Giardiavirus internal ribosome entry site has an apparently unique mechanism of initiating translation.

Giardiavirus (GLV) utilizes an internal ribosome entry site (IRES) for translation initiation in the early branching eukaryote Giardia lamblia. Unlike most of the viral IRESs among higher eukaryotes, which localize primarily within the 5'-untranslated region (UTR), the GLV IRES comprises 253 nts of 5'UTR and the initial 264 nts in the open-reading-frame (ORF). To test if GLV IRES also functions in higher eukaryotic systems, we examined it in rabbit reticulocyte lysate (RRL) and found that it functions much less efficiently than the IRES from the Encephalomyocarditis virus (EMCV) or Cricket paralysis virus (CrPV). In contrast, both EMCV-IRES and CrPV-IRESs were inactive in transfected Giardia cells. Structure-function analysis indicated that only the stem-loop U5 from the 5'UTR and the stem-loop I plus the downstream box (Dbox) from the ORF of GLV IRES are required for limited IRES function in RRL. Edeine, a translation initiation inhibitor, did not significantly affect the function of GLV IRES in either RRL or Giardia, indicating that a pre-initiation complex is not required for GLV IRES-mediated translation initiation. However, the small ribosomal subunit purified from Giardia did not bind to GLV IRES, indicating that additional protein factors may be necessary. A member of the helicase family IBP1 and two known viral IRES binding proteins La autoantigen and SRp20 have been identified in Giardia that bind to GLV IRES in vitro. These three proteins could be involved in facilitating small ribosome recruitment for initiating translation

Defects Can Increase the Melting Temperature of DNA-Nanoparticle Assemblies

DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to developing reliable detection technology. We studied the effects of DNA base-pairing defects, such as mismatches and deletions, on the melting temperature of DNA-nanoparticle assemblies. We found that, contrary to the general assumption that defects lower the melting temperature of DNA, some defects increase the melting temperature of DNA-linked nanoparticle assemblies. The effects of mismatches and deletions were found to depend on the specific base pair, the sequence, and the location of the defects. Our results demonstrate that the surface-bound DNA exhibit hybridization behavior different from that of free DNA. Such findings indicate that a detailed understanding of DNA-nanoparticle assembly phase behavior is required for quantitative interpretation of DNA-nanoparticle aggregation.Comment: 12 pages, 3 figure

Polymers in Fluid Flows

The interaction of flexible polymers with fluid flows leads to a number of intriguing phenomena observed in laboratory experiments, namely drag reduction, elastic turbulence and heat transport modification in natural convection, and is one of the most challenging subjects in soft matter physics. In this paper we review our present knowledge on the subject. Our present knowledge is mostly based on direct numerical simulations performed in the last twenty years, which have successfully explained, at least qualitatively, most of the experimental results. Our goal is to disentangle as much as possible the basic mechanisms acting in the system in order to capture the basic features underlying different theoretical approaches and explanations

Revisiting variable radius circles in constructive geometric constraint solving

Variable-radius circles are common constructs in planar constraint solving and are usually not handled fully by algebraic constraint solvers. We give a complete treatment of variable-radius circles when such a circle must be determined simultaneously with placing two groups of geometric entities. The problem arises for instance in solvers using triangle decomposition to reduce the complexity of the constraint problem.Postprint (published version

Development of EHD Ion-Drag Micropump for Microscale Electronics Cooling Systems

In this investigation, the numerical simulation of electrohydrodynamic (EHD) ion-drag micropumps with micropillar electrode geometries have been performed. The effect of micropillar height and electrode spacing on the performance of the micropumps was investigated. The performance of the EHD micropump improved with increased applied voltage and decreased electrode spacing. The optimum micropillar height for the micropump with electrode spacing of 40$\mu$m and channel height of 100$\mu$m at 200V was 40$\mu$m, where a maximum mass flow rate of 0.18g/min was predicted. Compared to that of planar electrodes, the 3D micropillar electrode geometry enhanced the overall performance of the EHD micropumps.Comment: Submitted on behalf of TIMA Editions (http://irevues.inist.fr/tima-editions

Statistically Preserved Structures and Anomalous Scaling in Turbulent Active Scalar Advection

The anomalous scaling of correlation functions in the turbulent statistics of active scalars (like temperature in turbulent convection) is understood in terms of an auxiliary passive scalar which is advected by the same turbulent velocity field. While the odd-order correlation functions of the active and passive fields differ, we propose that the even-order correlation functions are the same to leading order (up to a trivial multiplicative factor). The leading correlation functions are statistically preserved structures of the passive scalar decaying problem, and therefore universality of the scaling exponents of the even-order correlations of the active scalar is demonstrated.Comment: 4 pages, 5 figures, submitted to Phys. Rev. Let

Dependence of heat transport on the strength and shear rate of prescribed circulating flows

We study numerically the dependence of heat transport on the maximum velocity and shear rate of physical circulating flows, which are prescribed to have the key characteristics of the large-scale mean flow observed in turbulent convection. When the side-boundary thermal layer is thinner than the viscous boundary layer, the Nusselt number (Nu), which measures the heat transport, scales with the normalized shear rate to an exponent 1/3. On the other hand, when the side-boundary thermal layer is thicker, the dependence of Nu on the Peclet number, which measures the maximum velocity, or the normalized shear rate when the viscous boundary layer thickness is fixed, is generally not a power law. Scaling behavior is obtained only in an asymptotic regime. The relevance of our results to the problem of heat transport in turbulent convection is also discussed.Comment: 7 pages, 7 figures, submitted to European Physical Journal