microRNA-122 stimulates translation of hepatitis C virus RNA

Hepatitis C virus (HCV) is a positive strand RNA virus that propagates primarily in the liver. We show here that the liver-specific microRNA-122 (miR-122), a member of a class of small cellular RNAs that mediate post-transcriptional gene regulation usually by repressing the translation of mRNAs through interaction with their 3′-untranslated regions (UTRs), stimulates the translation of HCV. Sequestration of miR-122 in liver cell lines strongly reduces HCV translation, whereas addition of miR-122 stimulates HCV translation in liver cell lines as well as in the non-liver HeLa cells and in rabbit reticulocyte lysate. The stimulation is conferred by direct interaction of miR-122 with two target sites in the 5′-UTR of the HCV genome. With a replication-defective NS5B polymerase mutant genome, we show that the translation stimulation is independent of viral RNA synthesis. miR-122 stimulates HCV translation by enhancing the association of ribosomes with the viral RNA at an early initiation stage. In conclusion, the liver-specific miR-122 may contribute to HCV liver tropism at the level of translation

Structures Related to the Emplacement of Shallow-Level Intrusions

A systematic view of the vast nomenclature used to describe the structures of shallow-level intrusions is presented here. Structures are organised in four main groups, according to logical breaks in the timing of magma emplacement, independent of the scales of features: (1) Intrusion-related structures, formed as the magma is making space and then develops into its intrusion shape; (2) Magmatic flow-related structures, developed as magma moves with suspended crystals that are free to rotate; (3) Solid-state, flow-related structures that formed in portions of the intrusions affected by continuing flow of nearby magma, therefore considered to have a syn-magmatic, non-tectonic origin; (4) Thermal and fragmental structures, related to creation of space and impact on host materials. This scheme appears as a rational organisation, helpful in describing and interpreting the large variety of structures observed in shallow-level intrusions

Envelope Deglycosylation Enhances Antigenicity of HIV-1 gp41 Epitopes for Both Broad Neutralizing Antibodies and Their Unmutated Ancestor Antibodies

The HIV-1 gp41 envelope (Env) membrane proximal external region (MPER) is an important vaccine target that in rare subjects can elicit neutralizing antibodies. One mechanism proposed for rarity of MPER neutralizing antibody generation is lack of reverted unmutated ancestor (putative naive B cell receptor) antibody reactivity with HIV-1 envelope. We have studied the effect of partial deglycosylation under non-denaturing (native) conditions on gp140 Env antigenicity for MPER neutralizing antibodies and their reverted unmutated ancestor antibodies. We found that native deglycosylation of clade B JRFL gp140 as well as group M consensus gp140 Env CON-S selectively increased the reactivity of Env with the broad neutralizing human mAbs, 2F5 and 4E10. Whereas fully glycosylated gp140 Env either did not bind (JRFL), or weakly bound (CON-S), 2F5 and 4E10 reverted unmutated ancestors, natively deglycosylated JRFL and CON-S gp140 Envs did bind well to these putative mimics of naive B cell receptors. These data predict that partially deglycoslated Env would bind better than fully glycosylated Env to gp41-specific naïve B cells with improved immunogenicity. In this regard, immunization of rhesus macaques demonstrated enhanced immunogenicity of the 2F5 MPER epitope on deglyosylated JRFL gp140 compared to glycosylated JRFL gp140. Thus, the lack of 2F5 and 4E10 reverted unmutated ancestor binding to gp140 Env may not always be due to lack of unmutated ancestor antibody reactivity with gp41 peptide epitopes, but rather, may be due to glycan interference of binding of unmutated ancestor antibodies of broad neutralizing mAb to Env gp41

Data Mining the Brain to Decode the Mind

In recent years, neuroscience has begun to transform itself into a “big data” enterprise with the importation of computational and statistical techniques from machine learning and informatics. In addition to their translational applications such as brain-computer interfaces and early diagnosis of neuropathology, these tools promise to advance new solutions to longstanding theoretical quandaries. Here I critically assess whether these promises will pay off, focusing on the application of multivariate pattern analysis (MVPA) to the problem of reverse inference. I argue that MVPA does not inherently provide a new answer to classical worries about reverse inference, and that the method faces pervasive interpretive problems of its own. Further, the epistemic setting of MVPA and other decoding methods contributes to a potentially worrisome shift towards prediction and away from explanation in fundamental neuroscience

Multiple Signals Converge on a Differentiation MAPK Pathway

An important emerging question in the area of signal transduction is how information from different pathways becomes integrated into a highly coordinated response. In budding yeast, multiple pathways regulate filamentous growth, a complex differentiation response that occurs under specific environmental conditions. To identify new aspects of filamentous growth regulation, we used a novel screening approach (called secretion profiling) that measures release of the extracellular domain of Msb2p, the signaling mucin which functions at the head of the filamentous growth (FG) MAPK pathway. Secretion profiling of complementary genomic collections showed that many of the pathways that regulate filamentous growth (RAS, RIM101, OPI1, and RTG) were also required for FG pathway activation. This regulation sensitized the FG pathway to multiple stimuli and synchronized it to the global signaling network. Several of the regulators were required for MSB2 expression, which identifies the MSB2 promoter as a target “hub” where multiple signals converge. Accessibility to the MSB2 promoter was further regulated by the histone deacetylase (HDAC) Rpd3p(L), which positively regulated FG pathway activity and filamentous growth. Our findings provide the first glimpse of a global regulatory hierarchy among the pathways that control filamentous growth. Systems-level integration of signaling circuitry is likely to coordinate other regulatory networks that control complex behaviors

Carbon monoxide and respiratory symptoms in young adult passive smokers: A pilot study comparing waterpipe to cigarette

Objectives: Studies have correlated second hand smoke (SHS) with many diseases, especially respiratory effects. The goal of this study was to measure the impact of SHS on the respiratory symptoms and exhaled carbon monoxide. Material and Methods: The study population consisted of 50 young workers in restaurants serving waterpipes, 48 university students who sit frequently in the university cafeteria where cigarette smoking is allowed and 49 university students spending time in places where smoking is not allowed. Subjects completed questionnaires on socio-demographic characteristics, respiratory symptoms and exposure to SHS. Exhaled carbon monoxide levels were measured. ANOVA and Chi-square tests were used when applicable as well as linear and logistic regression analysis. Results: Exposure to cigarette smoke in university (adjusted odds ratio (ORa) = 6.06) and occupational exposure to waterpipe smoke (ORa = 7.08) were predictors of chronic cough. Being married (ORa = 6.40), living near a heavy traffic road (ORa = 9.49) or near a local power generator (ORa = 7.54) appeared responsible for chronic sputum production. Moreover, predictors of chronic allergies were: being male (ORa = 7.81), living near a local power generator (ORa = 5.52) and having a family history of chronic respiratory diseases (ORa = 17.01). Carbon monoxide levels were augmented by the number of weekly hours of occupational exposure to waterpipe smoke (β = 1.46) and the number of daily hours of exposure to cigarette smoke (β = 1.14). Conclusions: In summary, young non-smoker subjects demonstrated more chronic cough and elevated carbon monoxide levels when exposed to SHS while the effect of waterpipe was even more evident

Structural rearrangements maintain the Glycan Shield of an HIV-1 envelope trimer after the loss of a glycan

The HIV-1 envelope (Env) glycoprotein is the primary target of the humoral immune response and a critical vaccine candidate. However, Env is densely glycosylated and thereby substantially protected from neutralisation. Importantly, glycan N301 shields V3 loop and CD4 binding site epitopes from neutralising antibodies. Here, we use molecular dynamics techniques to evaluate the structural rearrangements that maintain the protective qualities of the glycan shield after the loss of glycan N301. We examined a naturally occurring subtype C isolate and its N301A mutant; the mutant not only remained protected against neutralising antibodies targeting underlying epitopes, but also exhibited an increased resistance to the VRC01 class of broadly neutralising antibodies. Analysis of this mutant revealed several glycans that were responsible, independently or through synergy, for the neutralisation resistance of the mutant. These data provide detailed insight into the glycan shield’s ability to compensate for the loss of a glycan, as well as the cascade of glycan movements on a protomer, starting at the point mutation, that affects the integrity of an antibody epitope located at the edge of the diminishing effect. These results present key, previously overlooked, considerations for HIV-1 Env glycan research and related vaccine studies.IS

Prime-boost immunization of rabbits with HIV-1 gp120 elicits potent neutralization activity against a primary viral isolate

<div><p>Development of a vaccine for HIV-1 requires a detailed understanding of the neutralizing antibody responses that can be experimentally elicited to difficult-to-neutralize primary isolates. Rabbits were immunized with the gp120 subunit of HIV-1 JR-CSF envelope (Env) using a DNA-prime protein-boost regimen. We analyzed five sera that showed potent autologous neutralizing activity (IC50s at ∼10³ to 10⁴ serum dilution) against pseudoviruses containing Env from the primary isolate JR-CSF but not from the related isolate JR-FL. Pseudoviruses were created by exchanging each variable and constant domain of JR-CSF gp120 with that of JR-FL or with mutations in putative N-glycosylation sites. The sera contained different neutralizing activities dependent on C3 and V5, C3 and V4, or V4 regions located on the glycan-rich outer domain of gp120. All sera showed enhanced neutralizing activity toward an Env variant that lacked a glycosylation site in V4. The JR-CSF gp120 epitopes recognized by the sera are generally distinct from those of several well characterized mAbs (targeting conserved sites on Env) or other type-specific responses (targeting V1, V2, or V3 variable regions). The activity of one serum requires specific glycans that are also important for 2G12 neutralization and this serum blocked the binding of 2G12 to gp120. Our findings show that different fine specificities can achieve potent neutralization of HIV-1, yet this strong activity does not result in improved breadth.</p> </div