Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.     

Mechanism of Perfluoroalkyl Halide Toxicity: Catalysis of Perfluoroalkylation by Reduced Forms of Cobalamin (Vitamin B12)

Perfluoroalkyl halides (PFHs) are synthetic products widely used in various fields. Perfluorooctyl bromide (PFB) is used in medicine as a component of blood substitutes and for artificial lung ventilation. In both cases, it is considered a completely inert compound acting as a solvent for oxygen. However, there are many reports of PFH-induced intoxication, including lethal cases. Mechanisms underlying toxic effects of this compound remain unknown. In this study, we demonstrate that the reduced form of cobalamin (vitamin B12) typical for B12-dependent enzymes can catalyze the reactions of perfluoroalkylation, aromatic substitution, or addition by double bonds. Synthesis of perfluoro derivatives from PFHs during catalysis by cob(I)alamin-like super nucleophiles is a new possible mechanism responsible for in vivo formation of highly toxic compounds from "chemically inert" substances widely used in medicine. Catalytic perfluoroalkylation might possibly contribute to nitric oxide depletion and modulation of activity of guanylate cyclase, cytochromes, NO-synthases, and other heme-containing proteins.     

AmylPepPred: Amyloidogenic Peptide Prediction tool

We present an efficient computational architecture designed using supervised machine learning model to predict amyloid fibril forming protein segments, named AmylPepPred. The proposed prediction model is based on bio-physio-chemical properties of primary sequences and auto-correlation function of their amino acid indices. AmylPepPred provides a user friendly web interface for the researchers to easily observe the fibril forming and non-fibril forming hexmers in a given protein sequence. We expect that this stratagem will be highly encouraging in discovering fibril forming regions in proteins thereby benefit in finding therapeutic agents that specifically aim these sequences for the inhibition and cure of amyloid illnesses.

Availability

AmylPepPred is available freely for academic use at www.zoommicro.in/amylpeppred     

Nicotine consumption before and during pregnancy affects not only newborn size but also birth modus

The associations between cigarette smoking before and during pregnancy and maternal body size (pre-pregnancy weight status, end of pregnancy weight status, weight gain during pregnancy) and newborn size (birth weight, length, head circumference, arcomial circumference), as well as birth modus, were tested in 7803 single full-term births in Vienna. Nicotine consumption before and during pregnancy was found to be associated with smaller and lighter newborns, although maternal weight status and weight gain during pregnancy was significantly higher in smokers. Furthermore, a higher incidence of Caesarean sections was found in smokers. A reduction in the number of daily smoked cigarettes was associated with a lower percentage of low weight newborns (<2500 g).     

Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection

Human immunodeficiency virus type 1 (HIV-1) isolates from 20 chronically infected patients who participated in a structured treatment interruption (STI) trial were studied to determine whether viral fitness influences reestablishment of viremia. Viruses derived from individuals who spontaneously controlled viremia had significantly lower in vitro replication capacities than viruses derived from individuals that did not control viremia after interruption of antiretroviral therapy (ART), and replication capacities correlated with pre-ART and post-STI viral set points. Of note, no clinically relevant improvement of viral loads upon STI occurred. Virus isolates from controlling and noncontrolling patients were indistinguishable in terms of coreceptor usage, genetic subtype, and sensitivity to neutralizing antibodies. In contrast, viruses from controlling patients exhibited increased sensitivity to inhibition by chemokines. Sensitivity to inhibition by RANTES correlated strongly with slower replication kinetics of the virus isolates, suggesting a marked dependency of these virus isolates on high coreceptor densities on the target cells. In summary, our data indicate that viral fitness is a driving factor in determining the magnitude of viral rebound and viral set point in chronic HIV-1 infection, and thus fitness should be considered as a parameter influencing the outcome of therapeutic intervention in chronic infection.     

Adjunctive passive immunotherapy in human immunodeficiency virus type 1-infected individuals treated with antiviral therapy during acute and early infection

Three neutralizing monoclonal antibodies (MAbs), 2G12, 2F5, and 4E10, with activity in vitro and in vivo were administered in an open-label, nonrandomized, proof-of-concept study to attempt to prevent viral rebound after interruption of antiretroviral therapy (ART). Ten human immunodeficiency virus type 1-infected individuals identified and treated with ART during acute and early infection were enrolled. The first six patients were administered 1.0 g of each of the three MAbs per infusion. The remaining four patients received 2G12 at 1.0 g/infusion and 2.0 g/infusion of 2F5 and 4E10. The MAbs were well tolerated. Grade I post-partial thromboplastin time prolongations were noted. Viral rebound was observed in 8/10 subjects (28 to 73 days post-ART interruption), and 2/10 subjects remained aviremic over the course of the study. In seven of eight subjects with viral rebound, clear resistance to 2G12 emerged, whereas reductions in the susceptibilities of plasma-derived recombinant viruses to 2F5 and 4E10 were neither sustained nor consistently measured. Viral rebound was associated with a preferential depletion of CD4(+) T cells within the gastrointestinal tract. Though safe, the use of MAbs generally delayed, but did not prevent, virologic rebound. Consideration should be given to further pilot studies with alternative combinations of MAbs and perhaps additional novel treatment modalities.     

Structure of chicken plasma retinol-binding protein.

The crystal structure of the specific carrier of retinol (retinol-binding protein, RBP) purified from chicken plasma has been determined (space group P2(1)2(1)2(1), with a=46.06(5) A, b=53.56(6) A, c=73.41(8) A, and one protein molecule in the asymmetric unit). Despite being obtained from a species phylogenetically distant from mammals, chicken holoRBP has an overall structure that closely resembles the previously determined structures of mammalian holoRBPs. The lack in chicken RBP of eight carboxy-terminal amino acid residues characteristic of mammalian RBPs does not significantly affect the protein structure. A distinctive feature of the avian protein is a better definition of the loop 63-67, close to the opening of the beta-barrel cavity accommodating the retinol molecule, which is rather disordered in the structures of mammalian RBPs.     

Liquid- and Air-Filled Catheters without Balloon as an Alternative to the Air-Filled Balloon Catheter for Measurement of Esophageal Pressure

Background

Measuring esophageal pressure (P_es) using an air-filled balloon catheter (BC) is the common approach to estimate pleural pressure and related parameters. However, P_es is not routinely measured in mechanically ventilated patients, partly due to technical and practical limitations and difficulties. This study aimed at comparing the conventional BC with two alternative methods for P_es measurement, liquid-filled and air-filled catheters without balloon (LFC and AFC), during mechanical ventilation with and without spontaneous breathing activity. Seven female juvenile pigs (32–42 kg) were anesthetized, orotracheally intubated, and a bundle of an AFC, LFC, and BC was inserted in the esophagus. Controlled and assisted mechanical ventilation were applied with positive end-expiratory pressures of 5 and 15 cmH₂O, and driving pressures of 10 and 20 cmH₂O, in supine and lateral decubitus.

Main Results

Cardiogenic noise in BC tracings was much larger (up to 25% of total power of P_es signal) than in AFC and LFC (<3%). Lung and chest wall elastance, pressure-time product, inspiratory work of breathing, inspiratory change and end-expiratory value of transpulmonary pressure were estimated. The three catheters allowed detecting similar changes in these parameters between different ventilation settings. However, a non-negligible and significant bias between estimates from BC and those from AFC and LFC was observed in several instances.

Conclusions

In anesthetized and mechanically ventilated pigs, the three catheters are equivalent when the aim is to detect changes in P_es and related parameters between different conditions, but possibly not when the absolute value of the estimated parameters is of paramount importance. Due to a better signal-to-noise ratio, and considering its practical advantages in terms of easier calibration and simpler acquisition setup, LFC may prove interesting for clinical use.