Internal friction and mode relaxation in a simple chain model

We consider equilibrium relaxation properties of the end-to-end distance and of principal components in a one-dimensional polymer chain model with nonlinear interaction between the beads. While for the single-well potentials these properties are similar to the ones of a Rouse chain, for the double-well interaction potentials, modeling internal friction, they differ vastly from the ones of the harmonic chain at intermediate times and intermediate temperatures. This minimal description within a one-dimensional model mimics the relaxation properties found in much more complex polymer systems. Thus, the relaxation time of the end-to-end distance may grow by orders of magnitude at intermediate temperatures. The principal components (whose directions are shown to coincide with the normal modes of the harmonic chain, whatever interaction potential is assumed) not only display larger relaxation times but also subdiffusive scaling

Control of gene conversion and somatic hypermutation by immunoglobulin promoter and enhancer sequences

It is thought that gene conversion (GCV) and somatic hypermutation (SHM) of immunoglobulin (Ig) genes occur in two steps: the generation of uracils in DNA by activation-induced cytidine deaminase, followed by their subsequent repair by various DNA repair pathways to generate sequence-diversified products. It is not known how either of the two steps is targeted specifically to Ig loci. Because of the tight link between transcription and SHM, we have investigated the role of endogenous Ig light chain (IgL) transcriptional control elements in GCV/SHM in the chicken B cell line DT40. Promoter substitution experiments led to identification of a strong RNA polymerase II promoter incapable of supporting efficient GCV/SHM. This surprising finding indicates that high levels of transcription are not sufficient for robust GCV/SHM in Ig loci. Deletion of the IgL enhancer in a context in which high-level transcription was not compromised showed that the enhancer is not necessary for GCV/SHM. Our results indicate that cis-acting elements are important for Ig gene diversification, and we propose that targeting specificity is achieved through the combined action of several Ig locus elements that include the promoter

Galaxy-Quasar correlations between APM galaxies and Hamburg-ESO QSOs

We detect angular galaxy-QSO cross-correlations between the APM Galaxy Catalogue and a preliminary release (consisting of roughly half of the anticipated final catalogue) of the Hamburg-ESO Catalogue of Bright QSOs as a function of source QSO redshift using multiple cross-correlation estimators. Each of the estimators yield very similar results, implying that the APM catalogue and the Hamburg-ESO survey are both fair samples of the respective true galaxy and QSO populations. Though the signal matches the expectations of gravitational lensing qualitatively, the strength of the measured cross-correlation signal is significantly greater than the CDM models of lensing by large scale structure would suggest. This same disagreement between models and observation has been found in several earlier studies. We estimate our confidence in the correlation detections versus redshift by generating 1000 random realizations of the Hamburg-ESO QSO survey: We detect physical associations between galaxies and low-redshift QSOs at 99% confidence and detect lensing associations at roughly 95% confidence for QSOs with redshifts between 0.6 and 1. Control cross-correlations between Galactic stars and QSOs show no signal. Finally, the overdensities (underdensities) of galaxies near QSO positions relative to those lying roughly 135 - 150 arcmin away are uncorrelated with differences in Galactic extinction between the two regions, implying that Galactic dust is not significantly affecting the QSO sample.Comment: 35 pages total, including 9 figures. Accepted by the Astrophysical Journa

Automated optical identification of a large complete northern hemisphere sample of flat spectrum radio sources with S_6cm > 200 mJy

This paper describes the automated optical APM identification of radio sources from the Jodrell Bank - VLA Astrometric Survey (JVAS), as used for the search for distant radio-loud quasars. The sample has been used to investigate possible relations between optical and radio properties of flat spectrum radio sources. From the 915 sources in the sample, 756 have an optical APM identification at a red (e) and/or blue (o) plate,resulting in an identification fraction of 83% with a completeness and reliability of 98% and 99% respectively. About 20% are optically identified with extended APM objects on the red plates, e.g. galaxies. However the distinction between galaxies and quasars can not be done properly near the magnitude limit of the POSS-I plates. The identification fraction appears to decrease from >90% for sources with a 5 GHz flux density of >1 Jy, to <80% for sources at 0.2 Jy. The identification fraction, in particular that for unresolved quasars, is found to be lower for sources with steeper radio spectra. In agreement with previous studies, we find that the quasars at low radio flux density levels also tend to have fainter optical magnitudes, although there is a large spread. In addition, objects with a steep radio-to-optical spectral index are found to be mainly highly polarised quasars, supporting the idea that in these objects the polarised synchrotron component is more prominent. It is shown that the large spread in radio-to-optical spectral index is possibly caused by source to source variations in the Doppler boosting of the synchrotron component [Abridged].Comment: LaTex, 17 pages, 5 gif figures, 4 tables. Accepted for publication in MNRAS. High resolution figures can be found at http://www.roe.ac.uk/~ignas

Size Bias in Galaxy Surveys

Only certain galaxies are included in surveys: those bright and large enough to be detectable as extended sources. Because gravitational lensing can make galaxies appear both brighter and larger, the presence of foreground inhomogeneities can scatter galaxies across not only magnitude cuts but also size cuts, changing the statistical properties of the resulting catalog. Here we explore this size bias, and how it combines with magnification bias to affect galaxy statistics. We demonstrate that photometric galaxy samples from current and upcoming surveys can be even more affected by size bias than by magnification bias.Comment: 4 pages; 3 figures. Accepted for publication in Phys. Rev. Let.; v2: incorporating referee's comments; v3: updated acknowledgment

Phylogenetic Analysis of the MS4A and TMEM176 Gene Families

The MS4A gene family in humans includes CD20 (MS4A1), FcRbeta (MS4A2), Htm4 (MS4A3), and at least 13 other syntenic genes encoding membrane proteins, most having characteristic tetraspanning topology. Expression of MS4A genes is variable in tissues throughout the body; however, several are limited to cells in the hematopoietic system where they have known roles in immune cell functions. Genes in the small TMEM176 group share significant sequence similarity with MS4A genes and there is evidence of immune function of at least one of the encoded proteins. In this study, we examined the evolutionary history of the MS4A/TMEM176 families as well as tissue expression of the phylogenetically earliest members, in order to investigate their possible origins in immune cells.Orthologs of human MS4A genes were found only in mammals; however, MS4A gene homologs were found in most jawed vertebrates. TMEM176 genes were found only in mammals and bony fish. Several unusual MS4A genes having 2 or more tandem MS4A sequences were identified in the chicken (Gallus gallus) and early mammals (opossum, Monodelphis domestica and platypus, Ornithorhyncus anatinus). A large number of highly conserved MS4A and TMEM176 genes was found in zebrafish (Danio rerio). The most primitive organism identified to have MS4A genes was spiny dogfish (Squalus acanthus). Tissue expression of MS4A genes in S. acanthias and D. rerio showed no evidence of expression restricted to the hematopoietic system.Our findings suggest that MS4A genes first appeared in cartilaginous fish with expression outside of the immune system, and have since diversified in many species into their modern forms with expression and function in both immune and nonimmune cells

Resonance-like phenomena of the mobility of a chain of nonlinear coupled oscillators in a two-dimensional periodic potential

We study the Langevin dynamics of a two-dimensional discrete oscillator chain absorbed on a periodic substrate and subjected to an external localized point force. Going beyond the commonly used harmonic bead-spring model, we consider a nonlinear Morse interaction between the next-nearest-neighbors. We focus interest on the activation of directed motion instigated by thermal fluctuations and the localized point force. In this context the local transition states are identified and the corresponding activation energies are calculated. As a novel feature it is found that the transport of the chain in point force direction is determined by stepwise escapes of a single unit or segments of the chain due to the existence of multiple locally stable attractors. The non-vanishing net current of the chain is quantitatively assessed by the value of the mobility of the center of mass. It turns out that the latter as a function of the ratio of the competing length scales of the system, that is the period of the substrate potential and the equilibrium distance between two chain units, shows a resonance behavior. More precisely there exist a set of optimal parameter values maximizing the mobility. Interestingly, the phenomenon of negative resistance is found, i.e. the mobility possesses a minimum at a finite value of the strength of the thermal fluctuations for a given overcritical external driving force.Comment: 25 pages, 12 figure

Defective DNA Repair and Increased Genomic Instability in Artemis-deficient Murine Cells

In developing lymphocytes, the recombination activating gene endonuclease cleaves DNA between V, D, or J coding and recombination signal (RS) sequences to form hairpin coding and blunt RS ends, which are fused to form coding and RS joins. Nonhomologous end joining (NHEJ) factors repair DNA double strand breaks including those induced during VDJ recombination. Human radiosensitive severe combined immunodeficiency results from lack of Artemis function, an NHEJ factor with in vitro endonuclease/exonuclease activities. We inactivated Artemis in murine embryonic stem (ES) cells by targeted mutation. Artemis deficiency results in impaired VDJ coding, but not RS, end joining. In addition, Artemis-deficient ES cells are sensitive to a radiomimetic drug, but less sensitive to ionizing radiation. VDJ coding joins from Artemis-deficient ES cells, which surprisingly are distinct from the highly deleted joins consistently obtained from DNA-dependent protein kinase catalytic subunit–deficient ES cells, frequently lack deletions and often display large junctional palindromes, consistent with a hairpin coding end opening defect. Strikingly, Artemis-deficient ES cells have increased chromosomal instability including telomeric fusions. Thus, Artemis appears to be required for a subset of NHEJ reactions that require end processing. Moreover, Artemis functions as a genomic caretaker, most notably in prevention of translocations and telomeric fusions. As Artemis deficiency is compatible with human life, Artemis may also suppress genomic instability in humans

Thermal Degradation of Adsorbed Bottle-Brush Macromolecules: Molecular Dynamics Simulation

The scission kinetics of bottle-brush molecules in solution and on an adhesive substrate is modeled by means of Molecular Dynamics simulation with Langevin thermostat. Our macromolecules comprise a long flexible polymer backbone with $L$ segments, consisting of breakable bonds, along with two side chains of length $N$, tethered to each segment of the backbone. In agreement with recent experiments and theoretical predictions, we find that bond cleavage is significantly enhanced on a strongly attractive substrate even though the chemical nature of the bonds remains thereby unchanged. We find that the mean bond life time decreases upon adsorption by more than an order of magnitude even for brush molecules with comparatively short side chains $N=1 \div 4$. The distribution of scission probability along the bonds of the backbone is found to be rather sensitive regarding the interplay between length and grafting density of side chains. The life time declines with growing contour length $L$ as $\propto L^{-0.17}$, and with side chain length as $\propto N^{-0.53}$. The probability distribution of fragment lengths at different times agrees well with experimental observations. The variation of the mean length $L(t)$ of the fragments with elapsed time confirms the notion of the thermal degradation process as a first order reaction.Comment: 15 pages, 7 figure

X-ray Spectral Survey of WGACAT Quasars, II: Optical and Radio Properties of Quasars with Low Energy X-ray Cut-offs

We have selected quasars with X-ray colors suggestive of a low energy cut-off, from the ROSAT PSPC pointed archive. We examine the radio and optical properties of these 13 quasars. Five out of the seven quasars with good optical spectra show associated optical absorption lines, with two having high delta-v candidate systems. Two other cut-off quasars show reddening associated with the quasar. We conclude that absorption is highly likely to be the cause of the X-ray cut-offs, and that the absorbing material associated with the quasars, not intervening along the line-of-sight. The suggestion that Gigahertz Peaked Sources are associated with X-ray cut-offs remains unclear with this expanded sample.Comment: 17 pages, LaTeX, including 2 Tables and 1 figure. Ap.J. in pres