A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes

We have derived a novel method to assess compositional biases in biological sequences, which is based on finding the lowest-probability subsequences for a given residue-type set. As a case study, the distribution of prion-like glutamine/asparagine-rich ((Q+N)-rich) domains (which are linked to amyloidogenesis) was assessed for budding and fission yeasts and four other eukaryotes. We find more than 170 prion-like (Q+N)-rich regions in budding yeast, and, strikingly, many fewer in fission yeast. Also, some residues, such as tryptophan or isoleucine, are unlikely to form biased regions in any eukaryotic proteome

Draft genome sequence of the Streptococcus pneumoniae Avery strain A66

We have used HiSeq 2000 technology to generate a draft genome sequence of Streptococcus pneumoniae strain A66. This is a common study strain used in investigations of pneumococcal bacterium-host interactions and was used in the seminal genetic studies of Avery et al

Portable Polarimetric Fiber Stress Sensor System for Visco-elastic and Biomimetic Material Analysis

Non-destructive materials characterization methods have significantly changed our fundamental understanding of material behavior and have enabled predictive models to be developed. However, the majority of these efforts have focused on crystalline and metallic materials, and transitioning to biomaterials, such as tissue samples, is non-trivial, as there are strict sample handling requirements and environmental controls which prevent the use of conventional equipment. Additionally, the samples are smaller and more complex in composition. Therefore, more advanced sample analysis methods capable of operating in these environments are needed. In the present work, we demonstrate an all-fiber-based material analysis system based on optical polarimetry. Unlike previous polarimetric systems which relied on free-space components, our method combines an in-line polarizer, polarization-maintaining fiber, and a polarimeter to measure the arbitrary polarization state of the output, eliminating all free-space elements. Additionally, we develop a more generalized theoretical analysis which allows more information about the polarization state to be obtained via the polarimeter. We experimentally verify our system using a series of elastomer samples made from polydimethylsiloxane (PDMS), a commonly used biomimetic material. By adjusting the base:curing agent ratio of the PDMS, we controllably tune the Young’s modulus of the samples to span over an order of magnitude. The measured results are in good agreement with those obtained using a conventional load-frame system. Our fiber-based polarimetric stress sensor shows promise for use as a simple research tool that is portable and suitable for a wide variety of applications

Spatiotemporal Fluorescent Detection Measurements Using Embedded Waveguide Sensors

Integrated waveguide biosensors, when combined with fluorescent labeling, have significantly impacted the field of biodetection. While there are numerous types of waveguide sensors, the fundamental excitation method is fairly consistent: the evanescent field of the waveguide excites a fluorophore whose emission is detected, either directly via imaging or indirectly via a decrease in power transfer. Recently, a sensor device was demonstrated which is able to back-couple the emitted light into the waveguide, allowing the signal to be detected directly. However, this previous work focused on the development of an empirical model, leaving many theoretical questions unanswered. Additionally, the results from the novel back-coupling route were not compared with the results from the more conventional imaging technique. In this study, we develop finite difference time domain simulations to predict the sensor\u27s performance both in air and aqueous environments. We also perform complementary experiments to verify the modeling, measuring the fluorescence coupled into the waveguide, and radiated perpendicular to the waveguide. Finally, we performed spatiotemporal measurements of the fluorescence on the waveguide. Utilizing these measurements, we are able to measure the fluorescent decay rate of the fluorescent dye at arbitrary points along the length of the waveguide

GALEX and Optical Light Curves of EF Eridanus During a Low State: the Puzzling Source of UV Light

Low state optical photometry of EF Eri during an extended low accretion state combined with GALEX near and far UV time-resolved photometry reveals a source of UV flux that is much larger than the underlying 9500K white dwarf, and that is highly modulated on the orbital period. The near UV and optical light curves can be modeled with a 20,000K spot but no spot model can explain both the large amplitude FUV variations and the SED. The limitations of limb darkening, cyclotron and magnetic white dwarf models in explaining the observations are discussed.Comment: 10 pages, 4 figures to be published in ApJ Letter

Structure and electronic properties of the quasi-one-dimensional Ba₂Co₁₋ₓZnₓS₃ series

This work focuses on the structure and physical properties of the solid solution Ba₂Co₁₋ₓZnₓS₃ (0 ≤ x ≤ 1), a family of quasi-one-dimensional sulfides with end members Ba₂CoS₃ and Ba₂ZnS₃. The structure of selected compounds with increasing Zn²⁺ content has been analysed using, neutron diffraction, TEM and EXAFS and the physical properties via magnetic susceptibility and resistivity measurements. The progressive substitution of the non-magnetic Zn²⁺ cation for Co²⁺ rapidly destroys the antiferromagnetic transition present at 46 K in the quasi one-dimensional Ba₂CoS₃, leading to paramagnetic behaviour down to the lowest investigated temperature (5K) for compounds with x > 0.25. For compounds with x ≥ 0.4, a pure CW regime is recovered around 300 K, yielding effective moments consistent with the g factor of the tetrahedrally coordinated Co²⁺ previously determined for Ba₂CoS₃. The Zn²⁺/Co²⁺ substitution also removes the metallic-like behaviour of Ba₂CoS₃ causing an increase in the value of the resistivity with all the Ba₂Co₁₋ₓZnₓS₃ compounds showing semiconducting behaviour. The negative magnetoresistance of Ba₂CoS₃ is improved by the Zn²⁺/Co²⁺ substitution, with values of – 6% for Ba₂Co₀.₇₅Zn₀.₂₅S₃, – 9% for Ba₂Co₀.₅Zn₀.₅S₃ and – 8% for Ba₂Co₀.₂₅Zn₀.₇₅S₃. However, there does not seem to be a correlation between the values of the resistivity and the magnetoresistance and the content of Zn²⁺, leading to the hypothesis that transport properties may be linked more closely to extrinsic properties

First observation of Bs0 → D*s2+Xμ-ν decays

Using data collected with the LHCb detector in proton–proton collisions at a centre-of-mass energy of 7 TeV, the semileptonic decays B0s→D+sXμ−ν and B0s→D0K+Xμ−ν are detected. Two structures are observed in the D0K+ mass spectrum at masses consistent with the known Ds1(2536)+ and D∗s22573)+ mesons. The measured branching fractions relative to the total B0s semileptonic rate are B(B0s→D∗+s2Xμ−ν)/B(B0s→Xμ−ν) = (3.3±1.0±0.4)%, and B(B0s→D+s1Xμ−ν)/B(B0s→Xμ−ν) = (5.4±1.2±0.5)%, where the first uncertainty is statistical and the second is systematic. This is the first observation of the D∗+s2 state in B0s decays; we also measure its mass and width

The emergence of mecC methicillin-resistant Staphylococcus aureus.

The report of methicillin-resistant Staphylococcus aureus (MRSA) encoding a divergent mecA gene in 2011 was highly significant. This homologue, designated mecC, poses diagnostic problems with the potential to be misdiagnosed as methicillin-sensitive S. aureus, with important potential consequences for individual patients and for the surveillance of MRSA. mecC MRSA have now been reported from 13 European countries and have been isolated from 14 different host species, with evidence of a recent increase in Denmark. The emergence of mecC MRSA is a topic of interest to human and veterinary microbiology, and we consider it timely to review here its discovery and subsequent investigation.Our work on S. aureus is supported by a Medical Research Council (MRC) Partnership Award to M.A.H and funding to G.K.P from PetPlan Charitable Trust, the British Society for Antimicrobial Chemotherapy, and the Cambridge–Africa Alborada Research Fund.This is the final published version distributed under a Creative Commons Attribution License 2.0, which can also be found on the publisher's website at: http://www.cell.com/trends/microbiology/abstract/S0966-842X(13)00226-

Serpentine Low Loss Trapezoidal Silica Waveguides on Silicon

We report the fabrication and characterization of straight and serpentine low loss trapezoidal silica waveguides integrated on a silicon substrate. The waveguide channel was defined using a dual photo-lithography and buffered HF etching and isolated from the silicon substrate using an isotropic silicon etchant. The waveguide is air-clad and thus has a core-cladding effective index contrast of approximately 25%. Measured at 658, 980 and 1550nm, the propagation loss was found to be 0.69, 0.59, and 0.41dB/cm respectively, with a critical bending radius less than 375μm. The waveguide’s polarization behavior was investigated both theoretically and experimentally. Additionally, the output power shows a linear response with input power up to 200mW