Comparative Analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans Protein Interaction Network

Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there has been considerable disagreement as to what extent other factors, such as protein abundance, modify this reported dependence. We compare the genomes of Saccharomyces cerevisiae and Caenorhabditis elegans with those of closely related species to elucidate the recent evolutionary history of their respective protein interaction networks. Interaction and expression data are studied in the light of a detailed phylogenetic analysis. The underlying network structure is incorporated explicitly into the statistical analysis. The increased phylogenetic resolution, paired with high-quality interaction data, allows us to resolve the way in which protein interaction network structure and abundance of proteins affect the evolutionary rate. We find that expression levels are better predictors of the evolutionary rate than a protein's connectivity. Detailed analysis of the two organisms also shows that the evolutionary rates of interacting proteins are not sufficiently similar to be mutually predictive. It appears that meaningful inferences about the evolution of protein interaction networks require comparative analysis of reasonably closely related species. The signature of protein evolution is shaped by a protein's abundance in the organism and its function and the biological process it is involved in. Its position in the interaction networks and its connectivity may modulate this but they appear to have only minor influence on a protein's evolutionary rate.Comment: Accepted for publication in BMC Evolutionary Biolog

Searches for Gravitational Waves from Binary Neutron Stars: A Review

A new generation of observatories is looking for gravitational waves. These waves, emitted by highly relativistic systems, will open a new window for ob- servation of the cosmos when they are detected. Among the most promising sources of gravitational waves for these observatories are compact binaries in the final min- utes before coalescence. In this article, we review in brief interferometric searches for gravitational waves emitted by neutron star binaries, including the theory, instru- mentation and methods. No detections have been made to date. However, the best direct observational limits on coalescence rates have been set, and instrumentation and analysis methods continue to be refined toward the ultimate goal of defining the new field of gravitational wave astronomy.Comment: 30 pages, 5 Figures, to appear in "Short-Period Binary Stars: Observations, Analyses, and Results", Ed.s Eugene F. Milone, Denis A. Leahy, David W. Hobil

Increased Yield of ttbb at Hadron Colliders in Low-Energy Supersymmetry

Light bottom squarks and gluinos have been invoked to explain the b quark pair production excess at the Tevatron. We investigate the associated production of ttbb at hadron colliders in this scenario, and find that the rates for this process are enhanced over the Standard Model prediction. If light gluinos exist, it may be possible to detect them at the Tevatron, and they could easily be observed at the LHC.Comment: 5p, references added, version accepted to PR

Minimal Brownian Ratchet: An Exactly Solvable Model

We develop an exactly-solvable three-state discrete-time minimal Brownian ratchet (MBR), where the transition probabilities between states are asymmetric. By solving the master equations we obtain the steady-state probabilities. Generally the steady-state solution does not display detailed balance, giving rise to an induced directional motion in the MBR. For a reduced two-dimensional parameter space we find the null-curve on which the net current vanishes and detailed balance holds. A system on this curve is said to be balanced. On the null-curve, an additional source of external random noise is introduced to show that a directional motion can be induced under the zero overall driving force. We also indicate the off-balance behavior with biased random noise.Comment: 4 pages, 4 figures, RevTex source, General solution added. To be appeared in Phys. Rev. Let

Elastic Instability Triggered Pattern Formation

Recent experiments have exploited elastic instabilities in membranes to create complex patterns. However, the rational design of such structures poses many challenges, as they are products of nonlinear elastic behavior. We pose a simple model for determining the orientational order of such patterns using only linear elasticity theory which correctly predicts the outcomes of several experiments. Each element of the pattern is modeled by a "dislocation dipole" located at a point on a lattice, which then interacts elastically with all other dipoles in the system. We explicitly consider a membrane with a square lattice of circular holes under uniform compression and examine the changes in morphology as it is allowed to relax in a specified direction.Comment: 15 pages, 7 figures, the full catastroph

Astrophysical Implications of the Binary Black Hole Merger GW150914

The discovery of the gravitational-wave (GW) source GW150914 with the Advanced LIGO detectors provides the first observational evidence for the existence of binary black hole (BH) systems that inspiral and merge within the age of the universe. Such BH mergers have been predicted in two main types of formation models, involving isolated binaries in galactic fields or dynamical interactions in young and old dense stellar environments. The measured masses robustly demonstrate that relatively heavy BHs (greater than or similar to 25M(circle dot)) can form in nature. This discovery implies relatively weak massive-star winds and thus the formation of GW150914 in an environment with a metallicity lower than about 1/2 of the solar value. The rate of binary-BH (BBH) mergers inferred from the observation of GW150914 is consistent with the higher end of rate predictions (greater than or similar to 1 Gpc(-3) yr(-1)) from both types of formation models. The low measured redshift (z similar or equal to 0.1) of GW150914 and the low inferred metallicity of the stellar progenitor imply either BBH formation in a low-mass galaxy in the local universe and a prompt merger, or formation at high redshift with a time delay between formation and merger of several Gyr. This discovery motivates further studies of binary-BH formation astrophysics. It also has implications for future detections and studies by Advanced LIGO and Advanced Virgo, and GW detectors in space

The Advanced LIGO Photon Calibrators

The two interferometers of the Laser Interferometry Gravitaional-wave Observatory (LIGO) recently detected gravitational waves from the mergers of binary black hole systems. Accurate calibration of the output of these detectors was crucial for the observation of these events, and the extraction of parameters of the sources. The principal tools used to calibrate the responses of the second-generation (Advanced) LIGO detectors to gravitational waves are systems based on radiation pressure and referred to as Photon Calibrators. These systems, which were completely redesigned for Advanced LIGO, include several significant upgrades that enable them to meet the calibration requirements of second-generation gravitational wave detectors in the new era of gravitational-wave astronomy. We report on the design, implementation, and operation of these Advanced LIGO Photon Calibrators that are currently providing fiducial displacements on the order of $10^{-18}$ m/$\sqrt{\textrm{Hz}}$ with accuracy and precision of better than 1 %.Comment: 14 pages, 19 figure

Circular Orbits in Einstein-Gauss-Bonnet Gravity

The stability under radial and vertical perturbations of circular orbits associated to particles orbiting a spherically symmetric center of attraction is study in the context of the n-dimensional: Newtonian theory of gravitation, Einstein's general relativity, and Einstein-Gauss-Bonnet theory of gravitation. The presence of a cosmological constant is also considered. We find that this constant as well as the Gauss-Bonnet coupling constant are crucial to have stability for $n>4$.Comment: 11 pages, 4 figs, RevTex, Phys. Rev. D, in pres

The \u3cem\u3elet-7\u3c/em\u3e MicroRNA Family Members \u3cem\u3emir\u3c/em\u3e-48, \u3cem\u3emir\u3c/em\u3e-84, and mir-241 Function Together to Regulate Developmental Timing in \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e

The microRNA let-7 is a critical regulator of developmental timing events at the larval-to-adult transition in C. elegans. Recently, microRNAs with sequence similarity to let-7 have been identified. We find that doubly mutant animals lacking the let-7 family microRNA genes mir-48 and mir-84 exhibit retarded molting behavior and retarded adult gene expression in the hypodermis. Triply mutant animals lacking mir-48, mir-84, and mir-241 exhibit repetition of L2-stage events in addition to retarded adult-stage events. mir-48, mir-84, and mir-241 function together to control the L2-to-L3 transition, likely by base pairing to complementary sites in the hbl-1 3′ UTR and downregulating hbl-1 activity. Genetic analysis indicates that mir-48, mir-84, and mir-241 specify the timing of the L2-to-L3 transition in parallel to the heterochronic genes lin-28 and lin-46. These results indicate that let-7 family microRNAs function in combination to affect both early and late developmental timing decisions

Proton stopping in C+C, d+C, C+Ta and d+Ta collisions at 4.2A GeV/c

The shape of proton rapidity distributions is analysed in terms of their Gaussian components, and the average rapidity loss is determined in order to estimate the amount of stopping in C+C, d+C, C+Ta and d+Ta collisions at 4.2A GeV/c. Three Gaussians correspond to the nuclear transparency and describe well all peripheral and also C+C central collisions. Two-component shape is obtained in case of d+C and C+Ta central collisions. Finally one Gaussian, found in d+Ta central collisions, corresponds to the full stopping. The calculated values of the average rapidity loss support the qualitative relationship between the number of Gaussian components and the corresponding stopping power. It is also observed, in central collisions, that the average rapidity loss increases with the ratio of the number of target and the number of projectile participants.Comment: 9 pages REVTeX, 1 PS figure replaced, to be published in Phys.Rev.