A toolbox of engineered mosquito lines to study salivary gland biology and malaria transmission.

Mosquito saliva is a vehicle for the transmission of vector borne pathogens such as Plasmodium parasites and different arboviruses. Despite the key role of the salivary glands in the process of disease transmission, knowledge of host-pathogen interactions taking place within this organ is very limited. To improve the experimental tractability of the salivary glands, we have generated fluorescent reporter lines in the African malaria mosquito Anopheles coluzzii using the salivary gland-specific promoters of the anopheline antiplatelet protein (AAPP), the triple functional domain protein (TRIO) and saglin (SAG) coding genes. Promoter activity was specifically observed in the distal-lateral lobes or in the median lobe of the salivary glands. Besides a comparison of the expression patterns of the selected promoters, the fluorescent probes allowed us to evaluate the inducibility of the selected promoters upon blood feeding and to measure intracellular redox changes. We also combined the aapp-DsRed fluorescent reporter line with a pigmentation-deficient yellow(-) mosquito mutant to assess the feasibility of in vivo microscopy of parasitized salivary glands. This combination allowed locating the salivary gland through the cuticle and imaging of individual sporozoites in vivo, which facilitates live imaging studies of salivary gland colonization by Plasmodium sporozoites.

Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches.

Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5' untranslated region of mRNA. Rearrangements of the RNA structure in response, e.g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modelling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behaviour in vivo critically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developed in silico methods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyse the influence of 5' hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free licence on GitHub (https://github.com/xileF1337/riboswitch_design).

Structural basis of tRNA recognition by the m3C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase.

Methylation of cytosine 32 in the anticodon loop of tRNAs to 3-methylcytosine (m3C) is crucial for cellular translation fidelity. Misregulation of the RNA methyltransferases setting this modification can cause aggressive cancers and metabolic disturbances. Here, we report the cryo-electron microscopy structure of the human m3C tRNA methyltransferase METTL6 in complex with seryl-tRNA synthetase (SerRS) and their common substrate tRNASer. Through the complex structure, we identify the tRNA-binding domain of METTL6. We show that SerRS acts as the tRNASer substrate selection factor for METTL6. We demonstrate that SerRS augments the methylation activity of METTL6 and that direct contacts between METTL6 and SerRS are necessary for efficient tRNASer methylation. Finally, on the basis of the structure of METTL6 in complex with SerRS and tRNASer, we postulate a universal tRNA-binding mode for m3C RNA methyltransferases, including METTL2 and METTL8, suggesting that these mammalian paralogs use similar ways to engage their respective tRNA substrates and cofactors.

IRFinder-S: a comprehensive suite to discover and explore intron retention.

Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention.

Functional insights from a surface antigen mRNA-bound proteome.

Trypanosoma brucei is the causative agent of human sleeping sickness. The parasites' variant surface glycoprotein (VSG) enables them to evade adaptive immunity via antigenic variation. VSG comprises 10% of total cell protein and the high stability of VSG mRNA is essential for trypanosome survival. To determine how VSG mRNA stability is maintained, we used mRNA affinity purification to identify all its associated proteins. CFB2 (cyclin F-box protein 2), an unconventional RNA-binding protein with an F-box domain, was specifically enriched with VSG mRNA. We demonstrate that CFB2 is essential for VSG mRNA stability, describe cis acting elements within the VSG 3'-untranslated region that regulate the interaction, identify trans-acting factors that are present in the VSG messenger ribonucleoprotein particle, and mechanistically explain how CFB2 stabilizes the mRNA of this key pathogenicity factor. Beyond T. brucei, the mRNP purification approach has the potential to supply detailed biological insight into metabolism of relatively abundant mRNAs in any eukaryote.

The mechanism of cavitation-induced scission of single-walled carbon nanotubes.

Aqueous suspensions of length selected single-walled carbon nanotubes were studied by atomic force microscopy (AFM) in order to probe the influence of sonication on nanotube scission. The maximum of the tube length distribution, lM, initially exhibits a power law dependence on the sonication time, t - roughly as lM approximately t(-0.5). This and the limiting behavior observed at longer times can be rationalized to first order in terms of a continuum model deriving from polymer physics. In this picture, the strain force associated with cavitation scales with the square of the nanotube length. Scission stops when the strain force falls below the critical value for nanotube disruption.

Raman spectroscopy of individual single-walled carbon nanotubes from various sources.

Resonance Raman spectroscopy/microscopy was used to study individualized single-walled carbon nanotubes (SWNTs) both in aqueous suspensions as well as after spin-coating onto Si/SiO2 surfaces. Four different SWNT materials containing nanotubes with diameters ranging from 0.7 to 1.6 nm were used. Comparison with Raman data obtained for suspensions shows that the surface does not dramatically affect the electronic properties of the deposited tubes. Raman features observed for deposited SWNTs are similar to what was measured for nanotubes directly fabricated on surfaces using chemical vapor deposition (CVD) methods. In particular, individual semiconducting tubes could be distinguished from metallic tubes by their different G-mode line shapes. It could also be shown that the high-power, short-time sonication used to generate individualized SWNT suspensions does not induce defects in great quantities. However, (additional) defects can be generated by laser irradiation of deposited SWNTs in air, thus giving rise to an increase of the D-mode intensity for even quite low power densities (approximately 10(4) W/cm2).

Intersubband decay of 1-D exciton resonances in carbon nanotubes.

We have studied intersubband decay of E22 excitons in semiconducting carbon nanotubes experimentally and theoretically. Photoluminescence excitation line widths of semiconducting nanotubes with chiral indicess (n,m) can be mapped onto a connectivity grid with curves of constant (n - m) and (2n + m). Moreover, the global behavior of E22 line widths is best characterized by a strong increase with energy irrespective of their (n-m)mod(3) = +/-1 family affiliation. Solution of the Bethe-Salpeter equations shows that the E22 line widths are dominated by phonon assisted coupling to higher momentum states of the E11 and E12 exciton bands. The calculations also suggest that the branching ratio for decay into exciton bands vs free carrier bands, respectively is about 10:1.

Direct observation of deep excitonic states in the photoluminescence spectra of single-walled carbon nanotubes.

Low-energy, dark excitonic states have recently been predicted to lie below the first bright (E11) exciton in semiconducting single-walled carbon nanotubes [Phys. Rev. Lett. 93, 157402 (2004)10.1103/PhysRevLett.93.157402]. Decay into such deep excitonic states is implicated as a mechanism which reduces photoluminescence quantum yields. In this study we report the first direct observation of deep excitons in SWNTs. Photoluminescence (PL) microscopy of suspended semiconducting single-walled carbon nanotubes (SWNTs) reveals weak emission satellites redshifted by approximately 38-45 and approximately 100-130 meV relative to the main E11 PL emission peaks. Similar satellites, redshifted by 95-145 meV depending on nanotube species, were also found in PL measurements of ensembles of SWNTs in water-surfactant dispersions. The relative intensities of these deep exciton emission features depend on the nanotube surroundings.

Spectroscopy of single- and double-wall carbon nanotubes in different environments.

Individual single-wall carbon nanotubes (SWNTs) and double-wall carbon nanotubes (DWNTs) were suspended in water for optical studies using sodium-cholate and other surfactants. We used time-resolved photoluminescence (PL) spectroscopy to study the influence of tube chirality and diameter as well as of the environment on nonradiative decay in small diameter tubes. The studies provide evidence for PL from small diameter core tubes in DWNTs and for a correlation of nonradiative decay with tube diameter and exciton red shift as induced by interaction with the environment.