RazerS - Fast Read Mapping with Sensitivity Control

Second-generation sequencing technologies deliver DNA sequence data at unprecedented high throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. Due to the large amounts of data, efficient algorithms and implementations are crucial for this task. We present an efficient read mapping tool called RazerS. It allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. Our tool can work either lossless or with a user-defined loss rate at higher speeds. Given the loss rate, we present an approach that guarantees not to lose more reads than specified. This enables the user to adapt to the problem at hand and provides a seamless tradeoff between sensitivity and running time

Segment-based multiple sequence alignment

Motivation: Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far. Results: We introduce a graph-based extension to the consistency-based, progressive alignment strategy. We apply the consistency notion to segments instead of single characters. The main problem we solve in this context is to define segments of the sequences in such a way that a graph-based alignment is possible. We implemented the algorithm using the SeqAn library and report results on amino acid and DNA sequences. The benefit of our approach is threefold: (1) sequences with conserved blocks can be rapidly aligned, (2) the implementation is conceptually easy, generic and fast and (3) the consistency idea can be extended to align multiple genomic sequences. Availability: The segment-based multiple sequence alignment tool can be downloaded from http://www.seqan.de/projects/msa.html. A novel version of T-Coffee interfaced with the tool is available from http://www.tcoffee.org. The usage of the tool is described in both documentations. Contact: [email protected]

Temperature dependence of the Kondo resonance and its satellites in CeCu_2Si_2

We present high-resolution photoemission spectroscopy studies on the Kondo resonance of the strongly-correlated Ce system CeCu$_2$Si$_2$. Exploiting the thermal broadening of the Fermi edge we analyze position, spectral weight, and temperature dependence of the low-energy 4f spectral features, whose major weight lies above the Fermi level $E_F$. We also present theoretical predictions based on the single-impurity Anderson model using an extended non-crossing approximation (NCA), including all spin-orbit and crystal field splittings of the 4f states. The excellent agreement between theory and experiment provides strong evidence that the spectral properties of CeCu$_2$Si$_2$ can be described by single-impurity Kondo physics down to $T \approx 5$ K.Comment: 4 pages, 3 figure

Shepherding DNA ends: Rif1 protects telomeres and chromosome breaks

Cells have evolved conserved mechanisms to protect DNA ends, such as those at the termini of linear chromosomes, or those at DNA double-strand breaks (DSBs). In eukaryotes, DNA ends at chromosomal termini are packaged into proteinaceous structures called telomeres. Telomeres protect chromosome ends from erosion, inadvertent activation of the cellular DNA damage response (DDR), and telomere fusion. In contrast, cells must respond to damage-induced DNA ends at DSBs by harnessing the DDR to restore chromosome integrity, avoiding genome instability and disease. Intriguingly, Rif1 (Rap1-interacting factor 1) has been implicated in telomere homeostasis as well as DSB repair. The protein was first identified in as being part of the proteinaceous telosome. In mammals, RIF1 is not associated with intact telomeres, but was found at chromosome breaks, where RIF1 has emerged as a key mediator of pathway choice between the two evolutionary conserved DSB repair pathways of non-homologous end-joining (NHEJ) and homologous recombination (HR). While this functional dichotomy has long been a puzzle, recent findings link yeast Rif1 not only to telomeres, but also to DSB repair, and mechanistic parallels likely exist. In this review, we will provide an overview of the actions of Rif1 at DNA ends and explore how exclusion of end-processing factors might be the underlying principle allowing Rif1 to fulfill diverse biological roles at telomeres and chromosome breaks

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

Motivation: The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map. Results: Here we present a method for ‘split’ read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant. Availability: SplazerS is available from http://www.seqan.de/projects/ splazers

Systematics of electronic and magnetic properties in the transition metal doped Sb2_2Te3_3 quantum anomalous Hall platform

The quantum anomalous Hall effect (QAHE) has recently been reported to emerge in magnetically-doped topological insulators. Although its general phenomenology is well established, the microscopic origin is far from being properly understood and controlled. Here we report on a detailed and systematic investigation of transition-metal (TM)-doped Sb$_2$Te$_3$. By combining density functional theory (DFT) calculations with complementary experimental techniques, i.e., scanning tunneling microscopy (STM), resonant photoemission (resPES), and x-ray magnetic circular dichroism (XMCD), we provide a complete spectroscopic characterization of both electronic and magnetic properties. Our results reveal that the TM dopants not only affect the magnetic state of the host material, but also significantly alter the electronic structure by generating impurity-derived energy bands. Our findings demonstrate the existence of a delicate interplay between electronic and magnetic properties in TM-doped TIs. In particular, we find that the fate of the topological surface states critically depends on the specific character of the TM impurity: while V- and Fe-doped Sb$_2$Te$_3$ display resonant impurity states in the vicinity of the Dirac point, Cr and Mn impurities leave the energy gap unaffected. The single-ion magnetic anisotropy energy and easy axis, which control the magnetic gap opening and its stability, are also found to be strongly TM impurity-dependent and can vary from in-plane to out-of-plane depending on the impurity and its distance from the surface. Overall, our results provide general guidelines for the realization of a robust QAHE in TM-doped Sb$_2$Te$_3$ in the ferromagnetic state.Comment: 40 pages, 13 figure

Amphibian Immune Defenses against Chytridiomycosis: Impacts of Changing Environments

Eco-immunology is the field of study that attempts to understand the functions of the immune system in the context of the host's environment. Amphibians are currently suffering devastating declines and extinctions in nearly all parts of the world due to the emerging infectious disease chytridiomycosis caused by the chytrid fungus, Batrachochytrium dendrobatidis. Because chytridiomycosis is a skin infection and remains confined to the skin, immune defenses of the skin are critical for survival. Skin defenses include secreted antimicrobial peptides and immunoglobulins as well as antifungal metabolites produced by symbiotic skin bacteria. Low temperatures, toxic chemicals, and stress inhibit the immune system and may impair natural defenses against B. dendrobatidis. Tadpoles' mouth parts can be infected by B. dendrobatidis. Damage to the mouth parts can impair growth, and the affected tadpoles maintain the pathogen in the environment even when adults have dispersed. Newly metamorphosing frogs appear to be especially vulnerable to infection and to the lethal effects of this pathogen because the immune system undergoes a dramatic reorganization at metamorphosis, and postmetamorphic defenses are not yet mature. Here we review our current understanding of amphibian immune defenses against B. dendrobatidis and the ability of the pathogen to resist those defenses. We also briefly review what is known about the impacts of temperature, environmental chemicals, and stress on the host-pathogen interactions and suggest future directions for researc

Lifetimes of electrons in the Shockley surface state band of Ag(111)

We present a theoretical many-body analysis of the electron-electron (e-e) inelastic damping rate $\Gamma$ of electron-like excitations in the Shockley surface state band of Ag(111). It takes into account ab-initio band structures for both bulk and surface states. $\Gamma$ is found to increase more rapidly as a function of surface state energy E than previously reported, thus leading to an improved agreement with experimental data

Towards high-order calculations of three-nucleon scattering in chiral effective field theory

We discuss the current status of chiral effective field theory in the three-nucleon sector and present selected results for nucleon–deuteron scattering observables based on semilocal momentum-space-regularized chiral two-nucleon potentials together with consistently regularized three-nucleon forces up to third chiral order. Using a Bayesian model for estimating truncation errors, the obtained results are found to provide a good description of the experimental data. We confirm our earlier findings that a high-precision description of nucleon–deuteron scattering data below pion production threshold will require the theory to be pushed to fifth chiral order. This conclusion is substantiated by an exploratory study of selected short-range contributions to the three-nucleon force at that order, which, as expected, are found to have significant effects on polarization observables at intermediate and high energies. We also outline the challenges that will need to be addressed in order to push the chiral expansion of three-nucleon scattering observables to higher orders