HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome

HIV-1 replication can be efficiently inhibited by intracellular expression of an siRNA targeting the viral RNA. However, HIV-1 escape variants emerged after prolonged culturing. These RNAi-resistant viruses contain nucleotide substitutions or deletions in or near the targeted sequence. We observed an inverse correlation between the level of resistance and the stability of the siRNA/target-RNA duplex. However, two escape variants showed a higher level of resistance than expected based on the duplex stability. We demonstrate that these mutations induce alternative folding of the RNA such that the target sequence is occluded from binding to the siRNA, resulting in reduced RNAi efficiency. HIV-1 can thus escape from RNAi-mediated inhibition not only through nucleotide substitutions or deletions in the siRNA target sequence, but also through mutations that alter the local RNA secondary structure. The results highlight the enormous genetic flexibility of HIV-1 and provide detailed molecular insight into the sequence specificity of RNAi and the impact of target RNA secondary structure

NMR parameters in alkali, alkaline earth and rare earth fluorides from first principle calculations

19F isotropic chemical shifts for alkali, alkaline earth and rare earth of column 3 basic fluorides are measured and the corresponding isotropic chemical shieldings are calculated using the GIPAW method. When using PBE exchange correlation functional for the treatment of the cationic localized empty orbitals of Ca2+, Sc3+ (3d) and La3+ (4f), a correction is needed to accurately calculate 19F chemical shieldings. We show that the correlation between experimental isotropic chemical shifts and calculated isotropic chemical shieldings established for the studied compounds allows to predict 19F NMR spectra of crystalline compounds with a relatively good accuracy. In addition, we experimentally determine the quadrupolar parameters of 25Mg in MgF2 and calculate the electric field gradient of 25Mg in MgF2 and 139La in LaF3 using both PAW and LAPW methods. The orientation of the EFG components in the crystallographic frame, provided by DFT calculations, is analysed in term of electron densities. It is shown that consideration of the quadrupolar charge deformation is essential for the analysis of slightly distorted environments or highly irregular polyhedra.Comment: 18 pages, 8 figures, 4 tables and ES

Kiezen voor dierenwelzijn

Om de consument beter te kunnen informeren over de diervriendelijkheid van vleesproducten heeft de Stichting Varkens in Nood (VIN) aan de voormalige Wetenschapswinkel Biologie (nu: Kennispunt Bètawetenschappen) in Utrecht gevraagd een “vleeswijzer” te ontwikkelen die uitgedeeld kan worden aan consumenten en waarop consumenten op een eenvoudige manier kunnen zien welke producten méér of juist minder diervriendelijk geproduceerd worden. Om deze vleeswijzer te ontwikkelen is in dit onderzoek een aantal dierenwelzijnsdeskundigen benaderd met de vraag de diervriendelijkheid van verschillende vleesproducten te beoordelen. In deze rapportage wordt dit onderzoek beschreven

Construction of a doxycycline-dependent simian immunodeficiency virus reveals a nontranscriptional function of tat in viral replication

In the quest for an effective vaccine against human immunodeficiency virus (HIV), live attenuated virus vaccines have proven to be very effective in the experimental model system of simian immunodeficiency virus (SIV) in macaques. However, live attenuated HIV vaccines are considered unsafe for use in humans because the attenuated virus may accumulate genetic changes during persistence and evolve to a pathogenic variant. As an alternative approach, we earlier presented a conditionally live HIV-1 variant that replicates exclusively in the presence of doxycycline (DOX). Replication of this vaccine strain can be limited to the time that is needed to provide full protection through transient DOX administration. Since the effectiveness and safety of such a conditionally live AIDS vaccine should be tested in macaques, we constructed a similar DOX-dependent SIVmac239 variant in which the Tat-TAR (trans-acting responsive) transcription control mechanism was functionally replaced by the DOX-inducible Tet-On regulatory mechanism. Moreover, this virus can be used as a tool in SIV biology studies and vaccine research because both the level and duration of replication can be controlled by DOX administration. Unexpectedly, the new SIV variant required a wild-type Tat protein for replication, although gene expression was fully controlled by the incorporated Tet-On system. This result suggests that Tat has a second function in SIV replication in addition to its role in the activation of transcriptio

The role of the dopamine D1 receptor in social cognition : Studies using a novel genetic rat model

Social cognitionisan endophenotype that is impaired in schizophrenia and several other (comorbid) psychiatric disorders. One of the modulators of social cognition is dopamine, but its role is not clear. The effects of dopamine are mediated through dopamine receptors, including the dopamine D1 receptor (Drd1). Because current Drd1 receptor agonists are not Drd1 selective, pharmacological tools are not sufficient to delineate the role of the Drd1. Here, we describe a novel rat model with a genetic mutation in Drd1 in which we measured basic behavioural phenotypes and social cognition. The I116S mutation was predicted to render the receptor less stable. In line with this computational prediction, this Drd1 mutation led to a decreased transmembrane insertion of Drd1, whereas Drd1 expression, as measured by Drd1 mRNA levels, remained unaffected. Owing to decreased transmembrane Drd1 insertion, the mutant rats displayed normal basic motoric and neurological parameters, as well as locomotor activity and anxiety-like behaviour. However, measures of social cognition like social interaction, scent marking, pup ultrasonic vocalizations and sociability, were strongly reduced in the mutant rats. This profile of the Drd1 mutant rat offers the field of neuroscience a novel genetic rat model to study a series of psychiatric disorders including schizophrenia, autism, depression, bipolar disorder and drug addiction

The role of the dopamine D1 receptor in social cognition: studies using a novel genetic rat model­

Social cognition is an endophenotype that is impaired in schizophrenia and several other (comorbid) psychiatric disorders. One of the modulators of social cognition is dopamine, but its role is not clear. The effects of dopamine are mediated through dopamine receptors, including the dopamine D1 receptor (Drd1). Because current Drd1 receptor agonists are not Drd1 selective, pharmacological tools are not sufficient to delineate the role of the Drd1. Here, we describe a novel rat model with a genetic mutation in Drd1 in which we measured basic behavioural phenotypes and social cognition. The I116S mutation was predicted to render the receptor less stable. In line with this computational prediction, this Drd1 mutation led to a decreased transmembrane insertion of Drd1, whereas Drd1 expression, as measured by Drd1 mRNA levels, remained unaffected. Owing to decreased transmembrane Drd1 insertion, the mutant rats displayed normal basic motoric and neurological parameters, as well as locomotor activity and anxiety-like behaviour. However, measures of social cognition like social interaction, scent marking, pup ultrasonic vocalizations and sociability, were strongly reduced in the mutant rats. This profile of the Drd1 mutant rat offers the field of neuroscience a novel genetic rat model to study a series of psychiatric disorders including schizophrenia, autism, depression, bipolar disorder and drug addiction

Diffusion-weighted MRI to assess response to chemoradiotherapy in rectal cancer:main interpretation pitfalls and their use for teaching

To establish the most common image interpretation pitfalls for non-expert readers using diffusion-weighted imaging (DWI) to assess response to chemoradiotherapy in patients with rectal cancer and to explore the use of these pitfalls in an expert teaching setting. Two independent non-expert readers (R1 and R2) scored the restaging DW MRI scans (b1,000 DWI, in conjunction with ADC maps and T2-W MRI scans for anatomical reference) in 100 patients for the likelihood of a complete response versus residual tumour using a five-point confidence score. The readers received expert feedback and the final response outcome for each case. The supervising expert documented any potential interpretation errors/pitfalls discussed for each case to identify the most common pitfalls. The most common pitfalls were the interpretation of low signal on the ADC map, small susceptibility artefacts, T2 shine-through effects, suboptimal sequence angulation and collapsed rectal wall. Diagnostic performance (area under the ROC curve) was 0.78 (R1) and 0.77 (R2) in the first 50 patients and 0.85 (R1) and 0.85 (R2) in the final 50 patients. Five main image interpretation pitfalls were identified and used for teaching and feedback. Both readers achieved a good diagnostic performance with an AUC of 0.85. aEuro cent Fibrosis appears hypointense on an ADC map and should not be mistaken for tumour. aEuro cent Susceptibility artefacts on rectal DWI are an important potential pitfall. aEuro cent T2 shine-through on rectal DWI is an important potential pitfall. aEuro cent These pitfalls are useful to teach non-experts how to interpret rectal DW