A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis

Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5′RACE-derivative method coined ‘5′tagRACE’, to perform the first search for non-coding RNAs (ncRNAs) encoded on the E. faecalis chromosome. We used the 5′tagRACE to simultaneously probe and characterize primary transcripts, and demonstrate here the simplicity, the reliability and the sensitivity of the method. The 5′tagRACE is complementary to tiling arrays or RNA-sequencing methods, and is also directly applicable to deep RNA sequencing and should significantly improve functional studies of bacterial RNA landscapes. From 45 selected loci of the E. faecalis chromosome, we discovered and mapped 29 novel ncRNAs, 10 putative novel mRNAs and 16 antisense transcriptional organizations. We describe in more detail the oxygen-dependent expression of one ncRNA located in an E. faecalis pathogenicity island, the existence of an ncRNA that is antisense to the ncRNA modulator of the RNA polymerase, SsrS and provide evidences for the functional interplay between two distinct toxin–antitoxin modules

Application of In Vivo Induced Antigen Technology (IVIAT) to Bacillus anthracis

In vivo induced antigen technology (IVIAT) is an immuno-screening technique that identifies bacterial antigens expressed during infection and not during standard in vitro culturing conditions. We applied IVIAT to Bacillus anthracis and identified PagA, seven members of a N-acetylmuramoyl-L-alanine amidase autolysin family, three P60 family lipoproteins, two transporters, spore cortex lytic protein SleB, a penicillin binding protein, a putative prophage holin, respiratory nitrate reductase NarG, and three proteins of unknown function. Using quantitative real-time PCR comparing RNA isolated from in vitro cultured B. anthracis to RNA isolated from BALB/c mice infected with virulent Ames strain B. anthracis, we confirmed induced expression in vivo for a subset of B. anthracis genes identified by IVIAT, including L-alanine amidases BA3767, BA4073, and amiA (pXO2-42); the bacteriophage holin gene BA4074; and pagA (pXO1-110). The exogenous addition of two purified putative autolysins identified by IVIAT, N-acetylmuramoyl-L-alanine amidases BA0485 and BA2446, to vegetative B. anthracis cell suspensions induced a species-specific change in bacterial morphology and reduction in viable bacterial cells. Many of the proteins identified in our screen are predicted to affect peptidoglycan re-modeling, and our results support significant cell wall structural remodeling activity during B. anthracis infection. Identification of L-alanine amidases with B. anthracis specificity may suggest new potential therapeutic targets

Raman Spectroscopic Study of Ruddlesden—Popper Tetragonal Sr₂VO₄

The lattice dynamics of tetragonal Sr2VO4 with a Ruddlesden—Popper-layered crystal structure was studied via Raman spectroscopy. We observed three of the four expected Raman-active modes under ambient conditions. Mode Grüneisen parameters and the implicit fractions of two A1g Raman-active modes were determined from high-pressure and high-temperature Raman spectroscopy experiments. The low-energy A1g Raman-active mode involving Sr motions along the c direction has a large isothermal Grüneisen parameter about seven times larger than that of the high-energy A1g Raman-active mode involving apical O motions along the c direction and is, therefore, more anharmonic. The thermodynamic Grüneisen parameter is significantly smaller in Sr2VO4 than in Sr2TiO4 due to the smaller Grüneisen parameter of the high-energy A1g Raman-active mode and other vibrational modes that still need to be identified. The explicit contribution of the low-energy A1g Raman-active mode is negative, and the implicit contribution due to volume change is much larger. Both volume implicit and anharmonic explicit contributions of the high-energy A1g Raman-active mode have similar positive values. The Raman experiment in the air shows that Sr2VO4 begins to decompose above 200 °C

Wavelength effect on polymer photooxidation under LED weathering conditions

International audienceThis paper is devoted to the investigation of the photooxidation of poly(N-vinylcarbazole (PVK) and polyethylene (LDPE) by exposure to λ ≥ 300 nm polychromatic light (SEPAP 12.24) or UV light produced by a new setup equipped with LEDs emitting at 365 nm (LED 365), both at a temperature of 60 °C. Photooxidation was studied by infrared and UV-visible spectroscopies and emission spectroscopy in the case of PVK. The mechanisms by which the oxidation products were formed in both polymers were recalled. Depending on the conditions of ageing, i.e., polychromatic light or exposure to LED 365, the same oxidation products were obtained but with different rates and different relative amounts. This result reflected the influence of the wavelengths on the mechanisms. In the case of PVK, the formation of oxidation photoproducts and yellowing were not impacted, but the kinetics of the decrease in excimer fluorescence, which is linked to the crosslinking of the polymer, were dramatically modified. In the case of LDPE, wavelength effects on the photolysis of ketones by Norrish reactions were observed. As a consequence, irradiations with the LED 365 setup could not be claimed to be representative of polychromatic irradiations because the shortest wavelengths ((300 nm < < 350 nm)) were missing and could not reproduce natural outdoor conditions of weathering

A revisited phonon assignment and electro-mechanical properties of chromium disilicide

International audienceWe report a complete study of the lattice dynamics, dielectric, elastic and piezolectric properties of the hexagonal semiconducting chromium disilicide (CrSi2). From a combined experimental and theoretical study, we have revisited the phonon mode assignments at the zone-center, so that the contradictions met in previous experimental studies between 250 and 300 cm-1 are now explained and understood. We found that the temperature dependence of the Raman frequencies is mainly due to an implicit volume contribution and related to the large Gruneisen parameter. This explains why CrSi2 has a moderate thermal conductivity although its Debye temperature is quite large. Optic and static dielectric constants have also been analyzed and discussed. The elastic constants of CrSi2 are large, but this compound is quite brittle. In addition, the relatively low Poisson coefficient associated to the large negative Cauchy pressure of CrSi2 indicate the angular nature of its bonding. The calculation of its piezoelectric coefficient shows a sizable value with a magnitude similar to that reported for α-quartz. This prediction requires, however, experimental confirmations

Vibrational Origin of the Thermal Stability in the Highly Distorted alpha-quartz-Type Material GeO2: an Experimental and Theoretical Study

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