Exact formulas for random growth with half-flat initial data

We obtain exact formulas for moments and generating functions of the height function of the asymmetric simple exclusion process at one spatial point, starting from special initial data in which every positive even site is initially occupied. These complement earlier formulas of E. Lee [J. Stat. Phys. 140 (2010) 635-647] but, unlike those formulas, ours are suitable in principle for asymptotics. We also explain how our formulas are related to divergent series formulas for half-flat KPZ of Le Doussal and Calabrese [J. Stat. Mech. 2012 (2012) P06001], which we also recover using the methods of this paper. These generating functions are given as a series without any apparent Fredholm determinant or Pfaffian structure. In the long time limit, formal asymptotics show that the fluctuations are given by the Airy$_{2\to1}$ marginals.Comment: Published at http://dx.doi.org/10.1214/15-AAP1099 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Variability of human pluripotent stem cell lines.

Human pluripotent stem cells derived from embryos (human Embryonic Stem Cells or hESCs) or generated by direct reprogramming of somatic cells (human Induced Pluripotent Stem Cells or hiPSCs) can proliferate almost indefinitely in vitro while maintaining the capacity to differentiate into a broad diversity of cell types. These two properties (self-renewal and pluripotency) confers human pluripotent stem cells a unique interest for clinical applications since they could allow the production of infinite quantities of cells for disease modelling, drug screening and cell based therapy. However, recent studies have clearly established that human pluripotent stem cell lines can display variable capacity to differentiate into specific lineages. Consequently, the development of universal protocols of differentiation which could work efficiently with any human pluripotent cell line is complicated substantially. As a consequence, each protocol needs to be adapted to every cell line thereby limiting large scale applications and precluding personalised therapies. Here, we summarise our knowledge concerning the origin of this variability and describe potential solutions currently available to bypass this major challenge

Kammmolch - Monitoring - Krefeld : Populationsökologie einer europaweit bedeutsamen Population des Kammmolches (<em>Triturus cristatus</em>) unter besonderer Berücksichtigung naturschutzrelevanter Fragestellungen

Im Rahmen des, sich über drei Untersuchungsjahre erstreckenden Forschungs- und Naturschutzprojektes „Kammmolch – Monitoring – Krefeld“, wurde die Dynamik benachbarter Populationen des Kammmolches (Triturus cristatus), sowie die mögliche Besiedelung neuer Gewässer dokumentiert und analysiert. Von besonderer Bedeutung waren hier die ungewöhnlich hohe Anzahl der im Jahr 2001 abgefangenen Amphibien und vor allem die Größe der nachgewiesenen Kammmolchpopulation mit ca. 4.500 erwachsenen Individuen. Diese Amphibienart genießt in Deutschland den höchsten Schutzstatus. Die Tatsachen, die bisher über diese Art bekannt sind, sprechen dafür, dass der Greiffenhorstpark im Krefelder Stadtteil Linn zu diesem Zeitpunkt eine der größten Populationen dieser bedrohten Art im gesamten Verbreitungsgebiet beherbergt. Von Anfang 2001 bis Anfang 2002 wurden, im Zuge der EUROGA 2002, umfassende Baumaßnahmen an diesem Gewässer durchgeführt und die oben genannte Zahl an Kammmolchenahe gelegene Gewässer umgesiedelt. Das übergeordnete Ziel des Projektes lag im Erreichen eines guten Erhaltungszustandes sowie in der Stabilisierung der Amphibienpopulation mit Schwerpunktsetzung auf die hier vorkommende, europaweit bedeutsame Population des Kammmolches. Um diese Ziele zu erreichen wurden insgesamt 30 verschiedene Gewässer mit, speziell für dieses Projekt konzipierten, Unterwassertrichterfallen untersucht. Zum Einsatz kamen verschiedene weitere populationsökologische sowie populationsgenetische Untersuchungsmethoden. Abschließend ist zu konstatieren, dass der Erhaltungszustand des Kammmolches im Untersuchungsgebiet als kritisch zu bewerten ist. Gleich an zwei Stellen im Untersuchungsgebiet sind die Populationen extrem eingebrochen. Im Greiffenhorstpark haben sich die Umbaumaßnahmen katastrophal für die Kammmolche ausgewirkt, so dass die Population um mehrere tausend Tiere zurückgegangen ist. Auf dem Gelände der SWK Aqua GmbH hatte die Verfüllung zweier Anreicherungsbecken ähnlich drastische Auswirkungen, welche die Restpopulation nachhaltig geschädigt haben. Zudem haben Verluste von Gewässern und Fischbesatz zu einer stärkeren Isolation der verbleibenden Populationen geführt. Um eine weitere Verschlechterung der Situation zu verhindern, ist die Anlage weiterer Gewässer sowie Pflegemaßnahmen an den meisten der übrigen Gewässer erforderlich. Bei beiden Populationen konnte ein signifikanter genetischer Bottleneck nachgewiesen werden. Dies ist als besonders kritisch zu anzusehen, da Populationen, die durch solch einen Bottleneck gegangen sind, eine deutlich geringere Überlebenschance in der Zukunft haben werden

PITX1, a specificity determinant in the HIF-1α-mediated transcriptional response to hypoxia

Hypoxia is an important developmental cue for multicellular organisms but it is also a contributing factor for several human pathologies, such as stroke, cardiovascular diseases and cancer. In cells, hypoxia activates a major transcriptional program coordinated by the Hypoxia Inducible Factor (HIF) family. HIF can activate more than one hundred targets but not all of them are activated at the same time, and there is considerable cell type variability. In this report we identified the paired-like homeodomain pituitary transcription factor (PITX1), as a transcription factor that helps promote specificity in HIF-1α dependent target gene activation. Mechanistically, PITX1 associates with HIF-1β and it is important for the induction of certain HIF-1 dependent genes but not all. In particular, PITX1 controls the HIF-1α-dependent expression of the histone demethylases; JMJD2B, JMJD2A, JMJD2C and JMJD1B. Functionally, PITX1 is required for the survival and proliferation responses in hypoxia, as PITX1 depleted cells have higher levels of apoptotic markers and reduced proliferation. Overall, our study identified PITX1 as a key specificity factor in HIF-1α dependent responses, suggesting PITX1 as a protein to target in hypoxic cancers

Cell cycle regulators control mesoderm specification in human pluripotent stem cells.

The mesoderm is one of the three germ layers produced during gastrulation from which muscle, bones, kidneys, and the cardiovascular system originate. Understanding the mechanisms that control mesoderm specification could inform many applications, including the development of regenerative medicine therapies to manage diseases affecting these tissues. Here, we used human pluripotent stem cells to investigate the role of cell cycle in mesoderm formation. To this end, using small molecules or conditional gene knockdown, we inhibited proteins controlling G1 and G2/M cell cycle phases during the differentiation of human pluripotent stem cells into lateral plate, cardiac, and presomitic mesoderm. These loss-of-function experiments revealed that regulators of the G1 phase, such as cyclin-dependent kinases and pRb (retinoblastoma protein), are necessary for efficient mesoderm formation in a context-dependent manner. Further investigations disclosed that inhibition of the G2/M regulator cyclin-dependent kinase 1 decreases BMP (bone morphogenetic protein) signaling activity specifically during lateral plate mesoderm formation while reducing fibroblast growth factor/extracellular signaling-regulated kinase 1/2 activity in all mesoderm subtypes. Taken together, our findings reveal that cell cycle regulators direct mesoderm formation by controlling the activity of key developmental pathways.This work was supported by the Wellcome Trust PhD program (PSAG/048 to L.Y.); the European Research Council advanced grant New-Chol (ERC: 741707 to L.V. and R.A.G), a BHF Senior Research Fellowship (FS/13/29/30024 to S.S.), a core support grant from the Wellcome and Medical Research Council to the Wellcome – Medical Research Council Cambridge Stem Cell Institute (PSAG028) and a core support grant from the Wellcome to the Wellcome Sanger Institute (WT206194)

Enzymatic degradation of polyethylene terephthalate nanoplastics analyzed in real time by isothermal titration calorimetry

Plastics are globally used for a variety of benefits. As a consequence of poor recycling or reuse, improperly disposed plastic waste accumulates in terrestrial and aquatic ecosystems to a considerable extent. Large plastic waste items become fragmented to small particles through mechanical and (photo)chemical processes. Particles with sizes ranging from millimeter (microplastics, <5 mm) to nanometer (nanoplastics, NP, <100 nm) are apparently persistent and have adverse effects on ecosystems and human health. Current research therefore focuses on whether and to what extent microorganisms or enzymes can degrade these NP. In this study, we addressed the question of what information isothermal titration calorimetry, which tracks the heat of reaction of the chain scission of a polyester, can provide about the kinetics and completeness of the degradation process. The majority of the heat represents the cleavage energy of the ester bonds in polymer backbones providing real-time kinetic information. Calorimetry operates even in complex matrices. Using the example of the cutinase-catalyzed degradation of polyethylene terephthalate (PET) nanoparticles, we found that calorimetry (isothermal titration calorimetry-ITC) in combination with thermokinetic models is excellently suited for an in-depth analysis of the degradation processes of NP. For instance, we can separately quantify i) the enthalpy of surface adsorption ∆AdsH = 129 ± 2 kJ mol−1, ii) the enthalpy of the cleavage of the ester bonds ∆EBH = −58 ± 1.9 kJ mol−1 and the apparent equilibrium constant of the enzyme substrate complex K = 0.046 ± 0.015 g L−1. It could be determined that the heat production of PET NP degradation depends to 95% on the reaction heat and only to 5% on the adsorption heat. The fact that the percentage of cleaved ester bonds (η = 12.9 ± 2.4%) is quantifiable with the new method is of particular practical importance. The new method promises a quantification of enzymatic and microbial adsorption to NP and their degradation in mimicked real-world aquatic conditions

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.

Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6-10 weeks post-conception. Our analysis reveals the transcriptional profile of cycling epithelial precursor cells; distinct from LGR5-expressing cells. We propose that these cells may contribute to differentiated cell subsets via the generation of LGR5-expressing stem cells and receive signals from surrounding mesenchymal cells. Furthermore, we draw parallels between the transcriptomes of ex vivo tissues and in vitro fetal organoids, revealing the maturation of organoid cultures in a dish. Lastly, we compare scRNA-seq profiles from pediatric Crohn's disease epithelium alongside matched healthy controls to reveal disease-associated changes in the epithelial composition. Contrasting these with the fetal profiles reveals the re-activation of fetal transcription factors in Crohn's disease. Our study provides a resource available at www.gutcellatlas.org, and underscores the importance of unraveling fetal development in understanding disease

Analysis of endothelial-to-haematopoietic transition at the single cell level identifies cell cycle regulation as a driver of differentiation

Funder: INTENS EU fp8 consortiumFunder: ERC advanced grant New-CholAbstract: Background: Haematopoietic stem cells (HSCs) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematopoietic transition (EHT). Despite the progress achieved in recent years, the molecular mechanisms driving EHT are still poorly understood, especially in human where the AGM region is not easily accessible. Results: In this study, we take advantage of a human pluripotent stem cell (hPSC) differentiation system and single-cell transcriptomics to recapitulate EHT in vitro and uncover mechanisms by which the haemogenic endothelium generates early haematopoietic cells. We show that most of the endothelial cells reside in a quiescent state and progress to the haematopoietic fate within a defined time window, within which they need to re-enter into the cell cycle. If cell cycle is blocked, haemogenic endothelial cells lose their EHT potential and adopt a non-haemogenic identity. Furthermore, we demonstrate that CDK4/6 and CDK1 play a key role not only in the transition but also in allowing haematopoietic progenitors to establish their full differentiation potential. Conclusion: We propose a direct link between the molecular machineries that control cell cycle progression and EHT

The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency.

The TGFβ pathway has essential roles in embryonic development, organ homeostasis, tissue repair and disease. These diverse effects are mediated through the intracellular effectors SMAD2 and SMAD3 (hereafter SMAD2/3), whose canonical function is to control the activity of target genes by interacting with transcriptional regulators. Therefore, a complete description of the factors that interact with SMAD2/3 in a given cell type would have broad implications for many areas of cell biology. Here we describe the interactome of SMAD2/3 in human pluripotent stem cells. This analysis reveals that SMAD2/3 is involved in multiple molecular processes in addition to its role in transcription. In particular, we identify a functional interaction with the METTL3-METTL14-WTAP complex, which mediates the conversion of adenosine to N6-methyladenosine (m6A) on RNA. We show that SMAD2/3 promotes binding of the m6A methyltransferase complex to a subset of transcripts involved in early cell fate decisions. This mechanism destabilizes specific SMAD2/3 transcriptional targets, including the pluripotency factor gene NANOG, priming them for rapid downregulation upon differentiation to enable timely exit from pluripotency. Collectively, these findings reveal the mechanism by which extracellular signalling can induce rapid cellular responses through regulation of the epitranscriptome. These aspects of TGFβ signalling could have far-reaching implications in many other cell types and in diseases such as cancer.We thank Cambridge Genomic Services for help in next generation sequencing. The work was 203 supported by the European Research Council starting grant “Relieve IMDs” (L.V., S.B., A.B., 204 P.M.); the Cambridge University Hospitals National Institute for Health Research Biomedical 205 Research Center (L.V., J.K., A.S.L.); the Wellcome Trust PhD program (A.O., L.Y.); a British 206 Heart Foundation PhD studentship (FS/11/77/39327 to A.B.); a Grant-in-Aid for JSPS Fellows 207 (16J08005 to S.N.); and a core support grant from the Wellcome Trust and Medical Research 208 Council to the Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute