Immune-Related Functions of the Hivep Gene Family in East African Cichlid Fishes

Immune-related genes are often characterized by adaptive protein evolution. Selection on immune genes can be particularly strong when hosts encounter novel parasites, for instance, after the colonization of a new habitat or upon the exploitation of vacant ecological niches in an adaptive radiation. We examined a set of new candidate immune genes in East African cichlid fishes. More specifically, we studied the signatures of selection in five paralogs of the human immunodeficiency virus type I enhancer-binding protein (Hivep) gene family, tested their involvement in the immune defense, and related our results to explosive speciation and adaptive radiation events in cichlids. We found signatures of long-term positive selection in four Hivep paralogs and lineage-specific positive selection in Hivep3b in two radiating cichlid lineages. Exposure of the cichlid Astatotilapia burtoni to a vaccination with Vibrio anguillarum bacteria resulted in a positive correlation between immune response parameters and expression levels of three Hivep loci. This work provides the first evidence for a role of Hivep paralogs in teleost immune defense and links the signatures of positive selection to host-pathogen interactions within an adaptive radiation

A Parameterization of the Energy Loss of Muons in the ATLAS Tracking Geometry

A parameterization of the muon energy loss in the ATLAS Calorimeters is presented. This parameterization is based on a GEANT4 simulation of the calorimeter absorber materials. The parameterization provides a calculation of the energy loss of muons in each calorimeter volume. This calculation has been integrated into the ATLAS Tracking Geometry to be used by tracking tools to improve the fit of candidate muon tracks traversing the calorimeters. The validation of this parameterization has been performed and compared to the ATLAS GEANT4 full simulation. Finally, possible uses of this parameterization as part of the tracking tools are discussed

Lasing and cooling in a hot cavity

We present a microscopic laser model for many atoms coupled to a single cavity mode, including the light forces resulting from atom-field momentum exchange. Within a semiclassical description, we solve the equations for atomic motion and internal dynamics to obtain analytic expressions for the optical potential and friction force seen by each atom. When optical gain is maximum at frequencies where the light field extracts kinetic energy from the atomic motion, the dynamics combines optical lasing and motional cooling. From the corresponding momentum diffusion coefficient we predict sub-Doppler temperatures in the stationary state. This generalizes the theory of cavity enhanced laser cooling to active cavity systems. We identify the gain induced reduction of the effective resonator linewidth as key origin for the faster cooling and lower temperatures, which implys that a bad cavity with a gain medium can replace a high-Q cavity. In addition, this shows the importance of light forces for gas lasers in the low-temperature limit, where atoms can arrange in a periodic pattern maximizing gain and counteracting spatial hole burning. Ultimately, in the low temperature limit, such a setup should allow to combine optical lasing and atom lasing in single device.Comment: 11 pages, 6 figure

Single Track Performance of the Inner Detector New Track Reconstruction (NEWT)

In a previous series of documents we have presented the new ATLAS track reconstruction chain (NEWT) and several of the involved components. It has become the default reconstruction application for the Inner Detector. However, a large scale validation of the reconstruction performance in both efficiency and track resolutions has not been given yet. This documents presents the results of a systematic single track validation of the new track reconstruction and puts it in comparison with results obtained with different reconstruction applications

A Sensory Bias Has Triggered the Evolution of Egg-Spots in Cichlid Fishes

Although, generally, the origin of sex-limited traits remains elusive, the sensory exploitation hypothesis provides an explanation for the evolution of male sexual signals. Anal fin egg-spots are such a male sexual signal and a key characteristic of the most species-rich group of cichlid fishes, the haplochromines. Males of about 1500 mouth-brooding species utilize these conspicuous egg-dummies during courtship – apparently to attract females and to maximize fertilization success. Here we test the hypothesis that the evolution of haplochromine egg-spots was triggered by a pre-existing bias for eggs or egg-like coloration. To this end, we performed mate-choice experiments in the basal haplochromine Pseudocrenilabrus multicolor, which manifests the plesiomorphic character-state of an egg-spot-less anal fin. Experiments using computer-animated photographs of males indeed revealed that females prefer images of males with virtual (‘in-silico’) egg-spots over images showing unaltered males. In addition, we tested for color preferences (outside a mating context) in a phylogenetically representative set of East African cichlids. We uncovered a strong preference for yellow, orange or reddish spots in all haplochromines tested and, importantly, also in most other species representing more basal lines. This pre-existing female sensory bias points towards high-quality (carotenoids-enriched) food suggesting that it is adaptive

Concepts, Design and Implementation of the ATLAS New Tracking (NEWT)

The track reconstruction of modern high energy physics experiments is a very complex task that puts stringent requirements onto the software realisation. The ATLAS track reconstruction software has been in the past dominated by a collection of individual packages, each of which incorporating a different intrinsic event data model, different data flow sequences and calibration data. Invoked by the Final Report of the Reconstruction Task Force, the ATLAS track reconstruction has undergone a major design revolution to ensure maintainability during the long lifetime of the ATLAS experiment and the flexibility needed for the startup phase. The entire software chain has been re-organised in modular components and a common Event Data Model has been deployed during the last three years. A complete new track reconstruction that concentrates on common tools aimed to be used by both ATLAS tracking devices, the Inner Detector and the Muon System, has been established. It has been already used during many large scale tests with data from Monte Carlo simulation and from detector commissioning projects such as the combined test beam 2004 and cosmic ray events. This document concentrates on the technical and conceptual details of the newly developed track reconstruction, also known as New Tracking

Treatment of energy loss and multiple scattering in the context of track parameter and covariance matrix propagation in continuous material in the ATLAS experiment

In this paper we study the energy loss, its fluctuations, and the multiple scattering of particles passing through matter, with an emphasis on muons. In addition to the well-known Bethe-Bloch and Bethe-Heitler equations describing the mean energy loss from ionization and bremsstrahlung respectively, new parameterizations of the mean energy loss of muons from the direct e+e- pair production and photonuclear interactions are presented along with new estimates of the most probable energy loss and its fluctuations in the ATLAS calorimeters. Moreover, a new adaptive Highland/Moliere approach to finding the multiple scattering angle is taken to accomodate a wide range of scatterer thicknesses. Furthermore, tests of the muon energy loss, its fluctuations, and multiple scattering are done in the ATLAS calorimeters. The material effects described in this paper are all part of the simultaneous track and error propagation (STEP) algorithm of the common ATLAS tracking software

Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika

Background and Aims Environmental DNA (eDNA) metabarcoding provides a highly sensitive method of surveying freshwater fish communities, although studies to date have largely been restricted to temperate ecosystems. Due to limited reference sequence availability and challenges identifying closely related and rare species in diverse tropical ecosystems, the effectiveness of metabarcoding methods for surveying tropical fish communities from eDNA samples remains uncertain. To address this, we applied an eDNA metabarcoding approach to survey Lake Tanganyika's (LT) species‐rich littoral fish communities. Materials and Methods As this system contains many closely related species, particularly cichlid fishes, we used four primer sets including a cichlid‐specific primer set (Cichlid_CR). A reference database was built for the 12s, 16s, and control region for 358 fish species including over 93% of known cichlids. Results and Discussion In silico and in situ results demonstrated wide variability in the taxonomic resolution of assignments by each primer with the cichlid‐specific marker (Cichlid_CR) enabling greater species‐level assignments for this highly diverse family. A greater number of non‐cichlid teleost species were detected at sites compared to the visual survey data. For cichlid species however, sequencing depth substantially influenced species richness estimates obtained from eDNA samples, with increased depths producing estimates comparable to that obtained from the visual survey data. Conclusions Our study highlights the importance of sequencing depth and local reference databases when undertaking metabarcoding studies within diverse ecosystems, as well as demonstrating the potential of eDNA metabarcoding for surveying diverse tropical fish communities, even those containing closely related species within evolutionary radiations

The Function of Anal Fin Egg-Spots in the Cichlid Fish Astatotilapia burtoni

Color and pigmentation patterns of animals are often targets of sexual selection because of their role in communication. Although conspicuous male traits are typically implicated with intersexual selection, there are examples where sex-specific displays play a role in an intrasexual context, e.g. when they serve as signals for aggression level and/or status. Here, we focus on the function of a conspicuous male ornament in the most species-rich tribe of cichlid fishes, the haplochromines. A characteristic feature of these ca. 1500 species are so-called egg-spots in form of ovoid markings on the anal fins of males, which are made up of carotenoid based pigment cells. It has long been assumed that these yellow, orange or reddish egg-spots play an important role in the courtship and spawning behavior of these maternal mouth-brooding fishes by mimicking the eggs of a conspecific female. The exact function of egg-spots remains unknown, however, and there are several hypotheses about their mode of action. To uncover the function of this cichlid-specific male ornament, we used female mate choice experiments and a male aggression test in the haplochromine species Astatotilapia burtoni. We manipulated the number and arrangement of egg-spots on the anal fins of males, or removed them entirely, and tested (1) female preference with visual contact only using egg-traps, (2) female preference with free contact using paternity testing with microsatellites and (3) male aggression. We found that females did not prefer males with many egg-spots over males with fewer egg-spots and that females tended to prefer males without egg-spots over males with egg-spots. Importantly, males without egg-spots sired clutches with the same fertilization rate as males with egg-spots. In male aggression trials, however, males with fewer egg-spots received significantly more attacks, suggesting that egg-spots are an important signal in intrasexual communication