On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei

Background: Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle. Results: Starting with 993 T. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA. Conclusions: Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host

Phase and amplitude scintillations of microwave signals over an elevated atmospheric path

Phase and amplitude scintillations of microwave signals over elevated atmospheric path for obtaining atmospheric density profile

Noncanonical quantum optics

Modification of the right-hand-side of canonical commutation relations (CCR) naturally occurs if one considers a harmonic oscillator with indefinite frequency. Quantization of electromagnetic field by means of such a non-CCR algebra naturally removes the infinite energy of vacuum but still results in a theory which is very similar to quantum electrodynamics. An analysis of perturbation theory shows that the non-canonical theory has an automatically built-in cut-off but requires charge/mass renormalization already at the nonrelativistic level. A simple rule allowing to compare perturbative predictions of canonical and non-canonical theories is given. The notion of a unique vacuum state is replaced by a set of different vacua. Multi-photon states are defined in the standard way but depend on the choice of vacuum. Making a simplified choice of the vacuum state we estimate corrections to atomic lifetimes, probabilities of multiphoton spontaneous and stimulated emission, and the Planck law. The results are practically identical to the standard ones. Two different candidates for a free-field Hamiltonian are compared.Comment: Completely rewritten version of quant-ph/0002003v2. There are overlaps between the papers, but sections on perturbative calculations show the same problem from different sides, therefore quant-ph/0002003v2 is not replace

A Comparative Analysis of the Chronic Effects of Fine Particulate Matter

The American Cancer Society study (ACS) and the Harvard Six Cities study (SCS) are the two landmark cohort studies for estimating the chronic effects of fine particulate matter PM2.5 on mortality. To date, no comparative analysis of these studies has been carried out using a different study design, study period, data, and modeling approach. In this paper, we estimate the chronic effects of PM on mortality for the period 2000-2002 by using mortality data from Medicare and \PM levels from the National Air Pollution Monitoring Network for the same counties included in the SCS and the ACS. We use a log-linear regression model which controls for individual-level risk factors (age and gender) and area-level covariates (education, income level, poverty and employment). We found that a 10 units increase in the yearly average PM2.5 is associated with 10.9% (95% CI: 9.0, 12.8) and with 20.8% (95% CI: 12.3, 30.0) increase in all-cause mortality by using Medicare data for the ACS and SCS counties. The results are similar to those reported by the original SCS and ACS indicating that fine particulate matter is still significantly associated with mortality when more recent air pollution and mortality data are used. Our findings suggest that national government based data, like the Medicare, are useful for advancing our understanding of the chronic effects of ambient air pollution on health

XO-5b: A Transiting Jupiter-sized Planet With A Four Day Period

The star XO-5 (GSC 02959-00729, V=12.1, G8V) hosts a Jupiter-sized, Rp=1.15+/-0.12 Rjup, transiting extrasolar planet, XO-5b, with an orbital period of P=4.187732+/-0.00002 days. The planet mass (Mp=1.15+/-0.08 Mjup) and surface gravity (gp=22+/-5 m/s^2) are significantly larger than expected by empirical Mp-P and Mp-P-[Fe/H] relationships. However, the deviation from the Mp-P relationship for XO-5b is not large enough to suggest a distinct type of planet as is suggested for GJ 436b, HAT-P-2b, and XO-3b. By coincidence XO-5 overlies the extreme H I plume that emanates from the interacting galaxy pair NGC 2444/NGC 2445 (Arp 143).Comment: 10 pages, 9 Figures, Submitted to Ap

Maximal entropy inference of oncogenicity from phosphorylation signaling

Point mutations in the phosphorylation domain of the Bcr-Abl fusion oncogene give rise to drug resistance in chronic myelogenous leukemia patients. These mutations alter kinase-mediated signaling function and phenotypic outcome. An information theoretic analysis of the correlation of phosphoproteomic profiling and transformation potency of the oncogene in different mutants is presented. The theory seeks to predict the leukemic transformation potency from the observed signaling by constructing a distribution of maximal entropy of site-specific phosphorylation events. The theory is developed with special reference to systems biology where high throughput measurements are typical. We seek sets of phosphorylation events most contributory to predicting the phenotype by determining the constraints on the signaling system. The relevance of a constraint is measured by how much it reduces the value of the entropy from its global maximum, where all events are equally likely. Application to experimental phospho-proteomics data for kinase inhibitor-resistant mutants shows that there is one dominant constraint and that other constraints are not relevant to a similar extent. This single constraint accounts for much of the correlation of phosphorylation events with the oncogenic potency and thereby usefully predicts the trends in the phenotypic output. An additional constraint possibly accounts for biological fine structure

The spatial distribution of coronae on Venus

Coronae on Venus are large, generally circular surface features that have distinctive tectonic, volcanic, and topographic expressions. They range in diameter from less than 200 km to at least 1000 km. Data from the Magellan spacecraft have now allowed complete global mapping of the spatial distribution of coronae on the planet. Unlike impact craters, which show a random (i.e., Poisson) spatial distribution, the distribution of coronae appears to be nonrandom. We investigate the distribution here in detail, and explore its implications in terms of mantle convection and surface modification processes

XO-2b: Transiting Hot Jupiter in a Metal-rich Common Proper Motion Binary

We report on a V=11.2 early K dwarf, XO-2 (GSC 03413-00005), that hosts a Rp=0.98+0.03/-0.01 Rjup, Mp=0.57+/-0.06 Mjup transiting extrasolar planet, XO-2b, with an orbital period of 2.615857+/-0.000005 days. XO-2 has high metallicity, [Fe/H]=0.45+/-0.02, high proper motion, mu_tot=157 mas/yr, and has a common proper motion stellar companion with 31" separation. The two stars are nearly identical twins, with very similar spectra and apparent magnitudes. Due to the high metallicity, these early K dwarf stars have a mass and radius close to solar, Ms=0.98+/-0.02 Msolar and Rs=0.97+0.02/-0.01 Rsolar. The high proper motion of XO-2 results from an eccentric orbit (Galactic pericenter, Rper<4 kpc) well confined to the Galactic disk (Zmax~100 pc). In addition, the phase space position of XO-2 is near the Hercules dynamical stream, which points to an origin of XO-2 in the metal-rich, inner Thin Disk and subsequent dynamical scattering into the solar neighborhood. We describe an efficient Markov Chain Monte Carlo algorithm for calculating the Bayesian posterior probability of the system parameters from a transit light curve.Comment: 14 pages, 10 Figures, Accepted in ApJ. Negligible changes to XO-2 system properties. Removed Chi^2 light curve analysis section, and simplified MCMC light curve analysis discussio

A Transiting Planet of a Sun-like Star

A planet transits an 11th magnitude, G1V star in the constellation Corona Borealis. We designate the planet XO-1b, and the star, XO-1, also known as GSC 02041-01657. XO-1 lacks a trigonometric distance; we estimate it to be 200+-20 pc. Of the ten stars currently known to host extrasolar transiting planets, the star XO-1 is the most similar to the Sun in its physical characteristics: its radius is 1.0+-0.08 R_Sun, its mass is 1.0+-0.03 M_Sun, V sini < 3 km/s, and its metallicity [Fe/H] is 0.015+-0.04. The orbital period of the planet XO-1b is 3.941534+-0.000027 days, one of the longer ones known. The planetary mass is 0.90+-0.07 M_Jupiter, which is marginally larger than that of other transiting planets with periods between 3 and 4 days. Both the planetary radius and the inclination are functions of the spectroscopically determined stellar radius. If the stellar radius is 1.0+-0.08 R_Sun, then the planetary radius is 1.30+-0.11 R_Jupiter and the inclination of the orbit is 87.7+-1.2 degrees. We have demonstrated a productive international collaboration between professional and amateur astronomers that was important to distinguishing this planet from many other similar candidates.Comment: 31 pages, 9 figures, accepted for part 1 of Ap

Dissecting the polar dichotomy of the noncondensable gas enhancement on Mars using the NASA Ames Mars General Circulation Model

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95628/1/jgre2298.pd