141 research outputs found
Entanglement-free Heisenberg-limited phase estimation
Measurement underpins all quantitative science. A key example is the
measurement of optical phase, used in length metrology and many other
applications. Advances in precision measurement have consistently led to
important scientific discoveries. At the fundamental level, measurement
precision is limited by the number N of quantum resources (such as photons)
that are used. Standard measurement schemes, using each resource independently,
lead to a phase uncertainty that scales as 1/sqrt(N) - known as the standard
quantum limit. However, it has long been conjectured that it should be possible
to achieve a precision limited only by the Heisenberg uncertainty principle,
dramatically improving the scaling to 1/N. It is commonly thought that
achieving this improvement requires the use of exotic quantum entangled states,
such as the NOON state. These states are extremely difficult to generate.
Measurement schemes with counted photons or ions have been performed with N <=
6, but few have surpassed the standard quantum limit and none have shown
Heisenberg-limited scaling. Here we demonstrate experimentally a
Heisenberg-limited phase estimation procedure. We replace entangled input
states with multiple applications of the phase shift on unentangled
single-photon states. We generalize Kitaev's phase estimation algorithm using
adaptive measurement theory to achieve a standard deviation scaling at the
Heisenberg limit. For the largest number of resources used (N = 378), we
estimate an unknown phase with a variance more than 10 dB below the standard
quantum limit; achieving this variance would require more than 4,000 resources
using standard interferometry. Our results represent a drastic reduction in the
complexity of achieving quantum-enhanced measurement precision.Comment: Published in Nature. This is the final versio
Heralded Noiseless Amplification of a Photon Polarization Qubit
Non-deterministic noiseless amplification of a single mode can circumvent the
unique challenges to amplifying a quantum signal, such as the no-cloning
theorem, and the minimum noise cost for deterministic quantum state
amplification. However, existing devices are not suitable for amplifying the
fundamental optical quantum information carrier, a qubit coherently encoded
across two optical modes. Here, we construct a coherent two-mode amplifier, to
demonstrate the first heralded noiseless linear amplification of a qubit
encoded in the polarization state of a single photon. In doing so, we increase
the transmission fidelity of a realistic qubit channel by up to a factor of
five. Qubit amplifiers promise to extend the range of secure quantum
communication and other quantum information science and technology protocols.Comment: 6 pages, 3 figure
Distinct Differences in Chromatin Structure at Subtelomeric X and Y' Elements in Budding Yeast
In Saccharomyces cerevisiae, all ends of telomeric DNA contain telomeric repeats of (TG1–3), but the number and position of subtelomeric X and Y' repeat elements vary. Using chromatin immunoprecipitation and genome-wide analyses, we here demonstrate that the subtelomeric X and Y' elements have distinct structural and functional properties. Y' elements are transcriptionally active and highly enriched in nucleosomes, whereas X elements are repressed and devoid of nucleosomes. In contrast to X elements, the Y' elements also lack the classical hallmarks of heterochromatin, such as high Sir3 and Rap1 occupancy as well as low levels of histone H4 lysine 16 acetylation. Our analyses suggest that the presence of X and Y' elements govern chromatin structure and transcription activity at individual chromosome ends
The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state
We introduce and analyze a minimal model of epigenetic silencing in budding
yeast, built upon known biomolecular interactions in the system. Doing so, we
identify the epigenetic marks essential for the bistability of epigenetic
states. The model explicitly incorporates two key chromatin marks, namely H4K16
acetylation and H3K79 methylation, and explores whether the presence of
multiple marks lead to a qualitatively different systems behavior. We find that
having both modifications is important for the robustness of epigenetic
silencing. Besides the silenced and transcriptionally active fate of chromatin,
our model leads to a novel state with bivalent (i.e., both active and
silencing) marks under certain perturbations (knock-out mutations, inhibition
or enhancement of enzymatic activity). The bivalent state appears under several
perturbations and is shown to result in patchy silencing. We also show that the
titration effect, owing to a limited supply of silencing proteins, can result
in counter-intuitive responses. The design principles of the silencing system
is systematically investigated and disparate experimental observations are
assessed within a single theoretical framework. Specifically, we discuss the
behavior of Sir protein recruitment, spreading and stability of silenced
regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the
controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page
Sub-Telomeric core X and Y' Elements in S.cerevisiae Suppress Extreme Variations in Gene Silencing
Telomere Position Effect (TPE) is governed by strong repression signals emitted by telomeres via the Sir2/3/4 Histone Deacetylase complex. These signals are then relayed by weak proto-silencers residing in the subtelomeric core X and Y' elements. Subtelomeres also contain Sub-Telomeric Anti-silencing Regions (STARs). In this study we have prepared telomeres built of different combinations of core X, Y' and STARs and have analyzed them in strains lacking Histone-Acetyltransferase genes as well as in cdc6-1 and Δrif1 strains. We show that core X and Y' dramatically reduce both positive and negative variations in TPE, that are caused by these mutations. We also show that the deletion of Histone-Acetyltransferase genes reduce the silencing activity of an ACS proto-silencer, but also reduce the anti-silencing activity of a STAR. We postulate that core X and Y' act as epigenetic “cushioning” cis-elements
Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts
Subtelomeric DNA in budding yeasts, like metazoan heterochromatin, is gene poor, repetitive, transiently silenced, and highly dynamic. The rapid evolution of subtelomeric regions is commonly thought to arise from transposon activity and increased recombination between repetitive elements. However, we found evidence of an additional factor in this diversification. We observed a surprising level of nucleotide divergence in transcriptionally silenced regions in inter-species comparisons of Saccharomyces yeasts. Likewise, intra-species analysis of polymorphisms also revealed increased SNP frequencies in both intergenic and synonymous coding positions of silenced DNA. This analysis suggested that silenced DNA in Saccharomyces cerevisiae and closely related species had increased single base-pair substitution that was likely due to the effects of the silencing machinery on DNA replication or repair
Dissipative and Non-dissipative Single-Qubit Channels: Dynamics and Geometry
Single-qubit channels are studied under two broad classes: amplitude damping
channels and generalized depolarizing channels. A canonical derivation of the
Kraus representation of the former, via the Choi isomorphism is presented for
the general case of a system's interaction with a squeezed thermal bath. This
isomorphism is also used to characterize the difference in the geometry and
rank of these channel classes. Under the isomorphism, the degree of decoherence
is quantified according to the mixedness or separability of the Choi matrix.
Whereas the latter channels form a 3-simplex, the former channels do not form a
convex set as seen from an ab initio perspective. Further, where the rank of
generalized depolarizing channels can be any positive integer upto 4, that of
amplitude damping ones is either 2 or 4. Various channel performance parameters
are used to bring out the different influences of temperature and squeezing in
dissipative channels. In particular, a noise range is identified where the
distinguishability of states improves inspite of increasing decoherence due to
environmental squeezing.Comment: 12 pages, 4 figure
Impact of digestive and oropharyngeal decontamination on the intestinal microbiota in ICU patients
Selective digestive microbial decontamination (SDD) is hypothesized to benefit patients in intensive care (ICU) by suppressing Gram-negative potential pathogens from the colon without affecting the anaerobic intestinal microbiota. The purpose of this study was to provide more insight to the effects of digestive tract and oropharyngeal decontamination on the intestinal microbiota by means of a prospective clinical trial in which faecal samples were collected from ICU patients for intestinal microbiota analysis. The faecal samples were collected from ICU patients enrolled in a multicentre trial to study the outcome of SDD and selective oral decontamination (SOD) in comparison with standard care (SC). Fluorescent in situ hybridization (FISH) was used to analyze the faecal microbiota. The numbers of bacteria from different bacterial groups were compared between the three regimens. The total counts of bacteria per gram faeces did not differ between regimens. The F. prausnitzii group of bacteria, representing an important group among intestinal microbiota, was significantly reduced in the SDD regimen compared to the SC and SOD. The Enterobacteriaceae were significantly suppressed during SDD compared to both SOD and SC; enterococci increased in SDD compared to both other regimens. The composition of the intestinal microbiota is importantly affected by SDD. The F. prausnitzii group was significantly suppressed during SDD. This group of microbiota is a predominant producer of butyrate, the main energy source for colonocytes. Reduction of this microbiota is an important trade-off while reducing gram-negative bacteria by SDD
Localization of telomeres and telomere-associated proteins in telomerase-negative Saccharomyces cerevisiae
Cells lacking telomerase cannot maintain their telomeres and undergo a telomere erosion phase leading to senescence and crisis in which most cells become nonviable. On rare occasions survivors emerge from these cultures that maintain their telomeres in alternative ways. The movement of five marked telomeres in Saccharomyces cerevisiae was followed in wild-type cells and through erosion, senescence/crisis and eventual survival in telomerase-negative (est2::HYG) yeast cells. It was found that during erosion, movements of telomeres in est2::HYG cells were indistinguishable from wild-type telomere movements. At senescence/crisis, however, most cells were in G2 arrest and the nucleus and telomeres traversed back and forth across the bud neck, presumably until cell death. Type I survivors, using subtelomeric Y′ amplification for telomere maintenance, continued to show this aberrant telomere movement. However, Type II survivors, maintaining telomeres by a sudden elongation of the telomere repeats, became indistinguishable from wild-type cells, consistent with growth properties of the two types of survivors. When telomere-associated proteins Sir2p, Sir3p and Rap1p were tagged, the same general trend was seen—Type I survivors retained the senescence/crisis state of protein localization, while Type II survivors were restored to wild type
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