ABSTRACT
BACKGROUND: HIV-1 can be inhibited by RNA interference in vitro through the expression of short hairpin RNAs (shRNAs) that target conserved genome sequences. In silico shRNA design for HIV has lacked a detailed study of virus variability constituting a possible breaking point in a clinical setting. We designed shRNAs against HIV-1 considering the variability observed in naïve and drug-resistant isolates available at public databases. METHODS: A Bioperl-based algorithm was developed to automatically scan multiple sequence alignments of HIV, while evaluating the possibility of identifying dominant and subdominant viral variants that could be used as efficient silencing molecules. Student t-test and Bonferroni Dunn correction test were used to assess statistical significance of our findings. RESULTS: Our in silico approach identified the most common viral variants within highly conserved genome regions, with a calculated free energy of ≥ -6.6 kcal/mol. This is crucial for strand loading to RISC complex and for a predicted silencing efficiency score, which could be used in combination for achieving over 90% silencing. Resistant and naïve isolate variability revealed that the most frequent shRNA per region targets a maximum of 85% of viral sequences. Adding more divergent sequences maintained this percentage. Specific sequence features that have been found to be related with higher silencing efficiency were hardly accomplished in conserved regions, even when lower entropy values correlated with better scores. We identified a conserved region among most HIV-1 genomes, which meets as many sequence features for efficient silencing. CONCLUSIONS: HIV-1 variability is an obstacle to achieving absolute silencing using shRNAs designed against a consensus sequence, mainly because there are many functional viral variants. Our shRNA cocktail could be truly effective at silencing dominant and subdominant naïve viral variants. Additionally, resistant isolates might be targeted under specific antiretroviral selective pressure, but in both cases these should be tested exhaustively prior to clinical use.
Subject(s)
Computational Biology/methods , HIV-1/genetics , RNA Interference , RNA, Small Interfering/genetics , Conserved Sequence , Drug Resistance, Viral/genetics , Genetic Variation , HIV Infections/virology , Humans , Models, Molecular , Mutation/genetics , Protein Structure, Tertiary , RNA, Small Interfering/chemistryABSTRACT
Se practicó adrenalectomía laparoscópica a una paciente femenina de 49 años de edad, con diagnóstico de tumor suprarrenal derecho con hiperaldosteronismo primario. El abordaje que se utilizó fue el laparoscópico transabdominal con cuatro puertos de trabajo. La paciente egresó en buenas condiciones, con mejoría de sus comorbilidades, sin complicaciones...(AU)
Subject(s)
Humans , Female , Adult , Middle Aged , Adrenalectomy/methods , Laparoscopy/statistics & numerical data , Hyperaldosteronism/diagnosis , Hyperaldosteronism/surgery , Adrenal Gland Diseases/diagnosis , Adrenal Gland Diseases/surgery , Adrenal Glands/surgery , Aldosterone/diagnosisABSTRACT
Se practicó adrenalectomía laparoscópica a una paciente femenina de 49 años de edad, con diagnóstico de tumor suprarrenal derecho con hiperaldosteronismo primario. El abordaje que se utilizó fue el laparoscópico transabdominal con cuatro puertos de trabajo. La paciente egresó en buenas condiciones, con mejoría de sus comorbilidades, sin complicaciones...