Photon lifetime in a cavity containing a slow-light medium

We investigate experimentally the lifetime of the photons in a cavity containing a medium exhibiting strong positive dispersion. This intracavity positive dispersion is provided by a metastable helium gas at room temperature in the electromagnetically induced transparency (EIT) regime, in which light propagates at a group velocity of the order of 10000 m/s. The results definitely prove that the lifetime of the cavity photons is governed by the group velocity of light in the cavity, and not its phase velocity.Comment: Accepted for publication in Optics Letter

Looking for a reliable method to follow the salmonella status of finishing pigs

A study was undertaken to answer questions about the epidemiology of Salmonella in pig production. Does the Salmonella excretion from a group of pigs (on the same farm) remain constant during time or is there variations ? Where, and how many samples do we have to take to follow these variations, if they exist? Are the techniques to analyse samples (bacteriological and serological) practicable ? How is the relationship between serological and bacteriological methods

Improved detection of intestinal helminth infections with a formalin ethyl-acetate-based concentration technique compared to a crude formalin concentration technique

Intestinal helminth infections are the most prevalent neglected tropical diseases, predominantly affecting rural and marginalised populations. The mainstay of diagnosis is the microscopic examination of faecal samples to detect parasites in the form of eggs, larvae and cysts. In an effort to improve the standard of care, the comparative accuracy in detecting helminth infections of the hitherto used formalin-based concentration method (FC) was compared to a previously developed formalin ethyl-acetate-based concentration technique (FECT), prior to the systematic deployment of the latter at a research and humanitarian unit operating on the Thailand-Myanmar border. A total of 693 faecal samples were available for the comparison of the two diagnostic methods. The FECT was superior in detecting hookworm, Trichuris trichiura and small liver flukes. Interestingly, there was no significant difference for Ascaris lumbricoides, possibly due to the high observed egg density. Despite the minor increase in material cost and the fact that the FECT is somewhat more time consuming, this method was implemented as the new routine technique

Zn-induced interactions between SARS-CoV-2 orf7a and BST2/Tetherin

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys(15) ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

<p/> <p>Background</p> <p>Brown algae of the genus <it>Ectocarpus </it>exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of <it>E. siliculosus </it>as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus <it>Ectocarpus </it>both at the genome and the transcriptome level.</p> <p>Results</p> <p>We used an <it>E. siliculosus </it>gene expression microarray based on EST sequences from the genome-sequenced strain (reference strain) to carry out comparative genome hybridizations for five <it>Ectocarpus </it>strains: four <it>E. siliculosus </it>isolates (the male genome strain, a female strain used for outcrosses with the genome strain, a strain isolated from freshwater, and a highly copper-tolerant strain), as well as one strain of the sister species <it>E. fasciculatus</it>. Our results revealed significant genomic differences between ecotypes of the same species, and enable the selection of conserved probes for future microarray experiments with these strains. In the two closely related strains (a male and a female strain used for crosses), genomic differences were also detected, but concentrated in two smaller genomic regions, one of which corresponds to a viral insertion site.</p> <p>Conclusion</p> <p>The high variability between strains supports the concept of <it>E. siliculosus </it>as a complex of cryptic species. Moreover, our data suggest that several parts of the <it>Ectocarpus </it>genome may have evolved at different rates: high variability was detected particularly in transposable elements and fucoxanthin chlorophyll a/c binding proteins.</p

Bacteriological assessment of the Salmonella status of market-aged pigs

The subclinical Salmonella enterica infection in pigs is associated with public health problems and can constitute a hindrance towards national and international trade. Many countries are starting the implementation of Salmonella national surveillance programs in pork. In spite of the increase of available data on the subject, no consensus seems to exist when assessing Salmonella status of finishing pigs

Out-of-plane orientation of luminescent excitons in atomically thin indium selenide flakes

Van der Waals materials offer a wide range of atomic layers with unique properties that can be easily combined to engineer novel electronic and photonic devices. A missing ingredient of the van der Waals platform is a two-dimensional crystal with naturally occurring out-of-plane luminescent dipole orientation. Here we measure the far-field photoluminescence intensity distribution of bulk InSe and two-dimensional InSe, WSe$_2$ and MoSe$_2$. We demonstrate, with the support of ab-initio calculations, that layered InSe flakes sustain luminescent excitons with an intrinsic out-of-plane orientation, in contrast with the in-plane orientation of dipoles we find in two-dimensional WSe$_2$ and MoSe$_2$ at room-temperature. These results, combined with the high tunability of the optical response and outstanding transport properties, position layered InSe as a promising semiconductor for novel optoelectronic devices, in particular for hybrid integrated photonic chips which exploit the out-of-plane dipole orientation.Comment: Published in Nature Communications. 12 pages, 5 figures. Link: https://www.nature.com/articles/s41467-019-11920-

The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin

In this paper, we provide evidence that Zn2+ ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments

Metal ion binding in wild-type and mutated frataxin: a stability study

This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal

Nuclear target search at the single molecule level: protein interactions define the exploration landscape

Gene regulation relies on highly mobile transcription factors (TFs) exploring the nucleoplasm in search of their targets. Our view of the nucleus has evolved from that of an isotropic and homogenous reactor to that of a highly organized yet very dynamic organelle. However important questions remain on how these regulatory factors explore the nuclear environment in search of their DNA or protein targets, and how their exploration strategy affects the kinetics of transcriptional regulation. We implemented a single-molecule tracking assay to determine the TFs dynamics using photoactivatable tags in human cells. We investigated the mobility of several nuclear proteins, including the transcription factor c-Myc and the elongation factor P-TEFb. We found that, while their diffusion speed was comparable, these proteins largely differed in terms of their exploration geometry. We discovered that c-Myc is a global explorer diffusing in the nucleus without spatial constraints. In contrast, the positive transcription elongation factor P-TEFb is a local explorer that oversamples its environment, constrained by a fractal nuclear architecture. Consequently, each c-Myc molecule is equally available for all nuclear sites while P-TEFb reaches its targets in a position-dependent manner. We also measured the mobility of a P-TEFb mutant in which the interaction with the CTD of the RNA Pol II was truncated. In this case, the single-molecule experiments suggested a global exploration of the P-TEFb mutant, consistent with free diffusion. Our observations are in line with a model in which the exploration geometry of TFs is constrained by their interactions and not by exclusion properties. Our findings have strong implications on how proteins react in the nucleus and how their function can be regulated in space and time