involved and we focus here on the role of IL-17. In addition, the chronic nature of joint inflammation may contribute to reduced response and enhanced chronicity. Therefore we studied the capacity of IL-17 to regulate synoviolin, an E3 ubiquitin ligase implicated in synovial hyperplasia in human rheumatoid arthritis (RA) FLS and in chronic reactivated streptococcal cell wall (SCW)-induced arthritis.<p></p> Methodology/Principal Findings: Chronic reactivated SCW-induced arthritis was examined in IL-17R deficient and wild-type mice. Synoviolin expression was analysed by real-time RT-PCR, Western Blot or immunostaining in RA FLS and tissue, and p53 assessed by Western Blot. Apoptosis was detected by annexin V/propidium iodide staining, SS DNA apoptosis ELISA kit or TUNEL staining and proliferation by PCNA staining. IL-17 receptor A (IL-17RA), IL-17 receptor C (IL-17-RC) or synoviolin inhibition were achieved by small interfering RNA (siRNA) or neutralizing antibodies. IL-17 induced sustained synoviolin expression in RA FLS. Sodium nitroprusside (SNP)-induced RA FLS apoptosis was associated with reduced synoviolin expression and was rescued by IL-17 treatment with a corresponding increase in synoviolin expression. IL-17RC or IL-17RA RNA interference increased SNP-induced apoptosis, and decreased IL-17-induced synoviolin. IL-17 rescued RA FLS from apoptosis induced by synoviolin knockdown. IL-17 and TNF had additive effects on synoviolin expression and protection against apoptosis induced by synoviolin knowndown. In IL-17R deficient mice, a decrease in arthritis severity was characterized by increased synovial apoptosis, reduced proliferation and a marked reduction in synoviolin expression. A distinct absence of synoviolin expressing germinal centres in IL-17R deficient mice contrasted with synoviolin positive B cells and Th17 cells in synovial germinal centre-like structures.<p></p> Conclusion/Significance: IL-17 induction of synoviolin may contribute at least in part to RA chronicity by prolonging the survival of RA FLS and immune cells in germinal centre reactions. These results extend the role of IL-17 to synovial hyperplasia.<p></p&gt

Three small planets transiting the bright young field star K2-233

We report the detection of three small transiting planets around the young K3 dwarf K2-233 (2MASS J15215519-2013539) from observations during Campaign 15 of the K2 mission. The star is relatively nearby ($d$ = 69 pc) and bright ($V$ = 10.7 mag, $K_s$ = 8.4 mag), making the planetary system an attractive target for radial velocity follow-up and atmospheric characterization with the James Webb Space Telescope. The inner two planets are hot super-Earths ($R_b$ = 1.40 $\pm$ 0.06 R$_\oplus$, $R_c$ = 1.34 $\pm$ 0.08 R$_\oplus$), while the outer planet is a warm sub-Neptune ($R_d$ = 2.6 $\pm$ 0.1 R$_\oplus$). We estimate the stellar age to be 360$^{+490}_{-140}$ Myr based on rotation, activity, and kinematic indicators. The K2-233 system is particularly interesting given recent evidence for inflated radii in planets around similarly-aged stars, a trend potentially related to photo-evaporation, core-cooling, or both mechanisms.Comment: Accepted to AJ. 15 pages, 6 figures, 3 table