950 research outputs found
Anaerobic Carbon Monoxide Dehydrogenase Diversity in the Homoacetogenic Hindgut Microbial Communities of Lower Termites and the Wood Roach
Anaerobic carbon monoxide dehydrogenase (CODH) is a key enzyme in the Wood-Ljungdahl (acetyl-CoA) pathway for acetogenesis performed by homoacetogenic bacteria. Acetate generated by gut bacteria via the acetyl-CoA pathway provides considerable nutrition to wood-feeding dictyopteran insects making CODH important to the obligate mutualism occurring between termites and their hindgut microbiota. To investigate CODH diversity in insect gut communities, we developed the first degenerate primers designed to amplify cooS genes, which encode the catalytic (β) subunit of anaerobic CODH enzyme complexes. These primers target over 68 million combinations of potential forward and reverse cooS primer-binding sequences. We used the primers to identify cooS genes in bacterial isolates from the hindgut of a phylogenetically lower termite and to sample cooS diversity present in a variety of insect hindgut microbial communities including those of three phylogenetically-lower termites, Zootermopsis nevadensis, Reticulitermes hesperus, and Incisitermes minor, a wood-feeding cockroach, Cryptocercus punctulatus, and an omnivorous cockroach, Periplaneta americana. In total, we sequenced and analyzed 151 different cooS genes. These genes encode proteins that group within one of three highly divergent CODH phylogenetic clades. Each insect gut community contained CODH variants from all three of these clades. The patterns of CODH diversity in these communities likely reflect differences in enzyme or physiological function, and suggest that a diversity of microbial species participate in homoacetogenesis in these communities
Formation of regulatory modules by local sequence duplication
Turnover of regulatory sequence and function is an important part of
molecular evolution. But what are the modes of sequence evolution leading to
rapid formation and loss of regulatory sites? Here, we show that a large
fraction of neighboring transcription factor binding sites in the fly genome
have formed from a common sequence origin by local duplications. This mode of
evolution is found to produce regulatory information: duplications can seed new
sites in the neighborhood of existing sites. Duplicate seeds evolve
subsequently by point mutations, often towards binding a different factor than
their ancestral neighbor sites. These results are based on a statistical
analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome,
and a comparison set of intergenic regulatory sequence in Saccharomyces
cerevisiae. In fly regulatory modules, pairs of binding sites show
significantly enhanced sequence similarity up to distances of about 50 bp. We
analyze these data in terms of an evolutionary model with two distinct modes of
site formation: (i) evolution from independent sequence origin and (ii)
divergent evolution following duplication of a common ancestor sequence. Our
results suggest that pervasive formation of binding sites by local sequence
duplications distinguishes the complex regulatory architecture of higher
eukaryotes from the simpler architecture of unicellular organisms
Trajectory curvature in saccade sequences:spatiotopic influences vs. residual motor activity
Saccades curve away from locations of previous fixation. Varying stimulus timing demonstrates the effects of both 1) spatiotopic representation and 2) motor residual activity from previous saccades. The spatiotopic effect can be explained if current models are augmented with an excitatory top-down spatiotopic signal.
When decisions drive saccadic eye movements, traces of the decision process can be inferred from the movement trajectories. For example, saccades can curve away from distractor stimuli, which was thought to reflect cortical inhibition biasing activity in the superior colliculus. Recent neurophysiological work does not support this theory, and two recent models have replaced top-down inhibition with lateral interactions in the superior colliculus or neural fatigue in the brainstem saccadic burst generator. All current models operate in retinotopic coordinates and are based on single saccade paradigms. To extend these models to sequences of saccades, we assessed whether and how saccade curvature depends on previously fixated locations and the direction of previous saccades. With a two-saccade paradigm, we first demonstrated that second saccades curved away from the initial fixation stimulus. Furthermore, by varying the time from fixation offset and the intersaccadic duration, we distinguished the extent of curvature originating from the spatiotopic representation of the previous fixation location or residual motor activity of the previous saccade. Results suggest that both factors drive curvature, and we discuss how these effects could be implemented in current models. In particular, we propose that the collicular retinotopic maps receive an excitatory spatiotopic update from the lateral interparial region
Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean
Background: Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 µm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone.
Methodology/Principal Findings: In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated.
Conclusions/Significance: Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups
Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic
Permafrost-affected soils of the Siberian Arctic were investigated with regard to identification of nitrite oxidizing bacteria active at low temperature. Analysis of the fatty acid profiles of enrichment cultures grown at 4°C, 10°C and 17°C revealed a pattern that was different from that of known nitrite oxidizers but was similar to fatty acid profiles of Betaproteobacteria. Electron microscopy of two enrichment cultures grown at 10°C showed prevalent cells with a conspicuous ultrastructure. Sequence analysis of the 16S rRNA genes allocated the organisms to a so far uncultivated cluster of the Betaproteobacteria, with Gallionella ferruginea as next related taxonomically described organism. The results demonstrate that a novel genus of chemolithoautotrophic nitrite oxidizing bacteria is present in polygonal tundra soils and can be enriched at low temperatures up to 17°C. Cloned sequences with high sequence similarities were previously reported from mesophilic habitats like activated sludge and therefore an involvement of this taxon in nitrite oxidation in nonarctic habitats is suggested. The presented culture will provide an opportunity to correlate nitrification with nonidentified environmental clones in moderate habitats and give insights into mechanisms of cold adaptation. We propose provisional classification of the novel nitrite oxidizing bacterium as 'Candidatus Nitrotoga arctica'
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An Interferon-Driven Oxysterol-Based Defense against Tumor-Derived Extracellular Vesicles
Tumor-derived extracellular vesicles (TEV) “educate” healthy cells to promote metastases. We found that melanoma TEV downregulated type I interferon (IFN) receptor and expression of IFN-inducible cholesterol 25-hydroxylase (CH25H). CH25H produces 25-hydroxycholesterol, which inhibited TEV uptake. Low CH25H levels in leukocytes from melanoma patients correlated with poor prognosis. Mice incapable of downregulating the IFN receptor and Ch25h were resistant to TEV uptake, TEV-induced pre-metastatic niche, and melanoma lung metastases; however, ablation of Ch25h reversed these phenotypes. An anti-hypertensive drug, reserpine, suppressed TEV uptake and disrupted TEV-induced formation of the pre-metastatic niche and melanoma lung metastases. These results suggest the importance of CH25H in defense against education of normal cells by TEV and argue for the use of reserpine in adjuvant melanoma therapy
Antibody Response to Shiga Toxins in Argentinean Children with Enteropathic Hemolytic Uremic Syndrome at Acute and Long-Term Follow-Up Periods
Shiga toxin (Stx)-producing Escherichia coli (STEC) infection is associated with a broad spectrum of clinical manifestations that include diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Systemic Stx toxemia is considered to be central to the genesis of HUS. Distinct methods have been used to evaluate anti-Stx response for immunodiagnostic or epidemiological analysis of HUS cases. The development of enzyme-linked immunosorbent assay (ELISA) and western blot (WB) assay to detect the presence of specific antibodies to Stx has introduced important advantages for serodiagnosis of HUS. However, application of these methods for seroepidemiological studies in Argentina has been limited. The aim of this work was to develop an ELISA to detect antibodies against the B subunit of Stx2, and a WB to evaluate antibodies against both subunits of Stx2 and Stx1, in order to analyze the pertinence and effectiveness of these techniques in the Argentinean population. We studied 72 normal healthy children (NHC) and 105 HUS patients of the urban pediatric population from the surrounding area of Buenos Aires city. Using the WB method we detected 67% of plasma from NHC reactive for Stx2, but only 8% for Stx1. These results are in agreement with the broad circulation of Stx2-expressing STEC in Argentina and the endemic behavior of HUS in this country. Moreover, the simultaneous evaluation by the two methods allowed us to differentiate acute HUS patients from NHC with a great specificity and accuracy, in order to confirm the HUS etiology when pathogenic bacteria were not isolated from stools
Measurement of the running of the QED coupling in small-angle Bhabha scattering at LEP
Using the OPAL detector at LEP, the running of the effective QED coupling
alpha(t) is measured for space-like momentum transfer from the angular
distribution of small-angle Bhabha scattering. In an almost ideal QED
framework, with very favourable experimental conditions, we obtain:
Delta alpha(-6.07GeV^2) - Delta alpha(-1.81GeV^2) = (440 pm 58 pm 43 pm 30) X
10^-5, where the first error is statistical, the second is the experimental
systematic and the third is the theoretical uncertainty. This agrees with
current evaluations of alpha(t).The null hypothesis that alpha remains constant
within the above interval of -t is excluded with a significance above 5sigma.
Similarly, our results are inconsistent at the level of 3sigma with the
hypothesis that only leptonic loops contribute to the running. This is
currently the most significant direct measurment where the running alpha(t) is
probed differentially within the measured t range.Comment: 43 pages, 12 figures, Submitted to Euro. Phys. J.
First Observation of and Decays
We have observed new channels for decays with an in the final
state. We study 3-prong tau decays, using the and
\eta\to 3\piz decay modes and 1-prong decays with two \piz's using the
channel. The measured branching fractions are
\B(\tau^{-}\to \pi^{-}\pi^{-}\pi^{+}\eta\nu_{\tau})
=(3.4^{+0.6}_{-0.5}\pm0.6)\times10^{-4} and \B(\tau^{-}\to
\pi^{-}2\piz\eta\nu_{\tau}
=(1.4\pm0.6\pm0.3)\times10^{-4}. We observe clear evidence for
substructure and measure \B(\tau^{-}\to
f_1\pi^{-}\nu_{\tau})=(5.8^{+1.4}_{-1.3}\pm1.8)\times10^{-4}. We have also
searched for production and obtain 90% CL upper limits
\B(\tau^{-}\to \pi^{-}\eta'\nu_\tau)<7.4\times10^{-5} and \B(\tau^{-}\to
\pi^{-}\piz\eta'\nu_\tau)<8.0\times10^{-5}.Comment: 11 page postscript file, postscript file also available through
http://w4.lns.cornell.edu/public/CLN
Search for the Decays B^0 -> D^{(*)+} D^{(*)-}
Using the CLEO-II data set we have searched for the Cabibbo-suppressed decays
B^0 -> D^{(*)+} D^{(*)-}. For the decay B^0 -> D^{*+} D^{*-}, we observe one
candidate signal event, with an expected background of 0.022 +/- 0.011 events.
This yield corresponds to a branching fraction of Br(B^0 -> D^{*+} D^{*-}) =
(5.3^{+7.1}_{-3.7}(stat) +/- 1.0(syst)) x 10^{-4} and an upper limit of Br(B^0
-> D^{*+} D^{*-}) D^{*\pm} D^\mp and
B^0 -> D^+ D^-, no significant excess of signal above the expected background
level is seen, and we calculate the 90% CL upper limits on the branching
fractions to be Br(B^0 -> D^{*\pm} D^\mp) D^+
D^-) < 1.2 x 10^{-3}.Comment: 12 page postscript file also available through
http://w4.lns.cornell.edu/public/CLNS, submitted to Physical Review Letter
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