Iodouracil-mediated photocrosslinking of DNA to EcoRII restriction endonuclease in catalytic conditions

We used a XeCl excimer laser with 50 ns pulses, a frequency of 0.3 Hz and a wavelength of 308 mn in appropriate conditions for the photocrosslinking of EcoRII restriction endonuclease to a 14-mer DNA duplex, containing a 5-iodo-2′-deoxyuridine residue (IdU). IdU replaced the thymidine residue within the EcoRII recognition sequence 5′-CCT/AGG. The binding of EcoRII endonuclease to the IdU-containing DNA duplex was analyzed by gel retardation assay in the presence of Ca2+ or Mg2+ ions. Photocrosslinking of EcoRII to the IdU-containing DNA duplex occurred in a pre-reactive complex formed in the presence of Ca2+ ions. Photocrosslinking yields as a function of time and UV-laser light intensity were studied.We thank Professor Alexander Yu. Borisov for valuable discussions and Robin Rycroft for assistance in preparation of the manuscript. We are grateful to Professor Ashok Bhagwat for providing us with the pR224 plasmid containing the ecoRII gene. This study was supported by the Russian Foundation of Fundamental Investigation (project no. 01–04–48637).Peer reviewe

DNA-controlled assembly of protein-modified gold nanocrystals

The controlled assembly in solution of gold nanocrystals modified by attachment of complementary protein-DNA conjugates is described. The size of the aggregates formed can be controlled by the addition of single-stranded DNA, which quickly terminates the assembly process. The rate of formation of the aggregates can also be controlled by varying the salt concentration. Consequently, two distinct regimes of aggregation kinetics are observed. At low salt concentrations, aggregation is shown to be dependent on the rate of duplex formation between the modified gold nanocrystals, i.e., reaction-limited. At higher salt concentrations, aggregation is shown to be dependent only on the rate of diffusion of the nanocrystals, i.e., diffusion-limited. The results presented provide important insights into the rates of formation of nanocrystal assemblies. Moreover, the approach adopted is modular, requiring only the relevant biotin linker chemistry to be developed for a given nanoparticle, while also precluding unfavorable interactions between the DNA and the streptavidin-coated nanoparticle. The ability to control the rate of formation and size of nanocrystal aggregates assembled is important new knowledge. Application of this knowledge will inform future studies of nanocrystal assembly in solution involving different types of nanocrystals, which is of increasing technological significance.This research was supported by a grant from the Petroleum Research Fund (Grant No. PRF# 32879-ACS). The Authors also thank Dr. Hakan Rensmo for helpful discussions and express their gratitude for the services provided by D. Cottell and the staff at the Electron Microscopy Centre, National University of Ireland, Dublin.Peer reviewe

BCN Rocks: aprendiendo geología urbana a través de una aplicación App interactiva

BCN Rocks is an application (App) for personal mobile devices (Android and iOS versions) suitable for secondary and high school students as well as people without background in Earth Sciences. The main objective of this App is to learn geology using the city facades and pavements of two emblematic spaces of the city of Barcelona, the Passeig de Gràcia and the Barri Gòtic. The application has three main sections (ELEMENTS, EXPLORE, and LABORATORY) that are intended to satisfy the different needs of users. In the first section, Elements, the user will find all the information about rocks forming the selected buildings as well as a brief explanation about the history and architecture of each edifice. The second section, Explore, aims to arise the curiosity of users. In this sense, several routes are proposed according to different criteria including geographic position and age of the edifices. Finally, the third section, Laboratory, allows all users to investigate several geological aspects by means of interactive experiments.Este trabajo se enmarca en un proyecto financiado por la Fundación Española para la Ciencia y la Tecnología, FECYT (ref. 8524) en el que ha participado la Universitat de Barcelona, el Instituto de Ciencias de la Tierra Jaume Almera del Consejo Superior de Investigaciones Científicas (ICTJA-CSIC) y la empresa FUSTA. AG agradece su contrato Ramón y Cajal (RYC-2012-11024).Peer Reviewe

Development of biosensors for detection of SARS-CoV-2 virus by Triplex Enhanced Nucleic Acid Detection Assay (TENADA).

SARS-CoV-2, a positive-strand RNA virus has caused devastating effects. The standard method for COVID diagnosis is based on polymerase chain reaction (PCR). The method needs expensive reagents and equipment and well-trained personnel and takes a few hours to be completed. The search for faster solutions has led to the development of immunological assays based on antibodies that recognize the viral proteins that are faster and do not require any special equipment. Here we explore an innovative analytical approach based on the sandwich oligonucleotide hybridization which can be adapted to several biosensing devices. PolyPurine Reverse Hoogsteen hairpins (PPRHs) oligonucleotides that form high affinity triplexes with the polypyrimidine target sequences are used for the efficient capture of the viral genome. Then, a second labelled oligonucleotide is used to detect the formation of a trimolecular complex in a similar way than antigen tests do. The limit of detection is around 0.01 nM (a few femtomoles) without the use of any amplification steps. The Triplex Enhanced Nucleic Acid Detection Assay (TENADA) can be readily adapted for the detection of any pathogen requiring only the knowledge of the pathogen genome sequence

Barcelona Rocks, a mobile app to learn geology in your city

Barcelona Rocks is an application for personal mobile devices suitable for secondary and high school students as well as the general public without a solid background in Earth Sciences. The main objective of this app is to teach Geology using as learning resource our city façades and pavements. Additionally, Barcelona Rocks provides a short explanation about the significance of the appearance of the different rock types at the different historical periods of the city. Although it has been designed as a playful learning resource for secondary school students, the level of knowledge also allows bringing some basic concepts and principles of Earth Sciences to the general public, irrespective of age.Peer Reviewe

Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa

HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed to characterize the HIV-1 IN gene in a South African context and identify resistance-associated mutations (RAMs) against available first and second generation Integrase strand-transfer inhibitors (InSTIs). We performed genetic analyses on 91 treatment-naïve HIV-1 infected patients, as well as 314 treatmentnaive South African HIV-1 IN-sequences, downloaded from Los Alamos HIV Sequence Database. Genotypic analyses revealed the absence of major RAMs in the cohort collected before the broad availability of combination antiretroviral therapy (cART) and INSTI in South Africa, however, occurred at a rate of 2.85% (9/314) in database derived sequences. RAMs were present at IN-positions 66, 92, 143, 147 and 148, all of which may confer resistance to Raltegravir (RAL) and Elvitegravir (EVG), but are unlikely to affect second-generation Dolutegravir (DTG), except mutations in the Q148 pathway. Furthermore, protein modeling showed, naturally occurring polymorphisms impact the stability of the intasome-complex and therefore may contribute to an overall potency against InSTIs. Our data suggest the prevalence of InSTI RAMs, against InSTIs, is low in South Africa, but natural polymorphisms and subtype-specific differences may influence the effect of individual treatment regimens

Yaws re-emergence and bacterial drug resistance selection after mass administration of azithromycin: a genomic epidemiology investigation.

BACKGROUND: In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum subspecies pertenue (T p pertenue). Here, we analyse genomic changes in the bacterial population using samples collected during the study. METHODS: We did whole bacterial genome sequencing directly on DNA extracted from 37 skin lesion swabs collected from patients on Lihir Island, Papua New Guinea, between April 1, 2013, and Nov 1, 2016. We produced phylogenies and correlated these with spatiotemporal information to investigate the source of new cases and the emergence of five macrolide-resistant cases. We used deep amplicon sequencing of surveillance samples to assess the presence of minority macrolide-resistant populations. FINDINGS: We recovered 20 whole T p pertenue genomes, and phylogenetic analysis showed that the re-emerging JG8 sequence type was composed of three bacterial sublineages characterised by distinct spatiotemporal patterns. Of five patients with resistant T p pertenue, all epidemiologically linked, we recovered genomes from three and found no variants. Deep sequencing showed that before treatment, the index patient had fixed macrolide-sensitive T p pertenue, whereas the post-treatment sample had a fixed resistant genotype, as did three of four contact cases. INTERPRETATION: In this study, re-emergence of yaws cases was polyphyletic, indicating multiple epidemiological sources. However, given the genomic and epidemiological linkage of resistant cases and the rarity of resistance alleles in the general population, azithromycin resistance is likely to have evolved only once in this study, followed by onward dissemination. FUNDING: Wellcome and Provincial Deputation of Barcelona