Search

The first obvious sign of bilateral symmetry in mammalian and avian embryos is the appearance of the primitive streak in the future posterior region of a radially symmetric disc. The primitive streak marks the midline of the future embryo. The mechanisms responsible for positioning the primitive streak remain largely unknown. Here we combine experimental embryology and mathematical modelling to analyse the role of the TGFβ-related molecules BMP4 and Vg1/GDF1 in positioning the primitive streak. Bmp4 and Vg1 are first expressed throughout the embryo, and then become localised to the future anterior and posterior regions of the embryo, where they will, respectively, inhibit or induce formation of the primitive streak. We propose a model based on paracrine signalling to account for the separation of the two domains starting from a homogeneous array of cells, and thus for the topological transformation of a radially symmetric disc to a bilaterally symmetric embryo.

Cardiac pacemaker cells, including cells of the sinoatrial node, are heterogeneous in size, morphology, and electrophysiological characteristics. The exact extent to which these cells differ electrophysiologically is unclear yet is critical to understanding their functioning. We examined major ionic currents in individual intercaval pacemaker cells (IPCs) sampled from the paracristal, intercaval region (including the sinoatrial node) that were spontaneously beating after enzymatic isolation from rabbit hearts. The beating rate was measured at baseline and after inhibition of the Ca(2+) pump with cyclopiazonic acid. Thereafter, in each cell, we consecutively measured the density of funny current (I(f)), delayed rectifier K(+) current (I(K)) (a surrogate of repolarization capacity), and L-type Ca(2+) current (I(Ca,L)) using whole cell patch clamp(.) The ionic current densities varied to a greater extent than previously appreciated, with some IPCs demonstrating very small or zero I(f) . The density of none of the currents was correlated with cell size, while I(Ca,L) and I(f) densities were related to baseline beating rates. I(f) density was correlated with I(K) density but not with that of I(Ca,L). Inhibition of Ca(2+) cycling had a greater beating rate slowing effect in IPCs with lower I(f) densities. Our numerical model simulation indicated that 1) IPCs with small (or zero) I(f) or small I(Ca,L) can operate via a major contribution of Ca(2+) clock, 2) I(f)-Ca(2+)-clock interplay could be important for robust pacemaking function, and 3) coupled I(f)-I(K) function could regulate maximum diastolic potential. Thus, we have demonstrated marked electrophysiological heterogeneity of IPCs. This heterogeneity is manifested in basal beating rate and response to interference of Ca(2+) cycling, which is linked to I(f). NEW & NOTEWORTHY In the present study, a hitherto unrecognized range of heterogeneity of ion currents in pacemaker cells from the intercaval region is demonstrated. Relationships between basal beating rate and L-type Ca(2+) current and funny current (I(f)) density are uncovered, along with a positive relationship between I(f) and delayed rectifier K(+) current. Links are shown between the response to Ca(2+) cycling blockade and I(f) density.

Perhaps even more important than the techniques themselves are the quality of the biological questions asked and the design of the experiments devised to answer them. This chapter summarizes some of the key issues and also touches on how the same principles affect scholarly use of the scientific literature and good peer-reviewing practices.

There is a rich tradition of surveys that aimed at identifying clusters of galaxies at higher and higher z. Although searches have preferentially looked for concentrations of red sequence and/or massive galaxies, or looking for signatures of the hot intracluster gas, they are exceedingly time-depending and require both depth and coverage as searches go to increasingly higher z. The limit of known clusters currently reaches z 2, also identified as a crucial epoch for cluster formation. A targeted cluster search would reduce the strain on telescope time. Our Spitzer/IRAC survey CARLA (Clusters Around Radio-Loud AGN) has, in that regard, targeted high-z radio-loud AGN, which are known to reside in dense environments. I will summarize a series of results and on-going studies from the CARLA collaboration that aimed at identifying cluster candidates in the field of RLAGN, investigating the formation scenario of the most massive cluster members by analyzing the evolution of the cluster luminosity function or red sequence color with redshift. I will also present CARLA-HST and CARLALMA, respectively the HST spectroscopic confirmation campaign and on-going ALMA follow-up of CARLA clusters.

Intracellular Ca signals represent a universal mechanism of cell function. Messages carried by Ca are local, rapid, and powerful enough to be delivered over the thermal noise. A higher signal to noise ratio is achieved by a cooperative action of Ca release channels such as IP3 receptors or ryanodine receptors arranged in clusters or release units containing a few to several hundred release channels. The release channels synchronize their openings via Ca-induced-Ca-release, generating high-amplitude local Ca signals known as puffs in neurons or sparks in muscle cells. Despite the high release amplitude and positive feedback nature of the activation, Ca signals are strictly confined in time and space by an unexplained termination mechanism. Here we show that the collective transition of release channels from an open to a closed state is identical to the phase transition associated with the reversal of magnetic field in an Ising ferromagnet. We demonstrate this mechanism using numerical model simulations of Ca sparks over a wide range of cluster sizes from 25 to 169 release channels. While prior studies suggested contributions of stochastic attrition and Ca store depletion, our new simple quantitative criterion closely predicts the depletion level required for spark termination for each cluster size. We further formulate exact requirements for a cluster of release channels to follow the Ising model in any cell type. Thus we describe deterministically the behaviour of a system on a coarser scale (release unit) which is random on a finer scale (release channels), bridging the gap between scales. Our results provide the first exact mapping of a nanoscale biological signalling model to an interacting particle system in statistical physics, making the extensive mathematical apparatus available to quantitative biology., Comment: 22 pages, 4 figures, 4 videos. Published in PNAS 2017

We present results from four new broadband X-ray observations of the extreme ultraluminous X-ray source Holmberg IX X-1 ($L_{\rm{X}} > 10^{40}$ erg/s), performed by $Suzaku$ and $NuSTAR$ in coordination. Combined with the archival data, we now have broadband observations of this remarkable source from six separate epochs. Two of these new observations probe lower fluxes than seen previously, allowing us to extend our knowledge of the broadband spectral variability exhibited. The spectra are well fit by two thermal blackbody components, which dominate the emission below 10 keV, as well as a steep ($\Gamma \sim 3.5$) powerlaw tail which dominates above $\sim$15 keV. Remarkably, while the 0.3-10.0 keV flux varies by a factor of $\sim$3 between all these epochs, the 15-40 keV flux varies by only $\sim$20%. Although the spectral variability is strongest in the $\sim$1-10 keV band, both of the thermal components are required to vary when all epochs are considered. We also re-visit the search for iron absorption features, leveraging the high-energy $NuSTAR$ data to improve our sensitivity to extreme velocity outflows in light of the ultra-fast outflow recently detected in NGC 1313 X-1. Iron absorption from a similar outflow along our line of sight can be ruled out in this case. We discuss these results in the context of super-Eddington accretion models that invoke a funnel-like geometry for the inner flow, and propose a scenario in which we have an almost face-on view of a funnel that expands to larger radii with increasing flux, resulting in an increasing degree of geometrical collimation for the emission from intermediate temperature regions., Comment: 11 pages, 6 Figures, accepted for publication in ApJ

SUMMARYMost cancer cells harbor multiple drivers whose epistasis and interactions with expression context clouds drug sensitivity prediction. We constructed a mechanistic computational model that is context-tailored by omics data to capture regulation of stochastic proliferation and death by pan-cancer driver pathways. Simulations and experiments explore how the coordinated dynamics of RAF/MEK/ERK and PI-3K/AKT kinase activities in response to synergistic mitogen or drug combinations control cell fate in a specific cellular context. In this context, synergistic ERK and AKT inhibitor-induced death is likely mediated by BIM rather than BAD. AKT dynamics explain S-phase entry synergy between EGF and insulin, but stochastic ERK dynamics seem to drive cell-to-cell proliferation variability, which in simulations are predictable from pre-stimulus fluctuations in C-Raf/B-Raf levels. Simulations predict MEK alteration negligibly influences transformation, consistent with clinical data. Our model mechanistically interprets context-specific landscapes between driver pathways and cell fates, moving towards more rational cancer combination therapy.

The chick embryo is a well-established representative of amniote embryos, which has been used to make many discoveries, including many major concepts, which have moved our knowledge of developmental biology in hugely important ways. The chick has a relatively compact genome and is easily amenable to embryological manipulations and in vivo imaging. Morpholino gene manipulations have been used in a variety of contexts, and constitute a quick and versatile molecular tool. Here we describe methods to deliver morpholinos to chick embryos, allowing targeting of specific cell populations at defined developmental stages, using two stages as examples: the epiblast of the embryo in the first day of incubation, when the primary germ layers of the embryo are specified, and in ovo electroporation of the neural tube as an example of a later stage. With slight modifications, these general methods can be used to target other embryonic tissues.

The most powerful sources among the blazar family are MeV blazars. Often detected at $z>2$, they usually display high X- and \gm-ray luminosities, larger-than-average jet powers and black hole masses $\gtrsim 10^9 M_{\odot}$. In the present work we perform a multiwavelength study of three high redshift blazars: 3FGL J0325.5+2223 ($z=2.06$), 3FGL J0449.0+1121 ($z= 2.15$), and 3FGL J0453.2$-$2808 ($z=2.56$), analysing quasi simultaneous data from GROND, \swift-UVOT and XRT, \nustar, and \fermi-LAT. Our main focus is on the hard X-ray band recently unveiled by \nustar~(3$-$79 keV) where these objects show a hard spectrum which enables us to constrain the inverse Compton peak and the jet power. We found that all three targets resemble the most powerful blazars, with the synchrotron peak located in the sub-millimeter range and the inverse Compton peak in the MeV range, and therefore belong to the MeV blazar class. Using a simple one zone leptonic emission model to reproduce the spectral energy distributions, we conclude that a simple combination of synchrotron and accretion disk emission reproduces the infrared-optical spectra while the X-ray to \gm-ray part is well reproduced by the inverse Compton scattering of low energy photons supplied by the broad line region. The black hole masses for each of the three sources are calculated to be $\gtrsim 4 \times 10^{8} M_{\odot}$. The three studied sources have jet power at the level of, or beyond, the accretion luminosity., 4 figures, 3 tables, accepted for publication in ApJ

To compare lesion detectability and positron-emission tomography (PET) metric measurements between early-PET/magnetic resonance imaging (MRI) acquisition and same-day PET/computed tomography (CT).The study was approved by the institutional review board and written informed consent was obtained from all patients. Twenty-one patients underwent non-time-of-flight (TOF) PET/MRI immediately followingSixty-one and 63 lesions were found on wbPET/MRI and wbPET/CT, respectively (K=0.95, 95% confidence interval (CI)=0.89-1.0) with very good correlation between PET metric measurements (r=0.91; p=0.001). Bland-Altman plots demonstrated a mean percentage difference between wbPET/CT with wbPET/MRI of 34.4% with 95% limits of agreement (LOA) between -39% to 107.9% for metabolic tumour volume (MTV) and a mean difference of 30% with LOA between -13.4% to 73.4% for peak standardised uptake value (SUVpeak).Early PET/MRI demonstrates very good lesion detectability agreement and correlation with PET metrics compared to same-day PET/CT. Nevertheless, LOA are far beyond the clinically acceptable range, and therefore, PET/CT and early PET/MRI metrics cannot be used interchangeably.

The WISE satellite surveyed the entire sky multiple times in four infrared wavelengths (3.4, 4.6, 12, and $22\,\mu$m; Wright et al. 2010). The unprecedented combination of coverage area and depth gives us the opportunity to measure the luminosity function of galaxies, one of the fundamental quantities in the study of them, at $2.4\ \mu$m to an unparalleled level of formal statistical accuracy in the near infrared. The big advantage of measuring luminosity functions at wavelengths in the window $\approx 2$ to $3.5\,\mu$m is that it correlates more closely to the total stellar mass in galaxies than others. In this paper we report on the parameters for the $2.4\,\mu$m luminosity function of galaxies obtained from applying the spectroluminosity functional based methods defined in Lake et al. (2017b) to the data sets described in Lake et al. (2017a) using the mean and covariance of $2.4\,\mu$m normalized SEDs from Lake & Wright (2016). In terms of single Schechter function parameters evaluated at the present epoch, the combined result is: $\phi_\star = 5.8 \pm [0.3_{\mathrm{stat}},\, 0.3_{\mathrm{sys}}] \times 10^{-3} \operatorname{Mpc}^{-3}$, $L_\star = 6.4 \pm [0.1_{\mathrm{stat}},\, 0.3_{\mathrm{sys}}] \times 10^{10}\, L_{2.4\,\mu\mathrm{m}\,\odot}$ ($M_\star = -21.67 \pm [0.02_{\mathrm{stat}},\, 0.05_{\mathrm{sys}}]\operatorname{AB\ mag}$), and $\alpha = -1.050 \pm [0.004_{\mathrm{stat}},\, 0.03_{\mathrm{sys}}]$, corresponding to a galaxy number density of $0.08\operatorname{Mpc}^{-3}$ brighter than $10^6\, L_{2.4\,\mu\mathrm{m}\,\odot}$ ($10^{-3} \operatorname{Mpc}^{-3}$ brighter than $L_\star$) and a $2.4\,\mu$m luminosity density equivalent to $3.8\times10^{8}\,L_{2.4\,\mu\mathrm{m}\,\odot}\operatorname{Mpc}^{-3}$. $\ldots$, Comment: 25 pages, 7 figures, 10 tables, posterior chains on Figshare under DOI 10.6084/m9.figshare.4109625, accepted by ApJ

The WISE satellite surveyed the entire sky multiple times in four infrared (IR) wavelengths ($3.4,\ 4.6,\ 12,$ and $22\, \mu$m, Wright et al. 2010). This all-sky IR photometric survey makes it possible to leverage many of the large publicly available spectroscopic redshift surveys to measure galaxy properties in the IR. While characterizing the cross-matching of WISE data to a single survey is a straightforward process, doing it with six different redshift surveys takes a fair amount of space to characterize adequately, because each survey has unique caveats and characteristics that need addressing. This work describes a data set that results from matching five public redshift surveys with the AllWISE data release, along with a reanalysis of the data described in Lake et al. 2012. The combined data set has an additional flux limit of $80\,\mu$Jy ($19.14$ AB mag) in WISE's W1 filter imposed in order to limit it to targets with high completeness and reliable photometry in the AllWISE data set. Consistent analysis of all of the data is only possible if the color bias discussed in Ilbert et al. (2004) is addressed (for example: the techniques explored in the first paper in this series Lake et al. 2017b). The sample defined herein is used in this paper's sequel paper, Lake et al. 2017a), to measure the luminosity function of galaxies at $2.4\, \mu$m rest frame wavelength, and the selection process of the sample is optimized for this purpose., Comment: 44 pages, 22 figures, 20 tables, associated data on Figshare under DOIs 10.6084/m9.figshare.3860016 and 10.6084/m9.figshare.4003680, accepted by ApJ

Pulmonary embolism (PE) is a frequently occurring complication in critically ill patients, and the simultaneous occurrence of PE and life-threatening bleeding is a therapeutic dilemma. Inferior vena cava filters (IVCF) may represent an important therapeutic alternative in these cases. The Angel® catheter (Bio2 Medical Inc., San Antonio, TX, USA) is a novel IVCF that provides temporary protection from PE and is implanted at bedside without fluoroscopy.The European Angel® Catheter Registry is an observational, multicenter study. In our German substudy, we investigated patients from three German hospitals and four intensive care units, who underwent Angel® catheter implantation between February 2016 and December 2016.A total of 23 critically ill patients (68 ± 9 years, 43% male) were included. The main indication for implantation was a high risk for or an established PE, combined with contraindications for prophylactic or therapeutic anticoagulation due to either an increased risk of bleeding (81%) or active bleeding (13%). The Angel® catheter was successfully inserted in all patients at bedside. No PE occurred in patients with an indwelling Angel® catheter. Clots with a diameter larger the 20 mm, indicating clot migration, were detected in 5% of the patients by cavography before filter retrieval. Filter retrieval was uneventful in all of our cases, while filter dislocation occurred in 3% of the patients.The German data from the multicenter European Angel® Catheter Registry show that the Angel® catheter is a safe and effective approach for critically ill patients with a high risk for the development of PE or an established PE, when an anticoagulation therapy is contraindicated.

Hot, Dust-Obscured Galaxies (Hot DOGs), selected from the WISE all sky infrared survey, host some of the most powerful Active Galactic Nuclei (AGN) known, and might represent an important stage in the evolution of galaxies. Most known Hot DOGs are at $z> 1.5$, due in part to a strong bias against identifying them at lower redshift related to the selection criteria. We present a new selection method that identifies 153 Hot DOG candidates at $z\sim 1$, where they are significantly brighter and easier to study. We validate this approach by measuring a redshift $z=1.009$, and an SED similar to higher redshift Hot DOGs for one of these objects, WISE J1036+0449 ($L_{\rm\,Bol}\simeq 8\times 10^{46}\rm\,erg\,s^{-1}$), using data from Keck/LRIS and NIRSPEC, SDSS, and CSO. We find evidence of a broadened component in MgII, which, if due to the gravitational potential of the supermassive black hole, would imply a black hole mass of $M_{\rm\,BH}\simeq 2 \times 10^8 M_{\odot}$, and an Eddington ratio of $\lambda_{\rm\,Edd}\simeq 2.7$. WISE J1036+0449 is the first Hot DOG detected by NuSTAR, and the observations show that the source is heavily obscured, with a column density of $N_{\rm\,H}\simeq(2-15)\times10^{23}\rm\,cm^{-2}$. The source has an intrinsic 2-10 keV luminosity of $\sim 6\times 10^{44}\rm\,erg\,s^{-1}$, a value significantly lower than that expected from the mid-infrared/X-ray correlation. We also find that the other Hot DOGs observed by X-ray facilities show a similar deficiency of X-ray flux. We discuss the origin of the X-ray weakness and the absorption properties of Hot DOGs. Hot DOGs at $z\lesssim1$ could be excellent laboratories to probe the characteristics of the accretion flow and of the X-ray emitting plasma at extreme values of the Eddington ratio., Comment: Accepted for publication in ApJ, 16 pages

Snail and Zeb transcription factors induce epithelial to mesenchymal transition (EMT) in embryonic and adult tissues by direct repression of E-Cadherin transcription. The repression of E-Cadherin transcription by the EMT inducers Snail1 and Zeb2 plays a fundamental role in defining embryonic territories in the mouse, as E-Cadherin needs to be downregulated in the primitive streak and in the epiblast concomitant with the formation of mesendodermal precursors and the neural plate, respectively. Here we show that in the chick embryo, E-Cadherin is weakly expressed in the epiblast at pre-primitive streak stages where it is substituted by P-Cadherin. We also show that Snail2 and Zeb2 repress P-Cadherin transcription in the primitive streak and the neural plate, respectively. This indicates that E- and P-Cadherin expression patterns evolved differently between chick and mouse. As such, the Snail1/E-Cadherin axis described in the early mouse embryo corresponds to Snail2/P-Cadherin in the chick, but both Snail factors and Zeb2 fulfill a similar role in chick and mouse in directly repressing ectodermal Cadherins to promote the delamination of mesendodermal precursors at gastrulation and the proper specification of the neural ectoderm during neural induction., This work was supported by grants from the Spanish Ministry of Economy and Competitiveness (BFU2008-01042 and BFU2014-53128-R), the Generalitat Valenciana (PR OMETEOII/2013/002) and the European Research Council (ERC AdG 322694) to M.A.N., who also acknowledges financial support from the Spanish State Research Age ncy, through the “Severo Ochoa” Programme for Centres of Excellence in R&D (SEV-2013-0317).

We present first results from a series of $NuSTAR$ observations of the black hole X-ray binary V404 Cyg obtained during its summer 2015 outburst, primarily focusing on observations during the height of this outburst activity. The $NuSTAR$ data show extreme variability in both the flux and spectral properties of the source. This is partly driven by strong and variable line-of-sight absorption, similar to previous outbursts. The latter stages of this observation are dominated by strong flares, reaching luminosities close to Eddington. During these flares, the central source appears to be relatively unobscured and the data show clear evidence for a strong contribution from relativistic reflection, providing a means to probe the geometry of the innermost accretion flow. Based on the flare properties, analogy with other Galactic black hole binaries, and also the simultaneous onset of radio activity, we argue that this intense X-ray flaring is related to transient jet activity during which the ejected plasma is the primary source of illumination for the accretion disk. If this is the case, then our reflection modelling implies that these jets are launched in close proximity to the black hole (as close as a few gravitational radii), consistent with expectations for jet launching models that tap either the spin of the central black hole, or the very innermost accretion disk. Our analysis also allows us to place the first constraints on the black hole spin for this source, which we find to be $a^* > 0.92$ (99% statistical uncertainty, based on an idealized lamppost geometry)., 23 pages, 16 figures, accepted for publication in ApJ

We present a study of the average X-ray spectral properties of the sources detected by the NuSTAR extragalactic survey, comprising observations of the E-CDFS, EGS and COSMOS fields. The sample includes 182 NuSTAR sources (64 detected at 8-24 keV), with 3-24 keV fluxes ranging between $f_{\rm 3-24 keV}\approx10^{-14}$ and $6\times10^{-13}$ erg/cm$^2$/s ($f_{\rm 8-24 keV}\approx3\times10^{-14}-3\times10^{-13}$ erg/cm$^2$/s) and redshifts of $z=0.04-3.21$. We produce composite spectra from the Chandra+NuSTAR data ($E\approx2-40$ keV, rest frame) for all the sources with redshift identifications (95%) and investigate the intrinsic, average spectra of the sources, divided into broad-line (BL) and narrow-line (NL) AGN, and also in different bins of X-ray column density and luminosity. The average power-law photon index for the whole sample is $\Gamma=1.65_{-0.03}^{+0.03}$, flatter than $\Gamma\approx1.8$ typically found for AGN. While the spectral slope of BL and X-ray unabsorbed AGN is consistent with typical values ($\Gamma=1.79_{-0.01}^{+0.01}$), a significant flattening is seen in NL AGN and heavily-absorbed sources ($\Gamma=1.60_{-0.05}^{+0.08}$ and $\Gamma=1.38_{-0.12}^{+0.12}$, respectively), likely due to the effect of absorption and to the contribution from Compton reflection to the high-energy flux (E>10 keV). We find that the typical reflection fraction in our spectra is $R\approx0.5$ (for $\Gamma=1.8$), with a tentative indication of an increase of the reflection strength with column density. While there is no significant evidence for a dependence of the photon index with X-ray luminosity in our sample, we find that $R$ decreases with luminosity, with relatively high levels of reflection ($R\approx1.2$) for $L_{\rm 10-40 keV}10^{44}$ erg/s AGN, assuming $\Gamma=1.8$., Comment: 19 pages, 14 figures, 4 tables. Accepted for publication in ApJ

We present an analysis of the joint $XMM$-$Newton$ and $NuSTAR$ observations of the radio-quiet quasar QSO B2202$-$209. Using an optical observation from the Hale Telescope at the Palomar Observatory, we revise the redshift of the source from the previously reported $z=1.77$ to $z=0.532$, and we estimate the mass of the central black hole, $\log (M_{\rm BH}/M_{\odot}) = 9.08 \pm 0.18$. The X-ray spectrum of this source can be well described by a power-law of photon index $\Gamma = 1.82 \pm 0.05$ with $E_{\rm cut} = 152_{-54}^{+103}\,{\rm keV}$, in the rest frame of the source. Assuming a Comptonisation model, we estimate the coronal temperature to be $kT_{\rm e}=42\pm 3 \,{\rm keV}$ and $kT_{\rm e}= 56 \pm 3\,{\rm keV}$ for a spherical and a slab geometry, respectively. The coronal properties are comparable to the ones derived for local AGN, despite a difference of around one order of magnitude in black hole mass and X-ray luminosity ($L_{2-10} = 1.93\times 10^{45}\,{\rm erg\,s^{-1}}$). The quasar is X-ray loud, with an unusually flat observed optical-to-X-ray spectral slope $\alpha_{\rm OX} = 1.00 \pm 0.02$, and has an exceptionally strong optical [O III] line. Assuming that both the X-ray emission and the [O III] line are isotropic, these two extreme properties can be explained by a nearly edge-on disk, leading to a reduction in the observed UV continuum light., Comment: 8 pages, 4 figures, accepted for publication in MNRAS

Perhaps even more important than the techniques themselves are the quality of the biological questions asked and the design of the experiments devised to answer them. This chapter summarizes some of the key issues and also touches on how the same principles affect scholarly use of the scientific literature and good peer-reviewing practices.

We present a detailed, broadband X-ray spectral analysis of the ULX pulsar NGC 7793 P13, a known super-Eddington source, utilizing data from the $XMM$-$Newton$, $NuSTAR$ and $Chandra$ observatories. The broadband $XMM$-$Newton+NuSTAR$ spectrum of P13 is qualitatively similar to the rest of the ULX sample with broadband coverage, suggesting that additional ULXs in the known population may host neutron star accretors. Through time-averaged, phase-resolved and multi-epoch studies, we find that two non-pulsed thermal blackbody components with temperatures $\sim$0.5 and $\sim$1.5 keV are required to fit the data below 10 keV, in addition to a third continuum component which extends to higher energies and is associated with the pulsed emission from the accretion column. The characteristic radii of the thermal components appear to be similar, and are too large to be associated with the neutron star itself, so the need for two components likely indicates the accretion flow outside the magnetosphere is complex. We suggest a scenario in which the thick inner disc expected for super-Eddington accretion begins to form, but is terminated by the neutron star's magnetic field soon after its onset, implying a limit of $B \lesssim 6 \times 10^{12}$ G for the dipolar component of the central neutron star's magnetic field. Evidence of similar termination of the disc in other sources may offer a further means of identifying additional neutron star ULXs. Finally, we examine the spectrum exhibited by P13 during one of its unusual 'off' states. These data require both a hard powerlaw component, suggesting residual accretion onto the neutron star, and emission from a thermal plasma, which we argue is likely associated with the P13 system., Comment: 17 pages, 12 figures, accepted for publication in MNRAS

Local Ca Releases (LCRs) are crucial events involved in cardiac pacemaker cell function. However, specific algorithms for automatic LCR detection and analysis have not been developed in live, spontaneously beating pacemaker cells. Here we measured LCRs using a high-speed 2D-camera in spontaneously contracting sinoatrial (SA) node cells isolated from rabbit and guinea pig and developed a new algorithm capable of detecting and analyzing the LCRs spatially in two-dimensions, and in time. Our algorithm tracks points along the midline of the contracting cell. It uses these points as a coordinate system for affine transform, producing a transformed image series where the cell does not contract. Action potential-induced Ca transients and LCRs were thereafter isolated from recording noise by applying a series of spatial filters. The LCR birth and death events were detected by a differential (frame-to-frame) sensitivity algorithm. An LCR was detected when its signal changes sufficiently quickly within a sufficiently large area. The LCR is considered to have died when its amplitude decays substantially, or when it merges into the rising whole cell Ca transient. Our algorithm provides major LCR parameters such as period, signal mass, duration, and path area. As LCRs propagate within cells, the algorithm identifies splitting and merging behaviors, indicating the importance of Ca-induced-Ca-release for the fate of LCRs and for generating a powerful ensemble Ca signal. Thus, our new computer algorithms eliminate motion artifacts and detect 2D local spatiotemporal Ca release events from recording noise and global signals. While the algorithms detect LCRs in sinoatrial nodal cells, they have the potential to be used in other applications in biophysics and cell physiology, for example, to detect Ca wavelets (abortive waves), sparks and embers in muscle cells and Ca puffs and syntillas in neurons., Comment: 43 pages, 7 figures, 2 tables, 5 videos (with web links)

The chick embryo is a well-established representative of amniote embryos, which has been used to make many discoveries, including many major concepts, which have moved our knowledge of developmental biology in hugely important ways. The chick has a relatively compact genome and is easily amenable to embryological manipulations and in vivo imaging. Morpholino gene manipulations have been used in a variety of contexts, and constitute a quick and versatile molecular tool. Here we describe methods to deliver morpholinos to chick embryos, allowing targeting of specific cell populations at defined developmental stages, using two stages as examples: the epiblast of the embryo in the first day of incubation, when the primary germ layers of the embryo are specified, and in ovo electroporation of the neural tube as an example of a later stage. With slight modifications, these general methods can be used to target other embryonic tissues.

Asymmetry is required by most numerical simulations of stellar core-collapse explosions, but the form it takes differs significantly among models. The spatial distribution of radioactive 44Ti, synthesized in an exploding star near the boundary between material falling back onto the collapsing core and that ejected into the surrounding medium, directly probes the explosion asymmetries. CassiopeiaA is a young, nearby, core-collapse remnant from which 44Ti emission has previously been detected but not imaged. Asymmetries in the explosion have been indirectly inferred from a high ratio of observed 44Ti emission to estimated 56Ni emission, from optical light echoes, and from jet-like features seen in the X-ray and optical ejecta. Here we report spatial maps and spectral properties of the 44Ti in Cassiopeia A. This may explain the unexpected lack of correlation between the 44Ti and iron X-ray emission, the latter being visible only in shock-heated material. The observed spatial distribution rules out symmetric explosions even with a high level of convective mixing, as well as highly asymmetric bipolar explosions resulting from a fast-rotating progenitor. Instead, these observations provide strong evidence for the development of low-mode convective instabilities in core-collapse supernovae., Comment: 32 pages, Figures Embedded

Numerical modeling indicates that hierarchical clustering of ryanodine receptors in cells of the sinoatrial node is crucial to the calcium clock and thereby to regulation of heart rate., The sinoatrial node, whose cells (sinoatrial node cells [SANCs]) generate rhythmic action potentials, is the primary pacemaker of the heart. During diastole, calcium released from the sarcoplasmic reticulum (SR) via ryanodine receptors (RyRs) interacts with membrane currents to control the rate of the heartbeat. This “calcium clock” takes the form of stochastic, partially periodic, localized calcium release (LCR) events that propagate, wave-like, for limited distances. The detailed mechanisms controlling the calcium clock are not understood. We constructed a computational model of SANCs, including three-dimensional diffusion and buffering of calcium in the cytosol and SR; explicit, stochastic gating of individual RyRs and L-type calcium channels; and a full complement of voltage- and calcium-dependent membrane currents. We did not include an anatomical submembrane space or inactivation of RyRs, the two heuristic components that have been used in prior models but are not observed experimentally. When RyRs were distributed in discrete clusters separated by >1 µm, only isolated sparks were produced in this model and LCR events did not form. However, immunofluorescent staining of SANCs for RyR revealed the presence of bridging RyR groups between large clusters, forming an irregular network. Incorporation of this architecture into the model led to the generation of propagating LCR events. Partial periodicity emerged from the interaction of LCR events, as observed experimentally. This calcium clock becomes entrained with membrane currents to accelerate the beating rate, which therefore was controlled by the activity of the SERCA pump, RyR sensitivity, and L-type current amplitude, all of which are targets of β-adrenergic–mediated phosphorylation. Unexpectedly, simulations revealed the existence of a pathological mode at high RyR sensitivity to calcium, in which the calcium clock loses synchronization with the membrane, resulting in a paradoxical decrease in beating rate in response to β-adrenergic stimulation. The model indicates that the hierarchical clustering of surface RyRs in SANCs may be a crucial adaptive mechanism. Pathological desynchronization of the clocks may explain sinus node dysfunction in heart failure and RyR mutations.

Avian embryos have reproductive organs with unique characteristics. In female, the gonads develop asymmetrically: the left gonad generates a functional ovary, whereas the right gonad and associated embryonic oviduct (Mullerian duct) regress. In males, however, both left and right gonads develop into testes. Recent evidence, however, revealed that left-right asymmetry can be detected in both sexes. Even male embryos have a greater number of germ cells in the left gonad. Moreover, pluripotency-associated markers, as well as SSEA1, the surface antigen that is strongly expressed in chick embryonic stem cells, also show asymmetric expression in both sexes both in germ cells and in stromal cells of the gonad. This review provides an update of the state of the field.

Cardiac pacemaking is a complex phenomenon that is still not completely understood. Together with experimental studies, numerical modeling has been traditionally used to acquire mechanistic insights in this research area. This review summarizes the present state of numerical modeling of the cardiac pacemaker, including approaches to resolve present paradoxes and controversies. Specifically we discuss the requirement for realistic modeling to consider symmetrical importance of both intracellular and cell membrane processes (within a recent “coupled-clock” theory). Promising future developments of the complex pacemaker system models include the introduction of local calcium control, mitochondria function, and biochemical regulation of protein phosphorylation and cAMP production. Modern numerical and theoretical methods such as multi-parameter sensitivity analyses within extended populations of models and bifurcation analyses are also important for the definition of the most realistic parameters that describe a robust, yet simultaneously flexible operation of the coupled-clock pacemaker cell system. The systems approach to exploring cardiac pacemaker function will guide development of new therapies such as biological pacemakers for treating insufficient cardiac pacemaker function that becomes especially prevalent with advancing age. Keywords:: cardiac pacemaker, sinoatrial node cell, numerical modeling, calcium, ion channel

We present the first full catalog and science results for the NuSTAR serendipitous survey. The catalog incorporates data taken during the first 40 months of NuSTAR operation, which provide ~20Ms of effective exposure time over 331 fields, with an areal coverage of 13 sq deg, and 497 sources detected in total over the 3-24 keV energy range. There are 276 sources with spectroscopic redshifts and classifications, largely resulting from our extensive campaign of ground-based spectroscopic followup. We characterize the overall sample in terms of the X-ray, optical, and infrared source properties. The sample is primarily comprised of active galactic nuclei (AGNs), detected over a large range in redshift from z = 0.002 - 3.4 (median of = 0.56), but also includes 16 spectroscopically confirmed Galactic sources. There is a large range in X-ray flux, from log( f_3-24keV / erg s^-1 cm^-2 ) ~ -14 to -11, and in rest-frame 10-40 keV luminosity, from log( L_10-40keV / erg s^-1 ) ~ 39 to 46, with a median of 44.1. Approximately 79% of the NuSTAR sources have lower energy ( 10^44 erg s^-1) to ~80% at the lowest luminosities (Lx < 10^43 erg s^-1). Our optical spectroscopic analysis finds that the observed fraction of optically obscured AGNs (i.e., the Type 2 fraction) is F_Type2 = 53(+14-15)%, for a well-defined subset of the 8-24 keV selected sample. This is higher, albeit at a low significance level, than the Type 2 fraction measured for redshift- and luminosity-matched AGNs selected by, 49 pages, 23 figures, 8 tables. Accepted for publication in ApJ

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.

In the above article, the name of the first author was spelled incorrectly. This has been corrected in the HTML and PDF versions of the article.

Rationale: Heart muscle contraction is activated by a synchronized systolic Ca release from sarcoplasmic reticulum (SR) via Ca sparks. In disease, Ca sparks fail to terminate, causing a diastolic Ca leak that decreases contraction amplitude and increases the risk of arrhythmia. The mechanisms and treatment of the abnormal Ca leak remain unclear. We have recently shown that spark termination emerges as collective behavior (synchronized closings) of Ca release channels (RyRs) that is identical to synchronization of spin orientation in ferromagnets described by a phase transition in Ising model. Objective: We employed the Ising approach to investigate and classify mechanisms of spark termination failure and Ca leak. Methods and Results: The key parameters determining whether spark termination succeeds or fails are SR Ca and RyR opening/closing rates. They define analogues of magnetic field $h$ and the inverse temperature ($\beta$) in Ising model. Sparks terminate via a phase transition known as "$h$ polarity reversal" and the leak emerges when $h$ fails to change its sign. This happens when the SR depletes insufficiently and RyR openings remained partially synchronized via Ca-induced-Ca-release, generating long-lasting sparks. Leak can also occur via $\beta$, known as Onsager's "order-disorder" transition. This happens at low SR Ca, reducing RyR current and RyRs interactions, resulting in independent RyR openings. The disorder leak is distinguished from synchronized leak by larger Peierls contour lengths reflecting degree of disorder. Conclusions: Abnormal leak results from either a probability imbalance during synchronized firing of RyRs or from disordered RyR firing. Each leak type requires different and balanced treatment to shift RyR operation towards normal spark termination.

The transferable potentials for phase equilibria (TraPPE) force field aims to be accurate, computationally efficient and applicable to a wide range of chemical compounds, state points and thermophy...

Summary Resistance to antimalarials targeting the folate pathway is widespread. GTP-cyclohydrolase (gch1), the first enzyme in this pathway, exhibits extensive copy number variation (CN) in parasite isolates from areas with a history of longstanding antifolate use. Increased CN of gch1 is associated with a greater number of point mutations in enzymes targeted by the antifolates, pyrimethamine and sulphadoxine. While these observations suggest that increases in gch1 CN are an adaptation to drug pressure, changes in CN have not been experimentally demonstrated to directly alter drug susceptibility. To determine if changes in gch1 expression alone modify pyrimethamine sensitivity, we manipulated gch1 CN in several parasite lines to test the effect on drug sensitivity. We report that increases in gch1 CN alter pyrimethamine resistance in most parasites lines. However we find evidence of a detrimental effect of very high levels of gch1 overexpression in parasite lines with high endogenous levels of gch1 expression, revealing the importance of maintaining balance in the folate pathway and implicating changes in gch1 expression in preserving proper metabolic flux. This work expands our understanding of parasite adaptation to drug pressure and provides a possible mechanism for how specific mutations become fixed within parasite populations.

The precise control of gene expression is critical in embryonic development. Quantitative assays, such as microarrays and RNA sequencing, provide gene expression levels for a large number of genes, but do not contain spatial information. In contrast, in situ methods, such as in situ hybridization and immunohistochemistry, provide spatial resolution, but poor quantification and can only reveal the expression of one, or very few genes at a time. Furthermore, the usual methods of documenting the results, by photographing whole mounts or sections, makes it very difficult to assess the three-dimensional (3D) relationships between expressing and nonexpressing cells. Optical projection tomography (OPT) can capture the full 3D expression pattern in a whole embryo at a reasonable level of resolution and at moderately high throughput. A large database containing spatio-temporal patterns of expression for the mouse (e-Mouse Atlas Project, EMAP, www.emouseatlas.org) has been created, incorporating 3D information. Like the mouse, the chick is an important model in developmental biology and translational studies. To facilitate comparisons between these important model organisms, we have created a 3D anatomical atlas, accompanied by an anatomical ontology of the chick embryo and a database of gene expression patterns during chick development. This database is publicly available (www.echickatlas.org). genesis 51:365-371.

The discovery of cis-regulatory elements is a challenging problem in bioinformatics, owing to distal locations and context-specific roles of these elements in controlling gene regulation. Here we review the current bioinformatics methodologies and resources available for systematic discovery of cis-acting regulatory elements and conserved transcription factor binding sites in the chick genome. In addition, we propose and make available, a novel workflow using computational tools that integrate CTCF analysis to predict putative insulator elements, enhancer prediction, and TFBS analysis. To demonstrate the usefulness of this computational workflow, we then use it to analyze the locus of the gene Sox2 whose developmental expression is known to be controlled by a complex array of cis-acting regulatory elements. The workflow accurately predicts most of the experimentally verified elements along with some that have not yet been discovered. A web version of the CTCF tool, together with instructions for using the workflow can be accessed from http://toolshed.g2.bx.psu.edu/view/mkhan1980/ctcf_analysis. For local installation of the tool, relevant Perl scripts and instructions are provided in the directory named "code" in the supplementary materials.

Most work on embryonic stem cell differentiation uses mammalian cells derived from the blastocyst stage and some of the most widely used protocols to induce differentiation involve growing these cells in monolayer culture. Equivalent stem cells can be obtained from embryos of non-mammalian vertebrates, but to date this has only been successful in birds. These cells can contribute to all somatic lineages in chimaeras and can be induced to differentiate into a variety of cell types in vitro via embryoid body formation. However to date there are no reliable methods for differentiating them into descendants from each of the germ layers in monolayer culture, comparable to the protocols used in mammals. Here we describe three simple and reproducible protocols for differentiation of chick embryonic stem cells into mesoderm (bone), endoderm and neuroectoderm (neurons and glia) in monolayer culture. These methods open the way for more direct comparisons of the properties of mammalian and avian embryonic stem cells that may highlight similarities and differences.

Calcium sparks in cardiac myocytes are brief, localized calcium releases from the sarcoplasmic reticulum (SR) believed to be caused by locally regenerative calcium-induced calcium release (CICR) via couplons, clusters of ryanodine receptors (RyRs). How such regeneration is terminated is uncertain. We performed numerical simulations of an idealized stochastic model of spark production, assuming a RyR gating scheme with only two states (open and closed). Local depletion of calcium in the SR was inevitable during a spark, and this could terminate sparks by interrupting CICR, with or without assumed modulation of RyR gating by SR lumenal calcium. Spark termination by local SR depletion was not robust: under some conditions, sparks could be greatly and variably prolonged, terminating by stochastic attrition–a phenomenon we dub “spark metastability.” Spark fluorescence rise time was not a good surrogate for the duration of calcium release. Using a highly simplified, deterministic model of the dynamics of a couplon, we show that spark metastability depends on the kinetic relationship of RyR gating and junctional SR refilling rates. The conditions for spark metastability resemble those produced by known mutations of RyR2 and CASQ2 that cause life-threatening triggered arrhythmias, and spark metastability may be mitigated by altering the kinetics of the RyR in a manner similar to the effects of drugs known to prevent those arrhythmias. The model was unable to explain the distributions of spark amplitudes and rise times seen in chemically skinned cat atrial myocytes, suggesting that such sparks may be more complex events involving heterogeneity of couplons or local propagation among sub-clusters of RyRs.

Setting up the body plan during embryonic development requires the coordinated action of many signals and transcriptional regulators in a precise temporal sequence and spatial pattern. The last decades have seen an explosion of information describing the molecular control of many developmental processes. The next challenge is to integrate this information into logic “wiring diagrams” that visualize gene actions and outputs, have predictive power and point to key control nodes. Here, we provide an experimental workflow on how to construct gene regulatory networks using the chick as model system. genesis 51:296–310, 2012.

Graphical abstract key: ADHD, attention deficit hyperactivity disorder; ASD, atrial septal defect; DD, developmental delay; EEG, electroencephalogram; Ht, height; ID, intellectual disability; OCD, obsessive-compulsive disorder; OFC, open fontanelle; PDA, patent ductus arteriosis; PFO, patent foramen ovale; VSD, ventricular septal defect; Wt, weight.

We present the 3-8 keV and 8-24 keV number counts of active galactic nuclei (AGN) identified in the NuSTAR extragalactic surveys. NuSTAR has now resolved 33-39% of the X-ray background in the 8-24 keV band, directly identifying AGN with obscuring columns up to approximately 1e25 /cm2. In the softer 3-8 keV band the number counts are in general agreement with those measured by XMM-Newton and Chandra over the flux range 5e-15 < S(3 - 8 keV)/(erg/cm2/s) < 1e-12 probed by NuSTAR. In the hard 8-24 keV band NuSTAR probes fluxes over the range 2e-14 < S(8-24 keV)/(erg/cm2/s) < 1e-12, a factor of approximately 100 fainter than previous measurements. The 8-24 keV number counts match predictions from AGN population synthesis models, directly confirming the existence of a population of obscured and/or hard X-ray sources inferred from the shape of the integrated cosmic X-ray background. The measured NuSTAR counts lie significantly above simple extrapolation with a Euclidian slope to low flux of the Swift/BAT 15-55 keV number counts measured at higher fluxes S(15-55 keV) > 1e-11 erg/cm2/s, reflecting the evolution of the AGN population between the Swift/BAT local (z, 8 pages; accepted by the Astrophysical Journal

Hard X-ray observations are crucial to study the non-thermal jet emission from high-redshift, powerful blazars. We observed two bright z>2 flat spectrum radio quasars (FSRQs) in hard X-rays to explore the details of their relativistic jets and their possible variability. S5 0014+81 (at z=3.366) and B0222+185 (at z=2.690) have been observed twice by the Nuclear Spectroscopic Telescope Array (NuSTAR) simultaneously with Swift/XRT, showing different variability behaviours. We found that NuSTAR is instrumental to explore the variability of powerful high-redshift blazars, even when no gamma-ray emission is detected. The two sources have proven to have respectively the most luminous accretion disk and the most powerful jet among known blazars. Thanks to these properties, they are located at the extreme end of the jet-accretion disk relation previously found for gamma-ray detected blazars, to which they are consistent., 10 pages, 7 figures, 3 tables, published on the Monthly Notices of the Royal Astronomical Society

The objective of this study was to evaluate effectiveness of educational intervention (EI) in the Pediatric Appropriate Use of Echocardiography (PAUSE) study to improve appropriateness of transthoracic echocardiograms (TTEs) ordered in pediatric cardiology clinics.Data were prospectively collected after the publication of the Appropriate Use Criteria (AUC) document during 2 phases: the pre-EI phase (1/1/15 to 4/30/15) and the post-EI phase (7/1/15 to 10/30/15). Pre-EI, site-investigators (SI) determined AUC indications, by reviewing the clinic records. Post-EI, providers assigned indications prior to obtaining TTE.Pediatric cardiology clinics at six centers.Those ≤18 years old, receiving initial outpatient TTE.EI included (i) sharing the pre-EI appropriateness ratings with providers, (ii) lecture on AUC, (iii) providers self-assigning indications, and (iv) monthly e-mail feedback by SI to individual providers.The primary outcome measure was a change in the proportion of studies for indications rated R following EI.Of the 4542 TTEs (1907 pre-EI, 2635 post-EI) ordered by 90 physicians, overall comparison of appropriateness ratings before and after EI showed an increase in Appropriate (72.5%-76.2%, P = .004), no change in May Be Appropriate, and a decline in Rarely Appropriate (R) from 9.6% to 7.4%, P = .008. Following EI, a significant decline in R was observed only in three centers and EI did not affect the variation in TTEs ordered for R indications among physicians (P = .467). Physicians with the highest proportion of TTEs ordered for R before EI, showed the most significant decline in R.Appropriateness of pediatric outpatient TTE varies substantially by center. A customized EI resulted in modest improvement in the appropriateness of TTEs in the PAUSE study, with an increase in Appropriate and a decrease in R TTEs. Multifaceted EIs are required to improve adherence to national standards such as AUC.

Intracellular Local Ca releases (LCRs) from sarcoplasmic reticulum (SR) regulate cardiac pacemaker cell function by activation of electrogenic Na/Ca exchanger (NCX) during diastole. Prior studies demonstrated the existence of powerful compensatory mechanisms of LCR regulation via a complex local cross-talk of Ca pump, release and NCX. One major obstacle to study these mechanisms is that LCR exhibit complex Ca release propagation patterns (including merges and separations) that have not been characterized. Here we developed new terminology, classification, and computer algorithms for automatic detection of numerically simulated LCRs and examined LCR regulation by SR Ca pumping rate (Pup) that provides a major contribution to fight-or-flight response. In our simulations the faster SR Ca pumping accelerates action potential-induced Ca transient decay and quickly clears Ca under the cell membrane in diastole, preventing premature releases. Then the SR generates an earlier, more synchronized, and stronger diastolic LCR signal activating an earlier and larger inward NCX current. LCRs at higher Pup exhibit larger amplitudes and faster propagation with more collisions to each other. The LCRs overlap with Ca transient decay, causing an elevation of the average diastolic [Ca] nadir to ~200 nM (at Pup = 24 mM/s). Background Ca (in locations lacking LCRs) quickly decays to resting Ca levels (, Author summary Life’s vital rhythm, the heartbeat is guaranteed by specialized, cardiac pacemaker cells. Based upon the Hodgkin-Huxley membrane excitation theory and its application to cardiac cells, the cardiac pacemaker clock has been, for a long time, to be considered essentially a surface membrane oscillator, i.e. a membrane clock, driven by an ensemble of time- and voltage-dependent ion channels. More recent studies, however, discovered a tight integration of the membrane clock with an intracellular Ca oscillator (dubbed Ca clock). The Ca clock generates rhythmic, diastolic locally propagating Ca releases from sarcoplasmic reticulum, a cell major Ca store, that is refilled with Ca via a Ca pump. The released Ca activates Na/Ca exchanger that generates an inward current and accelerates the diastolic depolarization. Despite their importance, the local releases have not been systematically studied. Here we developed a new computer algorithm for automatic detection, classification, and analysis of local Ca releases generated by a recent computational model of a sinoatrial node cell. Then we investigated how the releases are regulated by the Ca pump, a major functional component of Ca clock. We discovered counterintuitive behaviors stabilizing diastolic Ca signal mass and ensuring fail-safe pacemaker operation at various pumping rates.

Initiation of the primitive streak in avian embryos provides a well-studied example of a pattern-forming event that displays a striking capacity for regulation. The mechanisms underlying the regulative properties are, however, poorly understood and are not easily accounted for by traditional models of pattern formation, such as reaction–diffusion models. In this paper, we propose a new activator–inhibitor model for streak initiation. We show that the model is consistent with experimental observations, both in its pattern-forming properties and in its ability to form these patterns on the correct time-scales for biologically realistic parameter values. A key component of the model is a travelling wave of inhibition. We present a mathematical analysis of the speed of such waves in both diffusive and juxtacrine relay systems. We use the streak initiation model to make testable predictions. By varying parameters of the model, two very different types of patterning can be obtained, suggesting that our model may be applicable to other processes in addition to streak initiation.

Segmentation of the vertebrate body axis is established in the embryo by formation of somites, which give rise to the axial muscles (myotome) and vertebrae (sclerotome). To allow a muscle to attach to two successive vertebrae, the myotome and sclerotome must be repositioned by half a segment with respect to each other. Two main models have been put forward: ‘resegmentation’ proposes that each half‐sclerotome joins with the half‐sclerotome from the next adjacent somite to form a vertebra containing cells from two successive somites on each side of the midline. The second model postulates that a single vertebra is made from a single somite and that the sclerotome shifts with respect to the myotome. There is conflicting evidence for these models, and the possibility that the mechanism may vary along the vertebral column has not been considered. Here we use DiI and DiO to trace somite contributions to the vertebrae in different axial regions in the chick embryo. We demonstrate that vertebral bodies and neural arches form by resegmentation but that sclerotome cells shift in a region‐specific manner according to their dorsoventral position within a segment. We propose a ‘resegmentation‐shift’ model as the mechanism for amniote vertebral patterning.