Conformational Dynamics of the HIV-Vif Protein Complex.

Human immunodeficiency virus-1 viral infectivity factor (Vif) is an intrinsically disordered protein responsible for the ubiquitination of the APOBEC3 (A3) antiviral proteins. Vif folds when it binds Cullin-RING E3 ligase 5 and the transcription cofactor CBF-ß. A five-protein complex containing the substrate receptor (Vif, CBF-ß, Elongin-B, Elongin-C (VCBC)) and Cullin5 (CUL5) has a published crystal structure, but dynamics of this VCBC-CUL5 complex have not been characterized. Here, we use molecular dynamics (MD) simulations and NMR to characterize the dynamics of the VCBC complex with and without CUL5 and an A3 protein bound. Our simulations show that the VCBC complex undergoes global dynamics involving twisting and clamshell opening of the complex, whereas VCBC-CUL5 maintains a more static conformation, similar to the crystal structure. This observation from MD is supported by methyl-transverse relaxation-optimized spectroscopy NMR data, which indicates that the VCBC complex without CUL5 is dynamic on the µs-ms timescale. Our NMR data also show that the VCBC complex is more conformationally restricted when bound to the antiviral APOBEC3F (one of the A3 proteins), consistent with our MD simulations. Vif contains a flexible linker region located at the hinge of the VCBC complex, which changes conformation in conjunction with the global dynamics of the complex. Like other substrate receptors, VCBC can exist alone or in complex with CUL5 and other proteins in cells. Accordingly, the VCBC complex could be a good target for therapeutics that would inhibit full assembly of the ubiquitination complex by stabilizing an alternate VCBC conformation.

Concise, Simple, and Not Wrong: In Search of a Short-Hand Interpretation of Statistical Significance.

One challenge when communicating science to practitioners and the general public is accurately representing statistical results. In particular, describing the meaning of statistical significance to a non-scientific audience is especially difficult given the technical nature of a correct definition. Correct interpretations of statistical significance can be unintuitive, nuanced, and use unfamiliar technical language. As a result, when researchers are tasked with providing short and understandable interpretations of statistical significance it can be tempting to default to convenient but incorrect interpretations. In the current paper, we offer a concise, simple, and correct interpretation of statistical significance that is suitable for communications targeting a general audience.

A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability.

The dicistrovirus, Cricket paralysis virus (CrPV) encodes an RNA interference (RNAi) suppressor, 1A, which modulates viral virulence. Using the Drosophila model, we combined structural, biochemical, and virological approaches to elucidate the strategies by which CrPV-1A restricts RNAi immunity. The atomic resolution structure of CrPV-1A uncovered a flexible loop that interacts with Argonaute 2 (Ago-2), thereby inhibiting Ago-2 endonuclease-dependent immunity. Mutations disrupting Ago-2 binding attenuates viral pathogenesis in wild-type but not Ago-2-deficient flies. CrPV-1A also contains a BC-box motif that enables the virus to hijack a host Cul2-Rbx1-EloBC ubiquitin ligase complex, which promotes Ago-2 degradation and virus replication. Our study uncovers a viral-based dual regulatory program that restricts antiviral immunity by direct interaction with and modulation of host proteins. While the direct inhibition of Ago-2 activity provides an efficient mechanism to establish infection, the recruitment of a ubiquitin ligase complex enables CrPV-1A to amplify Ago-2 inactivation to restrict further antiviral RNAi immunity.

Prediction Interval: What to Expect When You're Expecting A Replication.

A challenge when interpreting replications is determining whether the results of a replication "successfully" replicate the original study. Looking for consistency between two studies is challenging because individual studies are susceptible to many sources of error that can cause study results to deviate from each other and the population effect in unpredictable directions and magnitudes. In the current paper, we derive methods to compute a prediction interval, a range of results that can be expected in a replication due to chance (i.e., sampling error), for means and commonly used indexes of effect size: correlations and d-values. The prediction interval is calculable based on objective study characteristics (i.e., effect size of the original study and sample sizes of the original study and planned replication) even when sample sizes across studies are unequal. The prediction interval provides an a priori method for assessing if the difference between an original and replication result is consistent with what can be expected due to sample error alone. We provide open-source software tools that allow researchers, reviewers, replicators, and editors to easily calculate prediction intervals.

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.

HIV-1 encodes the accessory protein Vif, which hijacks a host Cullin-RING ubiquitin ligase (CRL) complex as well as the non-canonical cofactor CBFß, to antagonize APOBEC3 antiviral proteins. Non-canonical cofactor recruitment to CRL complexes by viral factors, to date, has only been attributed to HIV-1 Vif. To further study this phenomenon, we employed a comparative approach combining proteomic, biochemical, structural, and virological techniques to investigate Vif complexes across the lentivirus genus, including primate (HIV-1 and simian immunodeficiency virus macaque [SIVmac]) and non-primate (FIV, BIV, and MVV) viruses. We find that CBFß is completely dispensable for the activity of non-primate lentiviral Vif proteins. Furthermore, we find that BIV Vif requires no cofactor and that MVV Vif requires a novel cofactor, cyclophilin A (CYPA), for stable CRL complex formation and anti-APOBEC3 activity. We propose modular conservation of Vif complexes allows for potential exaptation of functions through the acquisition of non-CRL-associated host cofactors while preserving anti-APOBEC3 activity.

A mutually assured destruction mechanism attenuates light signaling in Arabidopsis.

After light-induced nuclear translocation, phytochrome photoreceptors interact with and induce rapid phosphorylation and degradation of basic helix-loop-helix transcription factors, such as PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), to regulate gene expression. Concomitantly, this interaction triggers feedback reduction of phytochrome B (phyB) levels. Light-induced phosphorylation of PIF3 is necessary for the degradation of both proteins. We report that this PIF3 phosphorylation induces, and is necessary for, recruitment of LRB [Light-Response Bric-a-Brack/Tramtrack/Broad (BTB)] E3 ubiquitin ligases to the PIF3-phyB complex. The recruited LRBs promote concurrent polyubiqutination and degradation of both PIF3 and phyB in vivo. These data reveal a linked signal-transmission and attenuation mechanism involving mutually assured destruction of the receptor and its immediate signaling partner.

Expectations for Replications: Are Yours Realistic?

Failures to replicate published psychological research findings have contributed to a "crisis of confidence." Several reasons for these failures have been proposed, the most notable being questionable research practices and data fraud. We examine replication from a different perspective and illustrate that current intuitive expectations for replication are unreasonable. We used computer simulations to create thousands of ideal replications, with the same participants, wherein the only difference across replications was random measurement error. In the first set of simulations, study results differed substantially across replications as a result of measurement error alone. This raises questions about how researchers should interpret failed replication attempts, given the large impact that even modest amounts of measurement error can have on observed associations. In the second set of simulations, we illustrated the difficulties that researchers face when trying to interpret and replicate a published finding. We also assessed the relative importance of both sampling error and measurement error in producing variability in replications. Conventionally, replication attempts are viewed through the lens of verifying or falsifying published findings. We suggest that this is a flawed perspective and that researchers should adjust their expectations concerning replications and shift to a meta-analytic mind-set.

Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G.

Cellular restriction factors help to defend humans against human immunodeficiency virus (HIV). HIV accessory proteins hijack at least three different Cullin-RING ubiquitin ligases, which must be activated by the small ubiquitin-like protein NEDD8, in order to counteract host cellular restriction factors. We found that conjugation of NEDD8 to Cullin-5 by the NEDD8-conjugating enzyme UBE2F is required for HIV Vif-mediated degradation of the host restriction factor APOBEC3G (A3G). Pharmacological inhibition of the NEDD8 E1 by MLN4924 or knockdown of either UBE2F or its RING-protein binding partner RBX2 bypasses the effect of Vif, restoring the restriction of HIV by A3G. NMR mapping and mutational analyses define specificity determinants of the UBE2F NEDD8 cascade. These studies demonstrate that disrupting host NEDD8 cascades presents a novel antiretroviral therapeutic approach enhancing the ability of the immune system to combat HIV.

Examining workgroup diversity effects: does playing by the (group-retention) rules help or hinder?

Group diversity researchers are often faced with the problem of calculating diversity indices for groups that are incomplete due to participant nonresponse. Because participant nonresponse may attenuate the correlations that are observed between group diversity scores and outcome variables, some researchers use group-retention rules based on within-group response rates. With this approach, only those groups that have a within-group response rate at, or higher than, the rate prescribed by the group-retention rule are retained for subsequent analyses. We conducted two sets of experiments using computer simulations to determine the usefulness of group-retention rules. We found that group-retention rules are not a substitute for a high response rate and may decrease the accuracy of observed relations, and consequently, we advise against their use in diversity research.

Two-dimensional affective space: a new approach to orienting the axes.

What are the constructs that underlie affective experiences? Some authors have suggested Valence and Activation, whereas others have suggested Positive Activation and Negative Activation-both approaches are represented by different axis orientations in traditional two-mode (People x Adjectives) factor analysis. The authors provide new evidence for this debate by using three-mode (People x Adjectives x Occasions) parallel factor (PARAFAC) analysis to determine the appropriate axes (and hence constructs) for representing affective experiences. Unlike traditional factor analysis, with PARAFAC different orientations of the axes fit the data differently so it is possible to determine the best fitting axes. In Study 1, the authors assessed the extent to which the PARAFAC procedure was able recover the axes defining a two-dimensional factor space under different conditions. In both Study 2 (N = 112) and Study 3 (N = 349), undergraduate students rated their emotional states on a variety of occasions. The best fitting axes for two-dimensional affective space were Valence and Activation in both studies. Exploration of higher dimensional solutions in Study 3 revealed a three-factor solution that, in addition to an activation factor, supported the separation of positive and negative emotions.

Celluloid angels: a research study of nurses in feature films 1900-2007.

AIM: This paper is a report of a study examining the influence on how nursing and nurses are portrayed in feature films made between 1900 and 2007, with a nurse as their main or a principle character and a story-line related specifically to nursing. BACKGROUND: Nurses and the nursing profession are frequently portrayed negatively or stereotypically in the media, with nurses often being portrayed as feminine and caring but not as leaders or professionals capable of autonomous practice. METHODS: A mixed method approach was used to examine feature films made in the Western world. Over 36,000 feature film synopses were reviewed (via CINAHL, ProQuest and relevant movie-specific literature) for the keywords 'nurse'/'nursing'. Identified films were analysed quantitatively to determine their country of production, genre, plot(s) and other relevant data, and qualitatively to identify the emergence of themes related to the image of nurses/nursing in films. FINDINGS: For the period from 1900 to 2007, 280 relevant feature films were identified. Most films were made in the United States of America or United Kingdom, although in recent years films have been increasingly produced in other countries. Early films portrayed nurses as self-sacrificial heroines, sex objects and romantics. More recent films increasingly portray them as strong and self-confident, professionals. CONCLUSION: Nurse-related films offer a unique insight into the image of nurses and how they have been portrayed. Nurses need to be aware of the impact the film industry has on how nurses and nursing are perceived and represented in feature films.

Assessing dissimilarity relations under missing data conditions: evidence from computer simulations.

The extensive research examining relations between group member dissimilarity and outcome measures has yielded inconsistent results. In the present research, the authors used computer simulations to examine the impact that a methodological feature of such research, participant nonresponse, can have on dissimilarity-outcome relations. Results suggest that using only survey responders to calculate dissimilarity typically results in underestimation of true dissimilarity effects and that these effects can occur even when response rates are high.

Delta and mu opioid receptors from the brain of a urodele amphibian, the rough-skinned newt Taricha granulosa: cloning, heterologous expression, and pharmacological characterization.

Two full-length cDNAs, encoding delta (delta) and mu (mu) opioid receptors, were cloned from the brain of the rough-skinned newt Taricha granulosa, complementing previous work from our laboratory describing the cloning of newt brain kappa (kappa) and ORL1 opioid receptors. The newt delta receptor shares 82% amino acid sequence identity with a frog delta receptor and lower (68-70%) identity with orthologous receptors cloned from mammals and zebrafish. The newt mu receptor shares 79% sequence identity with a frog mu receptor, 72% identity with mammalian mu receptors, and 66-69% identity with mu receptors cloned from teleost fishes. Membranes isolated from COS-7 cells transiently expressing the newt delta receptor possessed a single, high-affinity (Kd = 2.4 nM) binding site for the nonselective opioid antagonist [3H]naloxone. In competition binding assays, the newt delta receptor displayed highest affinity for Met-enkephalin, relatively low affinity for Leu-enkephalin, beta-endorphin, and [D-penicillamine, D-penicillamine] enkephalin (DPDPE) (a delta-selective agonist in mammals), and very low affinity for mu-, kappa-, or ORL1-selective agonists. COS-7 cells expressing the newt mu receptor also possessed a high-affinity (Kd = 0.44 nM) naloxone-binding site that showed highest affinity for beta-endorphin, moderate-to-low affinity for Met-enkephalin and Leu-enkephalin and DAMGO (a mu-selective agonist in mammals), and very low affinity for DPDPE and kappa- or ORL1-selective agonists. COS-7 cells expressing either receptor type (delta or mu) showed very high affinity (Kd = 0.1-0.3 nM) for the nonselective opioid antagonist diprenorphine. Taricha granulosa expresses the same four subtypes (delta, mu, kappa, and ORL1) of opioid receptors found in other vertebrate classes, but ligand selectivity appears less stringent in the newt than has been documented in mammals.