Mar Álvarez

Development of nanomechanical biosensors for detection of the pesticide DDT.

We report the use of a novel technique for detection of the organochlorine insecticide compound dichlorodiphenyltrichloroethane (DDT) by measuring the nanometer-scale bending of a microcantilever produced by differential surface stress. A synthetic hapten of the pesticide conjugated with bovine serum albumin (BSA) was covalently immobilised on the gold-coated side of the cantilever by using thiol self assembled monolayers. The immobilisation process is characterised by monitoring the cantilever deflection in real-time. Then specific detection is achieved by exposing the cantilever to a solution of a specific monoclonal antibody to the DDT hapten derivative. The specific binding of the antibodies on the cantilever sensitised side is measured with nanomolar sensitivity. Direct detection is proved by performing competitive assays, in which the cantilever is exposed to a mixed solution of the monoclonal antibody and DDT. The future prospects and limitations to be overcome for the application of nanomechanical sensors for pesticide detection are discussed.

Cell Cycle Control and HIV-1 Susceptibility Are Linked by CDK6-Dependent CDK2 Phosphorylation of SAMHD1 in Myeloid and Lymphoid Cells

Proliferating cells are preferentially susceptible to infection by retroviruses. Sterile α motif and HD domain–containing protein-1 (SAMHD1) is a recently described deoxynucleotide phosphohydrolase controlling the size of the intracellular deoxynucleotide triphosphate (dNTP) pool, a limiting factor for retroviral reverse transcription in noncycling cells. Proliferating (Ki67+) primary CD4+ T cells or macrophages express a phosphorylated form of SAMHD1 that corresponds with susceptibility to infection in cell culture. We identified cyclin-dependent kinase (CDK) 6 as an upstream regulator of CDK2 controlling SAMHD1 phosphorylation in primary T cells and macrophages susceptible to infection by HIV-1. In turn, CDK2 was strongly linked to cell cycle progression and coordinated SAMHD1 phosphorylation and inactivation. CDK inhibitors specifically blocked HIV-1 infection at the reverse transcription step in a SAMHD1-dependent manner, reducing the intracellular dNTP pool. Our findings identify a direct relationship between control of the cell cycle by CDK6 and SAMHD1 activity, which is important for replication of lentiviruses, as well as other viruses whose replication may be regulated by intracellular dNTP availability.

Nucleoside/nucleotide analog inhibitors of hepatitis B virus polymerase: mechanism of action and resistance

Hepatitis B virus (HBV) polymerase and human immunodeficiency virus (HIV) reverse transcriptase are structurally related. However, the HBV enzyme has a protein priming activity absent in the HIV enzyme. Approved nucleoside/nucleotide inhibitors of the HBV polymerase include lamivudine, adefovir, telbivudine, entecavir and tenofovir. Although most of them target DNA elongation, guanosine and adenosine analogs (e.g. entecavir and tenofovir, respectively) also impair protein priming. Major mutational patterns conferring nucleoside/nucleotide analog resistance include the combinations rtL180M/rtM204(I/V) (for lamivudine, entecavir, telbivudine and clevudine) and rtA181V/rtN236T (for adefovir and tenofovir). However, development of drug resistance is very slow for entecavir and tenofovir. Novel nucleoside/nucleotide analogs in advanced clinical trials include phosphonates similar to adefovir or tenofovir, and new tenofovir derivatives with improved pharmacological properties.

Antiretroviral therapy and drug resistance in human immunodeficiency virus type 2 infection

One to two million people worldwide are infected with the human immunodeficiency virus type 2 (HIV-2), with highest prevalences in West African countries, but also present in Western Europe, Asia and North America. Compared to HIV-1, HIV-2 infection undergoes a longer asymptomatic phase and progresses to AIDS more slowly. In addition, HIV-2 shows lower transmission rates, probably due to its lower viremia in infected individuals. There is limited experience in the treatment of HIV-2 infection and several antiretroviral drugs used to fight HIV-1 are not effective against HIV-2. Effective drugs against HIV-2 include nucleoside analogue reverse transcriptase (RT) inhibitors (e.g. zidovudine, tenofovir, lamivudine, emtricitabine, abacavir, stavudine and didanosine), protease inhibitors (saquinavir, lopinavir and darunavir), and integrase inhibitors (raltegravir, elvitegravir and dolutegravir). Maraviroc, a CCR5 antagonist blocking coreceptor binding during HIV entry, is active in vitro against CCR5-tropic HIV-2 but more studies are needed to validate its use in therapeutic treatments against HIV-2 infection. HIV-2 strains are naturally resistant to a few antiretroviral drugs developed to suppress HIV-1 propagation such as nonnucleoside RT inhibitors, several protease inhibitors and the fusion inhibitor enfuvirtide. Resistance selection in HIV-2 appears to be faster than in HIV-1. In this scenario, the development of novel drugs specific for HIV-2 is an important priority. In this review, we discuss current anti-HIV-2 therapies and mutational pathways leading to drug resistance.

Real-time profile of microcantilevers for sensing applications

An optical readout technique has been developed for real-time monitoring of the profile of microcantilever arrays for sensing applications. The technique is based on the automated two-dimensional scanning of a laser beam by using voice-coil actuators. Cantilever profiles are obtained with subnanometer resolution and a processing speed of about ten cantilevers per second. The technique is applied for real-time monitoring of the adsorption of the alkylthiol mercaptohexanol in an aqueous environment by using an array of five microcantilevers. Molecular adsorption produces a cantilever strain that significantly differs from the Stoney’s model. Main strain changes are strongly located near the cantilever clamping.

Surface vibration induced spatial ordering of periodic polymer patterns on a substrate.

We demonstrate the possibility of producing regular, long-range, spatially ordered polymer patterns without requiring the use of physical or chemical templating through the interfacial destabilization of a thin polymer film driven by surface acoustic waves (SAWs). The periodicity and spot size of the pattern are observed to be dependent on a single parameter, that is, the SAW frequency (or wavelength), therefore offering a rapid, simple, yet novel method for self-organized regular spatial polymer pattern formation that is far more tunable than conventional polymer patterning procedures.

Increased thermostability and fidelity of DNA synthesis of wild-type and mutant HIV-1 group O reverse transcriptases.

Reverse transcription coupled with DNA amplification has become a well-established and powerful molecular technique for studying ribonucleic acids. However, the efficiency of those reactions is largely dependent on the molecular properties of currently used reverse transcriptases (RTs). Engineered and natural RT variants with improved thermostability and fidelity of DNA synthesis should be of great utility in the amplification of RNA targets. In this study, we demonstrate that the wild-type (WT) HIV-1 group O (O_WT) RT shows increased thermostability in comparison with Moloney murine leukemia virus RT and a prototypic HIV-1 group M:subtype B (BH10_WT) RT, while rendering higher yields in reverse transcription PCRs that included a cDNA synthesis step performed at a high temperature range (57-69 degrees C). In addition, the O_WT RT showed 2.5-fold increased accuracy in M13 lacZalpha forward mutation assays in comparison with the BH10_WT RT. Unlike the BH10_WT enzyme, O_WT RT showed a very low error rate for frameshifts. Mutational hot spots induced by O_WT RT occurred at nucleotide runs, suggesting a dislocation-mediated mechanism for the generation of base substitutions. In HIV-1 group O RT, substituting Ile75 for Val rendered an enzyme that was 1.9 and 4.7 times more faithful than O_WT RT and BH10_WT RTs, respectively, in forward mutation assays. The mutant RT also showed increased misinsertion and mispair extension fidelity in kinetic assays. However, its mutational spectrum was similar to that obtained with the WT group O polymerase. V75I caused a loss of efficiency of reverse transcription PCR amplifications at 65 and 68 degrees C in comparison with O_WT RT. However, a double mutant devoid of RNase H activity (V75I/E478Q) was found to reverse-transcribe at temperatures as high as 68 degrees C, while maintaining the increased accuracy of the V75I mutant.

Scanning force microscopy three-dimensional modes applied to the study of the dielectric response of adsorbed DNA molecules

We have developed a set of working modes for scanning probe microscopy?(SPM), which generalizes the usual method of acquiring data. We call these modes three-dimensional?(3D) modes. Using these modes it is possible to measure typical SPM magnitudes, such as, for example, the tunnel current, the normal force and the amplitude or frequency of the cantilever oscillation, as a function of any other two magnitudes of the system: f(x1,x2). In this paper we present different examples of 3D modes. In particular, we have applied 3D modes to the study of the electrostatic interaction of co-adsorbed single walled carbon nanotubes and individual DNA molecules with a metallic scanning force microscopy tip. The data indicate that adsorbed DNA has a dielectric constant similar to that of the glass substrate.

Direct detection of protein biomarkers in human fluids using site-specific antibody immobilization strategies.

Design of an optimal surface biofunctionalization still remains an important challenge for the application of biosensors in clinical practice and therapeutic follow-up. Optical biosensors offer real-time monitoring and highly sensitive label-free analysis, along with great potential to be transferred to portable devices. When applied in direct immunoassays, their analytical features depend strongly on the antibody immobilization strategy. A strategy for correct immobilization of antibodies based on the use of ProLinker™ has been evaluated and optimized in terms of sensitivity, selectivity, stability and reproducibility. Special effort has been focused on avoiding antibody manipulation, preventing nonspecific adsorption and obtaining a robust biosurface with regeneration capabilities. ProLinker™-based approach has demonstrated to fulfill those crucial requirements and, in combination with PEG-derivative compounds, has shown encouraging results for direct detection in biological fluids, such as pure urine or diluted serum. Furthermore, we have implemented the ProLinker™ strategy to a novel nanoplasmonic-based biosensor resulting in promising advantages for its application in clinical and biomedical diagnosis.

Rapid production of protein-loaded biodegradable microparticles using surface acoustic waves

We present a straightforward and rapid surface acoustic wave (SAW) atomization-based technique for encapsulating proteins into 10 mum order particles composed of a biodegradable polymeric excipient, using bovine serum albumin (BSA) as an exemplar. Scans obtained from confocal microscopy provide qualitative proof of encapsulation and show the fluorescent conjugated protein to be distributed in a relatively uniform manner within the polymer shell. An ELISA assay of the collected particles demonstrates that the BSA survives the atomization, particle formation, and collection process with a yield of approximately 55%. The SAW atomization universally gave particles with a textured morphology, and increasing the frequency and polymer concentration generally gave smaller particles (to 3 mum average) with reduced porosity.