Purifying Selection and Molecular Adaptation in the Genome of Verminephrobacter, the Heritable Symbiotic Bacteria of Earthworms

While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60–130 Myr) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it with the genomes of Verminephrobacter eiseniae and two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A–T bias. We characterized the strength of purifying selection (ω = dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (ω = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher ω values and less codon usage bias in symbiont compared with reference genomes. Relaxation was not evenly distributed among functional gene categories but was overrepresented in genes involved in signal transduction and cell envelope biogenesis. The same gene categories also harbored instances of positive selection in the Verminephrobacter clade. In total, positive selection was detected in 89 genes, including also genes involved in DNA metabolism, tRNA modification, and TonB-dependent iron uptake, potentially highlighting functions important in symbiosis. Our results suggest that the transition to symbiosis was accompanied by molecular adaptation, while purifying selection was only moderately relaxed, despite the evolutionary age and stability of the host association. We hypothesize that biparental transmission of symbionts and rare genetic mixing during transmission can prevent genome erosion in heritable symbionts

Effects of pretreatment hypothermia during resuscitated porcine hemorrhagic shock

OBJECTIVES: Accidental hypothermia increases mortality and morbidity after hemorrhage, but controversial data are available on the effects of therapeutic hypothermia. Therefore, we tested the hypothesis whether moderate pretreatment hypothermia would beneficially influence organ dysfunction during long-term, porcine hemorrhage and resuscitation. DESIGN: Prospective, controlled, randomized study. SETTING: University animal research laboratory. SUBJECTS: Twenty domestic pigs of either gender. INTERVENTIONS: Using an extracorporeal heat exchanger, anesthetized and instrumented animals were maintained at 38 degrees C, 35 degrees C, or 32 degrees C core temperature and underwent 4 hours of hemorrhage (removal of 40% of the blood volume and subsequent blood removal/retransfusion to maintain mean arterial pressure at 30 mm Hg). Resuscitation comprised of hydroxyethyl starch and norepinephrine infusion titrated to maintain mean arterial pressure at preshock values. MEASUREMENTS AND MAIN RESULTS: Before, immediately at the end of, and 12 and 22 hours after hemorrhage, we measured systemic and regional hemodynamics (portal vein, hepatic and right kidney artery ultrasound flow probes) and oxygen transport, and nitric oxide and cytokine production. Hemostasis was assessed by rotation thromboelastometry. Postmortem biopsies were analyzed for histomorphology (hematoxylin and eosin staining) and markers of apoptosis (kidney Bcl-xL and caspase-3 expression). Hypothermia at 32 degrees C attenuated the shock-related lactic acidosis but caused metabolic acidosis, most likely resulting from reduced carbohydrate oxidation. Although hypothermia did not further aggravate shock-related coagulopathy, it caused a transitory attenuation of kidney and liver dysfunction, which was ultimately associated with reduced histological damage and more pronounced apoptosis. CONCLUSIONS: During long-term porcine hemorrhage and resuscitation, moderate pretreatment hypothermia was associated with a transitory attenuation of organ dysfunction and less severe histological tissue damage despite more pronounced metabolic acidosis. This effect is possibly due to a switch from necrotic to apoptotic cell death, ultimately resulting from reduced tissue energy deprivation during the shock phase

The FORS Deep Field: Field selection, photometric observations and photometric catalog

The FORS Deep Field project is a multi-colour, multi-object spectroscopic investigation of an approx. 7 times 7 region near the south galactic pole based mostly on observations carried out with the FORS instruments attached to the VLT telescopes. It includes the QSO Q 0103-260 (z = 3.36). The goal of this study is to improve our understanding of the formation and evolution of galaxies in the young Universe. In this paper the field selection, the photometric observations, and the data reduction are described. The source detection and photometry of objects in the FORS Deep Field is discussed in detail. A combined B and I selected UBgRIJKs photometric catalog of 8753 objects in the FDF is presented and its properties are briefly discussed. The formal 50% completeness limits for point sources, derived from the co-added images, are 25.64, 27.69, 26.86, 26.68, 26.37, 23.60 and 21.57 in U, B, g, R, I, J and Ks (Vega-system), respectively. A comparison of the number counts in the FORS Deep Field to those derived in other deep field surveys shows very good agreement.Comment: 15 pages, 11 figures (included), accepted for publication in A&

Sfermion Precision Measurements at a Linear Collider

At future e+- e- linear colliders, the event rates and clean signals of scalar fermion production - in particular for the scalar leptons - allow very precise measurements of their masses and couplings and the determination of their quantum numbers. Various methods are proposed for extracting these parameters from the data at the sfermion thresholds and in the continuum. At the same time, NLO radiative corrections and non-zero width effects have been calculated in order to match the experimental accuracy. The substantial mixing expected for the third generation sfermions opens up additional opportunities. Techniques are presented for determining potential CP-violating phases and for extracting tan(beta) from the stau sector, in particular at high values. The consequences of possible large mass differences in the stop and sbottom system are explored in dedicated analyses.Comment: Expanded version of contributions to the proceedings of ICHEP'02 (Amsterdam) and LCWS 2002 (Jeju Island

Early and Middle Holocene Hunter-Gatherer Occupations in Western Amazonia: The Hidden Shell Middens

We report on previously unknown early archaeological sites in the Bolivian lowlands, demonstrating for the first time early and middle Holocene human presence in western Amazonia. Multidisciplinary research in forest islands situated in seasonally-inundated savannahs has revealed stratified shell middens produced by human foragers as early as 10,000 years ago, making them the oldest archaeological sites in the region. The absence of stone resources and partial burial by recent alluvial sediments has meant that these kinds of deposits have, until now, remained unidentified. We conducted core sampling, archaeological excavations and an interdisciplinary study of the stratigraphy and recovered materials from three shell midden mounds. Based on multiple lines of evidence, including radiocarbon dating, sedimentary proxies (elements, steroids and black carbon), micromorphology and faunal analysis, we demonstrate the anthropogenic origin and antiquity of these sites. In a tropical and geomorphologically active landscape often considered challenging both for early human occupation and for the preservation of hunter-gatherer sites, the newly discovered shell middens provide evidence for early to middle Holocene occupation and illustrate the potential for identifying and interpreting early open-air archaeological sites in western Amazonia. The existence of early hunter-gatherer sites in the Bolivian lowlands sheds new light on the region's past and offers a new context within which the late Holocene "Earthmovers" of the Llanos de Moxos could have emerged. © 2013 Lombardo et al