A yeast three-hybrid system that reconstitutes mammalian hypoxia inducible factor regulatory machinery

Background: Several human pathologies, including neoplasia and ischemic cardiovascular diseases, course with an unbalance between oxygen supply and demand ( hypoxia). Cells within hypoxic regions respond with the induction of a specific genetic program, under the control of the Hypoxia Inducible Factor (HIF), that mediates their adaptation to the lack of oxygen. The activity of HIF is mainly regulated by the EGL-nine homolog (EGLN) enzymes that hydroxylate the alpha subunit of this transcription factor in an oxygen-dependent reaction. Hydroxylated HIF is then recognized and ubiquitinilated by the product of the tumor suppressor gene, pVHL, leading to its proteosomal degradation. Under hypoxia, the hydroxylation of HIF by the EGLNs is compromised due to the lack of oxygen, which is a reaction cosubstrate. Thus, HIF escapes degradation and drives the transcription of its target genes. Since the progression of the aforementioned pathologies might be influenced by activation of HIF-target genes, development of small molecules with the ability to interfere with the HIF-regulatory machinery is of great interest.Results: Herein we describe a yeast three-hybrid system that reconstitutes mammalian HIF regulation by the EGLNs and VHL. In this system, yeast growth, under specific nutrient restrictions, is driven by the interaction between the beta domain of VHL and a hydroxyproline-containing HIF alpha peptide. In turn, this interaction is strictly dependent on EGLN activity that hydroxylates the HIFa peptide. Importantly, this system accurately preserves the specificity of the hydroxylation reaction toward specific substrates. We propose that this system, in combination with a matched control, can be used as a simple and inexpensive assay to identify molecules that specifically modulate EGLN activity. As a proof of principle we show that two known EGLN inhibitors, dimethyloxaloylglycine (DMOG) and 6-chlor-3-hydroxychinolin-2-carbonic acid-N-carboxymethylamide (S956711), have a profound and specific effect on the yeast HIF/EGLN/VHL system.Conclusion: The system described in this work accurately reconstitutes HIF regulation while preserving EGLN substrate specificity. Thus, it is a valuable tool to study HIF regulation, and particularly EGLN biochemistry, in a cellular context. In addition, we demonstrate that this system can be used to identify specific inhibitors of the EGLN enzymes

Equilibrium and Dynamical Evolution of Self-Gravitating System Embedded in a Potential Well

Isothermal and self-gravitating systems bound by non-conducting and conducting walls are known to be unstable if the density contrast between the center and the boundary exceeds critical values. We investigate the equilibrium and dynamical evolution of isothermal and self-gravitating system embedded in potential well, which can be the situation of many astrophysical objects such as the central parts of the galaxies, or clusters of galaxies with potential dominated by dark matter, but is still limited to the case where the potential well is fixed during the evolution. As the ratio between the depth of surrounding potential well and potential of embedded system becomes large, the potential well becomes effectively the same boundary condition as conducting wall, which behaves like a thermal heat bath. We also use the direct N-body simulation code, NBODY6 to simulate the dynamical evolution of stellar system embedded in potential wells and propose the equilibrium models for this system. In deep potential well, which is analogous to the heat bath with high temperature, the embedded self-gravitating system is dynamically hot, and loosely bound or can be unbound since the kinetic energy increases due to the heating by the potential well. On the other hand, the system undergoes core collapse by self-gravity when potential well is shallow. Binary heating can stop the collapse and leads to the expansion, but the evolution is very slow because the potential as a heat bath can absorb the energy generated by the binaries. The system can be regarded as quasi-static. Density and velocity dispersion profiles from the N-body simulations in the final quasi-equilibrium state are similar to our equilibrium models assumed to be in thermal equilibrium with the potential well.Comment: 12 pages, 12 figures, Submitted to MNRA

A dynamical model for longitudinal wave functions in light-front holographic QCD

We construct a Schrodinger-like equation for the longitudinal wave function of a meson in the valence qq-bar sector, based on the 't Hooft model for large-N two-dimensional QCD, and combine this with the usual transverse equation from light-front holographic QCD, to obtain a model for mesons with massive quarks. The computed wave functions are compared with the wave function ansatz of Brodsky and De Teramond and used to compute decay constants and parton distribution functions. The basis functions used to solve the longitudinal equation may be useful for more general calculations of meson states in QCD.Comment: 12 pages, 2 figures, RevTeX 4.1; expanded discussion, with calculation details moved to appendice

Nonlinear Evolution of Cosmological Structures in Warm Dark Matter Models

The dark energy dominated warm dark matter (WDM) model is a promising alternative cosmological scenario. We explore large-scale structure formation in this paradigm. We do this in two different ways: with the halo model approach and with the help of an ensemble of high resolution N-body simulations. Combining these quasi-independent approaches, leads to a physical understanding of the important processes which shape the formation of structures. We take a detailed look at the halo mass function, the concentrations and the linear halo bias of WDM. In all cases we find interesting deviations with respect to CDM. In particular, the concentration-mass relation displays a turnover for group scale dark matter haloes, for the case of WDM particles with masses of the order ~0.25 keV. This may be interpreted as a hint for top-down structure formation on small scales. We implement our results into the halo model and find much better agreement with simulations. On small scales the WDM halo model now performs as well as its CDM counterpart.Comment: accepted for publication in MNRA

Maternal Serum Meteorin Levels and the Risk of Preeclampsia

BACKGROUND: Meteorin (METRN) is a recently described neutrophic factor with angiogenic properties. This is a nested case-control study in a longitudinal cohort study that describes the serum profile of METRN during different periods of gestation in healthy and preeclamptic pregnant women. Moreover, we explore the possible application of METRN as a biomarker. METHODS AND FINDINGS: Serum METRN was measured by ELISA in a longitudinal prospective cohort study in 37 healthy pregnant women, 16 mild preeclamptic women, and 20 healthy non-pregnant women during the menstrual cycle with the aim of assessing serum METRN levels and its correlations with other metabolic parameters. Immunostaining for METRN protein was performed in placenta. A multivariate logistic regression model was proposed and a classifier model was formulated for predicting preeclampsia in early and middle pregnancy. The performance in classification was evaluated using measures such as sensitivity, specificity, and the receiver operating characteristic (ROC) curve. In healthy pregnant women, serum METRN levels were significantly elevated in early pregnancy compared to middle and late pregnancy. METRN levels are significantly lower only in early pregnancy in preeclamptic women when compared to healthy pregnant women. Decision trees that did not include METRN levels in the first trimester had a reduced sensitivity of 56% in the detection of preeclamptic women, compared to a sensitivity of 69% when METRN was included. CONCLUSIONS: The joint measurements of circulating METRN levels in the first trimester and systolic blood pressure and weight in the second trimester significantly increase the probabilities of predicting preeclampsia

Null Models of Economic Networks: The Case of the World Trade Web

In all empirical-network studies, the observed properties of economic networks are informative only if compared with a well-defined null model that can quantitatively predict the behavior of such properties in constrained graphs. However, predictions of the available null-model methods can be derived analytically only under assumptions (e.g., sparseness of the network) that are unrealistic for most economic networks like the World Trade Web (WTW). In this paper we study the evolution of the WTW using a recently-proposed family of null network models. The method allows to analytically obtain the expected value of any network statistic across the ensemble of networks that preserve on average some local properties, and are otherwise fully random. We compare expected and observed properties of the WTW in the period 1950-2000, when either the expected number of trade partners or total country trade is kept fixed and equal to observed quantities. We show that, in the binary WTW, node-degree sequences are sufficient to explain higher-order network properties such as disassortativity and clustering-degree correlation, especially in the last part of the sample. Conversely, in the weighted WTW, the observed sequence of total country imports and exports are not sufficient to predict higher-order patterns of the WTW. We discuss some important implications of these findings for international-trade models.Comment: 39 pages, 46 figures, 2 table

Clumpy galaxies at z~0.6: kinematics, stability, and comparison with analogs at other redshifts

Distant clumpy galaxies are thought to be Jeans-unstable disks, and an important channel for the formation of local galaxies, as suggested by recent spatially-resolved kinematic observations of z~2 galaxies. I study the kinematics of clumpy galaxies at z~0.6, and compare their properties with those of counterparts at higher and lower redshifts. I selected a sample of 11 clumpy galaxies at z~0.6 from the representative sample of emission line, intermediate-mass galaxies IMAGES. Selection was based on rest-frame UV morphology from HST/ACS images, mimicking the selection criteria commonly used at higher redshifts. Their spatially-resolved kinematics were derived in the frame of the IMAGES survey, using the VLT/FLAMES-GIRAFFE multi-integral field spectrograph. For those showing large-scale rotation, I derived the Toomre Q parameter, which characterizes the stability of their gaseous and stellar phases. I find that the fraction of UV-selected clumpy galaxies at z~0.6 is 20+/-12%. Roughly half of them (45+/-30%) have complex kinematics inconsistent with Jeans-unstable disks, while those in the remaining half (55+/-30%) show large-scale rotations. The latter reveal a stable gaseous phase, but the contribution of their stellar phase makes them globally unstable to clump formation. Clumpy galaxies appear to be less unstable at z~0.6 than at z~2, which could explain why the UV clumps tend to vanish in rest-frame optical images of z~0.6 clumpy galaxies, conversely to z~2 clumpy galaxies, in which the stellar phase can substantially fragment. This suggests that the former correspond to patchy star-formation regions superimposed on a smoother mass distribution. A possible and widespread scenario for driving clump formation relies on instabilities by cold streams penetrating the dark matter halos where clumpy galaxies inhabit. While such a gas accretion process is predicted to be significant in massive, z~2 haloes, it is also predicted to be strongly suppressed in similar, z~0.6 haloes, which could explain why lowest-z clumpy galaxies appear to be driven by a different mechanism. Instead, I found that interactions are probably the dominant driver leading to the formation of clumpy galaxies at z1 clumpy galaxies remains more uncertain. While cold flows could be an important driver at z~2, I also argue that the observed and cumulative merger fraction between z=2 and z=3 is large enough so that every z~2 galaxy might be the result of a merger that occurred within their past 1 Gyr. I conclude that it is premature to rule out mergers as a universal driver for galaxy evolution from z~2 down to z=0.Comment: Accepted for publication in MNRAS. 14 pages, 2 figures

The role of the right temporoparietal junction in perceptual conflict: detection or resolution?

The right temporoparietal junction (rTPJ) is a polysensory cortical area that plays a key role in perception and awareness. Neuroimaging evidence shows activation of rTPJ in intersensory and sensorimotor conflict situations, but it remains unclear whether this activity reflects detection or resolution of such conflicts. To address this question, we manipulated the relationship between touch and vision using the so-called mirror-box illusion. Participants' hands lay on either side of a mirror, which occluded their left hand and reflected their right hand, but created the illusion that they were looking directly at their left hand. The experimenter simultaneously touched either the middle (D3) or the ring finger (D4) of each hand. Participants judged, which finger was touched on their occluded left hand. The visual stimulus corresponding to the touch on the right hand was therefore either congruent (same finger as touch) or incongruent (different finger from touch) with the task-relevant touch on the left hand. Single-pulse transcranial magnetic stimulation (TMS) was delivered to the rTPJ immediately after touch. Accuracy in localizing the left touch was worse for D4 than for D3, particularly when visual stimulation was incongruent. However, following TMS, accuracy improved selectively for D4 in incongruent trials, suggesting that the effects of the conflicting visual information were reduced. These findings suggest a role of rTPJ in detecting, rather than resolving, intersensory conflict

A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2′-deoxyguanosine

The harmfulness of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8oxodG) damage resides on its dual coding potential, as it can pair with the correct dCMP (dC) or the incorrect dAMP (dA). Here, we investigate the translesional synthesis ability of family B ϕ29 DNA polymerase on 8oxodG-containing templates. We show that this polymerase preferentially inserts dC opposite 8oxodG, its 3′–5′ exonuclease activity acting indistinctly on both dA or dC primer terminus. In addition, ϕ29 DNA polymerase shows a favoured extension of the 8oxodG/dA pair, but with an efficiency much lower than that of the canonical dG/dC pair. Additionally, we have analysed the role of the invariant tyrosine from motif B of family B DNA polymerases in translesional synthesis past 8oxodG, replacing the corresponding ϕ29 DNA polymerase Tyr390 by Phe or Ser. The lack of the aromatic portion in mutant Y390S led to a lost of discrimination against dA insertion opposite 8oxodG. On the contrary, the absence of the hydroxyl group in the Y390F mutant precluded the favoured extension of 8oxodG:dA base pair with respect to 8oxodG:dC. Based on the results obtained, we propose that this Tyr residue contributes to dictate nucleotide insertion and extension preferences during translesion synthesis past 8oxodG by family B replicases