253 research outputs found
Phase-dependent which-way information
We introduce a new observable for reading out a which-way detector in a
Young-type interferometer whose eigenstates either contain full which-way
information or none at all. We calculate the which-way knowledge K that can be
retrieved from this observable and find that K depends on the phase difference
\delta that the interfering object accumulates on its way from either slit to
the detector. In particular, it turns out that K(\delta) has an upper bound of
1, almost independent of the visibility V of the interference pattern generated
by the interfering object on a screen, which is in marked contrast to the
well-known inequality K^2 + V^2 <= 1 (cf. B.-G. Englert, Phys. Rev. Lett. 77,
2154 (1996)).Comment: 7 pages, 4 figure
Evaluating the utility of B/Ca ratios in planktic foraminifera as a proxy for the carbonate system: A case study of Globigerinoides ruber
B/Ca ratios in foraminifera have attracted considerable scientific attention as a proxy for past ocean carbonate system. However, the carbonate system controls on B/Ca ratios are not straightforward, with ?[ inline image] ([ inline image]in situ β [ inline image]at saturation) correlating best with B/Ca ratios in benthic foraminifera, rather than pH, inline image, or inline image (as a simple model of boron speciation in seawater and incorporation into CaCO3 would predict). Furthermore, culture experiments have shown that in planktic foraminifera properties such as salinity and [B]sw can have profound effects on B/Ca ratios beyond those predicted by simple partition coefficients. Here, we investigate the controls on B/Ca ratios in G. ruber via a combination of culture experiments and core-top measurements, and add to a growing body of evidence that suggests B/Ca ratios in symbiont-bearing foraminiferal carbonate are not a straightforward proxy for past seawater carbonate system conditions. We find that while B/Ca ratios in culture experiments covary with pH, in open ocean sediments this relationship is not seen. In fact, our B/Ca data correlate best with [ inline image] (a previously undocumented association) and in most regions, salinity. These findings might suggest a precipitation rate or crystallographic control on boron incorporation into foraminiferal calcite. Regardless, our results underscore the need for caution when attempting to interpret B/Ca records in terms of the ocean carbonate system, at the very least in the case of mixed-layer planktic foraminifera
Efficiency of complex production in changing environment
This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens
Avoiding Coral Reef Functional Collapse Requires Local and Global Action
oral reefs face multiple anthropogenic threats, from pollution and overfishing to the dual effects of greenhouse gas emissions: rising sea temperature and ocean acidification [1]. While the abundance of coral has declined in recent decades [2, 3], the implications for humanity are difficult to quantify because they depend on ecosystem function rather than the corals themselves. Most reef functions and ecosystem services are founded on the ability of reefs to maintain their three-dimensional structure through net carbonate accumulation [4]. Coral growth only constitutes part of a reef's carbonate budget; bioerosion processes are influential in determining the balance between net structural growth and disintegration [5, 6]. Here, we combine ecological models with carbonate budgets and drive the dynamics of Caribbean reefs with the latest generation of climate models. Budget reconstructions using documented ecological perturbations drive shallow (6-10 m) Caribbean forereefs toward an increasingly fragile carbonate balance. We then projected carbonate budgets toward 2080 and contrasted the benefits of local conservation and global action on climate change. Local management of fisheries (specifically, no-take marine reserves) and the watershed can delay reef loss by at least a decade under "business-as-usual" rises in greenhouse gas emissions. However, local action must be combined with a low-carbon economy to prevent degradation of reef structures and associated ecosystem services
Systematic identification of abundant A-to-I editing sites in the human transcriptome
RNA editing by members of the double-stranded RNA-specific ADAR family leads
to site-specific conversion of adenosine to inosine (A-to-I) in precursor
messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is
essential for mammalian development. Currently, only a limited number of human
ADAR substrates are known, while indirect evidence suggests a substantial
fraction of all pre-mRNAs being affected. Here we describe a computational
search for ADAR editing sites in the human transcriptome, using millions of
available expressed sequences. 12,723 A-to-I editing sites were mapped in 1,637
different genes, with an estimated accuracy of 95%, raising the number of known
editing sites by two orders of magnitude. We experimentally validated our
method by verifying the occurrence of editing in 26 novel substrates. A-to-I
editing in humans primarily occurs in non-coding regions of the RNA, typically
in Alu repeats. Analysis of the large set of editing sites indicates the role
of editing in controlling dsRNA stability.Comment: Pre-print version. See http://dx.doi.org/10.1038/nbt996 for a reprin
Wavefront error of PHI/HRT on Solar Orbiter at various heliocentric distances
We use wavefront sensing to characterise the image quality of the the High
Resolution Telescope (HRT) of the Polarimetric and Helioseismic Imager (SO/PHI)
data products during the second remote sensing window of the Solar Orbiter (SO)
nominal mission phase. Our ultimate aims are to reconstruct the HRT data by
deconvolving with the HRT point spread function (PSF) and to correct for the
effects of optical aberrations on the data. We use a pair of focused--defocused
images to compute the wavefront error and derive the PSF of HRT by means of a
phase diversity (PD) analysis. The wavefront error of HRT depends on the
orbital distance of SO to the Sun. At distances \,au, the wavefront error
is small, and stems dominantly from the inherent optical properties of HRT. At
distances \,au, the thermo-optical effect of the Heat Rejection Entrance
Window (HREW) becomes noticeable. We develop an interpolation scheme for the
wavefront error that depends on the thermal variation of the HREW with the
distance of SO to the Sun. We also introduce a new level of image
reconstruction, termed `aberration correction', which is designed to reduce the
noise caused by image deconvolution while removing the aberrations caused by
the HREW. The computed PSF via phase diversity significantly reduces the
degradation caused by the HREW in the near-perihelion HRT data. In addition,
the aberration correction increases the noise by a factor of only
compared to the factor of increase that results from the usual PD
reconstructions
Stable Photosymbiotic Relationship under CO2-Induced Acidification in the Acoel Worm Symsagittifera Roscoffensis
As a consequence of anthropogenic CO2 emissions, oceans are becoming more acidic, a phenomenon known as ocean acidification. Many marine species predicted to be sensitive to this stressor are photosymbiotic, including corals and foraminifera. However, the direct impact of ocean acidification on the relationship between the photosynthetic and nonphotosynthetic organism remains unclear and is complicated by other physiological processes known to be sensitive to ocean acidification (e.g. calcification and feeding). We have studied the impact of extreme pH decrease/pCO2 increase on the complete life cycle of the photosymbiotic, non-calcifying and pure autotrophic acoel worm, Symsagittifera roscoffensis. Our results show that this species is resistant to high pCO2 with no negative or even positive effects on fitness (survival, growth, fertility) and/or photosymbiotic relationship till pCO2 up to 54 K Β΅atm. Some sub-lethal bleaching is only observed at pCO2 up to 270 K Β΅atm when seawater is saturated by CO2. This indicates that photosymbiosis can be resistant to high pCO2. If such a finding would be confirmed in other photosymbiotic species, we could then hypothesize that negative impact of high pCO2 observed on other photosymbiotic species such as corals and foraminifera could occur through indirect impacts at other levels (calcification, feeding)
A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing
While it is widely held that an organism's genomic information should remain constant, several protein families are known to modify it. Members of the AID/APOBEC protein family can deaminate DNA. Similarly, members of the ADAR family can deaminate RNA. Characterizing the scope of these events is challenging. Here we use large genomic data sets, such as the two billion sequences in the NCBI Trace Archive, to look for clusters of mismatches of the same type, which are a hallmark of editing events caused by APOBEC3 and ADAR. We align 603,249,815 traces from the NCBI trace archive to their reference genomes. In clusters of mismatches of increasing size, at least one systematic sequencing error dominates the results (G-to-A). It is still present in mismatches with 99% accuracy and only vanishes in mismatches at 99.99% accuracy or higher. The error appears to have entered into about 1% of the HapMap, possibly affecting other users that rely on this resource. Further investigation, using stringent quality thresholds, uncovers thousands of mismatch clusters with no apparent defects in their chromatograms. These traces provide the first reported candidates of endogenous DNA editing in human, further elucidating RNA editing in human and mouse and also revealing, for the first time, extensive RNA editing in Xenopus tropicalis. We show that the NCBI Trace Archive provides a valuable resource for the investigation of the phenomena of DNA and RNA editing, as well as setting the stage for a comprehensive mapping of editing events in large-scale genomic datasets
N-Cadherin in Neuroblastoma Disease: Expression and Clinical Significance
One of the first and most important steps in the metastatic cascade is the loss of cell-cell and cell-matrix interactions. N-cadherin, a crucial mediator of homotypic and heterotypic cell-cell interactions, might play a central role in the metastasis of neuroblastoma (NB), a solid tumor of neuroectodermal origin. Using Reverse Transcription Quantitative PCR (RT-qPCR), Western blot, immunocytochemistry and Tissue MicroArrays (TMA) we demonstrate the expression of N-cadherin in neuroblastoma tumors and cell lines. All neuroblastic tumors (nβ=β356) and cell lines (nβ=β10) expressed various levels of the adhesion protein. The N-cadherin mRNA expression was significantly lower in tumor samples from patients suffering metastatic disease. Treatment of NB cell lines with the N-cadherin blocking peptide ADH-1 (Exherin, Adherex Technologies Inc.), strongly inhibited tumor cell proliferation in vitro by inducing apoptosis. Our results suggest that N-cadherin signaling may play a role in neuroblastoma disease, marking involvement of metastasis and determining neuroblastoma cell viability
Jack of All Trades, Master of All: A Positive Association between Habitat Niche Breadth and Foraging Performance in Pit-Building Antlion Larvae
Species utilizing a wide range of resources are intuitively expected to be less efficient in exploiting each resource type compared to species which have developed an optimal phenotype for utilizing only one or a few resources. We report here the results of an empirical study whose aim was to test for a negative association between habitat niche breadth and foraging performance. As a model system to address this question, we used two highly abundant species of pit-building antlions varying in their habitat niche breadth: the habitat generalist Myrmeleon hyalinus, which inhabits a variety of soil types but occurs mainly in sandy soils, and the habitat specialist Cueta lineosa, which is restricted to light soils such as loess. Both species were able to discriminate between the two soils, with each showing a distinct and higher preference to the soil type providing higher prey capture success and characterizing its primary habitat-of-origin. As expected, only small differences in the foraging performances of the habitat generalist were evident between the two soils, while the performance of the habitat specialist was markedly reduced in the alternative sandy soil. Remarkably, in both soil types, the habitat generalist constructed pits and responded to prey faster than the habitat specialist, at least under the temperature range of this study. Furthermore, prey capture success of the habitat generalist was higher than that of the habitat specialist irrespective of the soil type or prey ant species encountered, implying a positive association between habitat niche-breadth and foraging performance. Alternatively, C. lineosa specialization to light soils does not necessarily confer upon its superiority in utilizing such habitats. We thus suggest that habitat specialization in C. lineosa is either an evolutionary dead-end, or, more likely, that this species' superiority in light soils can only be evident when considering additional niche axes
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