An all-optical trap for a gram-scale mirror

We report on a stable optical trap suitable for a macroscopic mirror, wherein the dynamics of the mirror are fully dominated by radiation pressure. The technique employs two frequency-offset laser fields to simultaneously create a stiff optical restoring force and a viscous optical damping force. We show how these forces may be used to optically trap a free mass without introducing thermal noise; and we demonstrate the technique experimentally with a 1 gram mirror. The observed optical spring has an inferred Young's modulus of 1.2 TPa, 20% stiffer than diamond. The trap is intrinsically cold and reaches an effective temperature of 0.8 K, limited by technical noise in our apparatus.Comment: Major revision. Replacement is version that appears in Phy. Rev. Lett. 98, 150802 (2007

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

BACKGROUND: DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2-5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. RESULTS: Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on CONCLUSION: Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6-8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2,3,10,11]

Achieving ground state and enhancing entanglement by recovering information

For cavity-assisted optomechanical cooling experiments, it has been shown in the literature that the cavity bandwidth needs to be smaller than the mechanical frequency in order to achieve the quantum ground state of the mechanical oscillator, which is the so-called resolved-sideband or good-cavity limit. We provide a new but physically equivalent insight into the origin of such a limit: that is information loss due to a finite cavity bandwidth. With an optimal feedback control to recover those information, we can surpass the resolved-sideband limit and achieve the quantum ground state. Interestingly, recovering those information can also significantly enhance the optomechanical entanglement. Especially when the environmental temperature is high, the entanglement will either exist or vanish critically depending on whether information is recovered or not, which is a vivid example of a quantum eraser.Comment: 9 figures, 18 page

Verschränkte Spiegel - ein realisierbares Gedankenexperiment

Die Herstellung von verschränkten Quantenobjekten aus Photonen oder Ionen ist bereits Routine. Da die Quantenmechanik der Größe und Schwere solcher Objekte keine prinzipielle Obergrenze setzt, sollten sich auch makroskopische Gegenstände miteinander verschränken lassen. Allerdings stellt das hohe Ansprüche an die Experimentiertechnik, vor allem im Bereich der Laser- und Kältetechnik, sowie an die Methoden zur Entkopplung der Objekte von der Umgebung. Die hier vorgestellte Idee nutzt einen Laserstrahl, um zwei massive Spiegel miteinander zu verschränken. Das entsprechende Experiment soll in den nächsten Jahren realisiert werden. Es könnte sogar eine Demonstration des Einstein-Podolsky-Rosen-Paradoxons mit makroskopischen Objekten ermöglichen

Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle

peer-reviewedCurrent bovine pregnancy detection methods are not reliable until at least day 28 post artificial insemination (AI). The bovine estrous cycle is approximately 21 days; consequently, producers miss an opportunity to rebreed at the next estrous event. Therefore, commercial interest exists for the discovery of novel biomarkers of pregnancy which could reliably detect pregnancy status at or before day 21 of pregnancy. The objective of the present study was to use liquid chromatography tandem mass spectrometry (LC-MS/MS) to perform a global, label-free, proteomics study on (i) milk whey and (ii) extracellular vesicle (EV) enriched milk whey samples, from day 21 of pregnancy, compared with day 21 of the estrous cycle, in order to identify potential protein biomarkers of early pregnancy. The estrous cycles of 10 dairy cows were synchronized, they went through one (control) estrous cycle and these cows were artificially inseminated during the following estrus. These cows were confirmed pregnant by ultrasound scanning. Milk whey samples were collected on day 21 of the estrous cycle and on day 21 post AI. Milk whey samples and EV enriched milk whey samples were analyzed by LC-MS/MS and subsequent analyzes of the label-free quantitative data was performed in MaxQuant and Perseus. Four proteins (APOB, SPADH1, PLIN2 and LPO) were differentially expressed between the proteomes of milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). Ten proteins (PIGR, PGD, QSOX1, MUC1, SRPRA, MD2, GAPDH, FOLR1, GPRC5B and HHIPL2) were differentially expressed between the proteomes of EV enriched milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). These proteins are potential milk whey biomarkers of early pregnancy

Interferometer readout-noise below the Standard Quantum Limit of a membrane

Here we report on the realization of a Michelson-Sagnac interferometer whose purpose is the precise characterization of the motion of membranes showing significant light transmission. Our interferometer has a readout noise spectral density (imprecision) of 3E-16 m/sqrt(Hz) at frequencies around the fundamental resonance of a SiN_x membrane at about 100 kHz, without using optical cavities. The readout noise demonstrated is more than 16 dB below the peak value of the membrane's standard quantum limit (SQL). This reduction is significantly higher than those of previous works with nano-wires [Teufel et al., Nature Nano. 4, 820 (2009); Anetsberger et al., Nature Phys. 5, 909 (2009)]. We discuss the meaning of the SQL for force measurements and its relation to the readout performance and conclude that neither our nor previous experiments achieved a total noise spectral density as low as the SQL

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications

Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3′ micro RNA uridine extensions and 5′ micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5′ deletions and 3′ uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications

Quantum Measurement Theory in Gravitational-Wave Detectors

The fast progress in improving the sensitivity of the gravitational-wave (GW) detectors, we all have witnessed in the recent years, has propelled the scientific community to the point, when quantum behaviour of such immense measurement devices as kilometer-long interferometers starts to matter. The time, when their sensitivity will be mainly limited by the quantum noise of light is round the corner, and finding the ways to reduce it will become a necessity. Therefore, the primary goal we pursued in this review was to familiarize a broad spectrum of readers with the theory of quantum measurements in the very form it finds application in the area of gravitational-wave detection. We focus on how quantum noise arises in gravitational-wave interferometers and what limitations it imposes on the achievable sensitivity. We start from the very basic concepts and gradually advance to the general linear quantum measurement theory and its application to the calculation of quantum noise in the contemporary and planned interferometric detectors of gravitational radiation of the first and second generation. Special attention is paid to the concept of Standard Quantum Limit and the methods of its surmounting.Comment: 147 pages, 46 figures, 1 table. Published in Living Reviews in Relativit