Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements

RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans. From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes with HIF-1–dependent expression that have opposite changes in expression in mutants of two genes that cooperate to negatively regulate HIF-1 abundance; however, the double mutant of these genes exhibits suppression epistasis. This class violates the classical model of HIF-1 regulation but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control

Helium, Oxygen, Proton, and Electron (HOPE) Mass Spectrometer for the Radiation Belt Storm Probes Mission

The HOPE mass spectrometer of the Radiation Belt Storm Probes (RBSP) mission (renamed the Van Allen Probes) is designed to measure the in situ plasma ion and electron fluxes over 4π sr at each RBSP spacecraft within the terrestrial radiation belts. The scientific goal is to understand the underlying physical processes that govern the radiation belt structure and dynamics. Spectral measurements for both ions and electrons are acquired over 1 eV to 50 keV in 36 log-spaced steps at an energy resolution ΔE FWHM/E≈15 %. The dominant ion species (H+, He+, and O+) of the magnetosphere are identified using foil-based time-of-flight (TOF) mass spectrometry with channel electron multiplier (CEM) detectors. Angular measurements are derived using five polar pixels coplanar with the spacecraft spin axis, and up to 16 azimuthal bins are acquired for each polar pixel over time as the spacecraft spins. Ion and electron measurements are acquired on alternate spacecraft spins. HOPE incorporates several new methods to minimize and monitor the background induced by penetrating particles in the harsh environment of the radiation belts. The absolute efficiencies of detection are continuously monitored, enabling precise, quantitative measurements of electron and ion fluxes and ion species abundances throughout the mission. We describe the engineering approaches for plasma measurements in the radiation belts and present summaries of HOPE measurement strategy and performance

Double-illumination photoacoustic microscopy

Recent developments of optical-resolution photoacoustic microscopy (OR-PAM) have improved its spatial resolution and imaging speed. However, the penetration depth of OR-PAM is still limited to ∼1  mm in tissue, owing to the strong tissue scattering. Here, we have developed double-illumination PAM (DI-PAM), which illuminates the sample from both top and bottom sides simultaneously. Through phantom and in vivo experiments, we have demonstrated for thin targets that DI-PAM has a penetration depth of ∼2  mm in tissue at 532 nm and a focal zone of 260 μm, both significant improvements over traditional reflection or transmission-mode OR-PAM

Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders

Nuclear factor κB (NF-κB) is a transcription factor that regulates various aspects of immune response, cell death, and differentiation as well as cancer. In this study we introduce the Py-Im polyamide 1 that binds preferentially to the sequences 5′-WGGWWW-3′ and 5′GGGWWW-3′. The compound is capable of binding to κB sites and reducing the expression of various NF-κB–driven genes including IL6 and IL8 by qRT-PCR. Chromatin immunoprecipitation experiments demonstrate a reduction of p65 occupancy within the proximal promoters of those genes. Genome-wide expression analysis by RNA-seq compares the DNA-binding polyamide with the well-characterized NF-κB inhibitor PS1145, identifies overlaps and differences in affected gene groups, and shows that both affect comparable numbers of TNF-α–inducible genes. Inhibition of NF-κB DNA binding via direct displacement of the transcription factor is a potential alternative to the existing antagonists

Chandra Observations of Type Ia Supernovae: Upper Limits to the X-ray Flux of SN 2002bo, SN 2002ic, SN 2005gj, and SN 2005ke

We set sensitive upper limits to the X-ray emission of four Type Ia supernovae (SNe Ia) using the Chandra X-ray Observatory. SN 2002bo, a normal, although reddened, nearby SN Ia, was observed 9.3 days after explosion. For an absorbed, high temperature bremsstrahlung model the flux limits are 3.2E-16 ergs/cm^2/s (0.5-2 keV band) and 4.1E-15 ergs/cm^2/s (2-10 keV band). Using conservative model assumptions and a 10 km/s wind speed, we derive a mass loss rate of \dot{M} ~ 2E-5 M_\odot/yr, which is comparable to limits set by the non-detection of Halpha lines from other SNe Ia. Two other objects, SN 2002ic and SN 2005gj, observed 260 and 80 days after explosion, respectively, are the only SNe Ia showing evidence for circumstellar interaction. The SN 2002ic X-ray flux upper limits are ~4 times below predictions of the interaction model currently favored to explain the bright optical emission. To resolve this discrepancy we invoke the mixing of cool dense ejecta fragments into the forward shock region, which produces increased X-ray absorption. A modest amount of mixing allows us to accommodate the Chandra upper limit. SN 2005gj is less well studied at this time. Assuming the same circumstellar environment as for SN 2002i, the X-ray flux upper limits for SN 2005gj are ~4 times below the predictions, suggesting that mixing of cool ejecta into the forward shock has also occurred here. Our reanalysis of Swift and Chandra data on SN 2005ke does not confirm a previously reported X-ray detection. The host galaxies NGC 3190 (SN 2002bo) and NGC 1371 (SN 2005ke) each harbor a low luminosity (L_X ~ 3-4E40 ergs/s) active nucleus in addition to wide-spread diffuse soft X-ray emission.Comment: 16 pages, to appear in ApJ (20 Nov 2007

Two-dimensional Navier--Stokes simulation of deformation and break up of liquid patches

The large deformations and break up of circular 2D liquid patches in a high Reynolds number (Re=1000) gas flow are investigated numerically. The 2D, plane flow Navier--Stokes equations are directly solved with explicit tracking of the interface between the two phases and a new algorithm for surface tension. The numerical method is able to pursue the simulation beyond the breaking or coalescence of droplets. The simulations are able to unveil the intriguing details of the non-linear interplay between the deforming droplets and the vortical structures in the droplet's wake.Comment: 13 pages including 4 postscript figures; Revised version as resubmitted to PRL. Title has change

Microwave Assisted Synthesis of Py-Im Polyamides

Microwave synthesis was utilized to rapidly build Py-Im polyamides in high yields and purity using Boc-protection chemistry on Kaiser oxime resin. A representative polyamide targeting the 5′-WGWWCW-3′ (W = A or T) subset of the consensus Androgen and Glucocorticoid Response Elements was synthesized in 56% yield after 20 linear steps and HPLC purification. It was confirmed by Mosher amide derivatization of the polyamide that a chiral α-amino acid does not racemize after several additional coupling steps

2006 SQ372: A Likely Long-Period Comet from the Inner Oort Cloud

We report the discovery of a minor planet (2006 SQ372) on an orbit with a perihelion of 24 AU and a semimajor axis of 796 AU. Dynamical simulations show that this is a transient orbit and is unstable on a timescale of 200 Myrs. Falling near the upper semimajor axis range of the scattered disk and the lower semimajor axis range of the Oort Cloud, previous membership in either class is possible. By modeling the production of similar orbits from the Oort Cloud as well as from the scattered disk, we find that the Oort Cloud produces 16 times as many objects on SQ372-like orbits as the scattered disk. Given this result, we believe this to be the most distant long-period comet ever discovered. Furthermore, our simulation results also indicate that 2000 OO67 has had a similar dynamical history. Unaffected by the "Jupiter-Saturn Barrier," these two objects are most likely long-period comets from the inner Oort Cloud

The European Union in the World — A Community of Values

These are momentous times in Europe. The Euro has been successfully introduced, the enlargement negotiations are approaching their climax, and the European Convention (“Convention”) is moving towards the drafting of a constitution for a new, continent-wide political entity. At the same time, unrest is manifest, particularly in two areas. On the one hand, many of our citizens, and not just the political elites, are dissatisfied with Europe\u27s performance on the world stage and are concerned about the maintenance of peace and security within the Union. In these areas they would like to see a strengthened, more effective entity-- “more Europe.” On the other hand, their disenchantment with the long reach of European Union (“EU” or “Union”) regulation in the first pillar area of economic policy is growing. The feeling of loss of local control over their destiny and a vague feeling of potential loss of identity within an ever more centralized polity is palpable. Here, they want “less Europe.” In the outside world, change is also the order of the day. The ice-sheet of bipolarity, which overlaid and hid the complexity of international relations during the Cold War, is breaking up at an ever-increasing speed and revealing a world in which two paradigms are competing to become the underlying ordering principles for the new century. The traditional paradigm of interacting Nation States, each pursuing its own separate interests, with alliances allowing the small to compete with the large, is alive and well, and its proponents like Machiavelli or Churchill continue to be in vogue in the literature of international relations and the rhetoric of world leaders. At the same time, there is a school of thought which points to the growing economic and ecological interdependence of our societies and the necessity for new forms of global governance to complement national action. It is also becoming abundantly clear that the concept of a “Nation State” is often a fiction, positing as it does an identity between the citizens of a State and the members of a culturally homogenous society. For both reasons, the concept of the Nation State as the principal actor on the world stage, is called into question. The experience of the Union with the sharing of State sovereignty is clearly related to the second paradigm and also to the EU\u27s firm support for the development of the United Nations (“U.N.”) as well as other elements of multilateral governance. It would hardly be wise to suggest that any foreign policy, and certainly not that of the EU, should be based only on this paradigm. Given the recurrent threats to security, which seem to be part of the human condition expressed by some as the “inevitability of war”--the defense of territorial integrity; action against threats of aggression; and resistance to crimes against humanity such as genocide--the ability to conduct a security policy based much more on the old paradigm of interacting interests will continue to be required. That the EU needs to develop such a capability will be taken here as a given. Such a crisis-management capability will be essential to the Union, but will be distinguished here from the more long-term elements of foreign policy, which can be thought of as being designed to reduce the need for crisis management in the context of a security policy to a minimum. The crisis-management area of policy will not be treated further here. The thesis of this Essay is that the same set of political concepts can serve as a guide to the future internal development of the EU and as the basis of such a long-term foreign policy. Furthermore, it suggests that neither should be seen in terms of the balancing of interests but rather, as the expression of a small list of fundamental values. The list is as follows: (1) the rule of law as the basis for relations between members of society; (2) the interaction between the democratic process and entrenched human rights in political decision-making; (3) the operation of competition within a market economy as the source of increasing prosperity; (4) the anchoring of the principle of solidarity among all members of society alongside that of the liberty of the individual; (5) the adoption of the principle of sustainability of all economic development; and (6) the preservation of separate identities and the maintenance of cultural diversity within society. These values can be seen as the answer to the question posed both, by citizens of the Union and by our fellow citizens of the world: “What does the EU stand for?” In exploring these values we should, however, remember that in the real world there will be occasions on which Realpolitik will intrude and the interest-based paradigm will prevail