Characterising plant deubiquitinases with in vitro activity-based labelling and ubiquitin chain disassembly assays

Post-translational modification of proteins by ubiquitin is an essential cellular signaling mechanism in all eukaryotes. Ubiquitin is removed from target proteins by a wide range of deubiquitinase (DUB) enzymes with different activities and substrate specificities. Understanding how DUBs function in vitro is a vital first step to uncovering their cellular roles. Here, we provide protocols for the rapid analysis of DUB activity in vitro by activity-based labelling with the suicide probe, HA-ubiquitin vinyl sulfone (HA-UbVS), and ubiquitin chain disassembly assays. We have previously used these methods to analyse the activity of the Arabidopsis thaliana DUB, UBP6, but in principle, these protocols are applicable to any DUB of interest

Patterns of gene expression in schistosomes: localization by whole mount in situ hybridization

rom the identification of genes to the characterization of their functions and interactions. Developmental biologists have long used whole mount in situ hybridization (WISH) to determine gene expression patterns, as a vital tool for formulating and testing hypotheses about function. This paper describes the application of WISH to the study of gene expression in larval and adult schistosomes. Fixed worms were permeablized by proteinase K treatment for hybridization with digoxygenin-labelled RNA probes, with binding being detected by alkaline phosphatase-coupled anti-digoxygenin antibodies, and BM Purple substrate. Discrete staining patterns for the transcripts of the molecules Sm29, cathepsin L, antigen 10.3 and chorion were observed in the tegument cell bodies, gut epithelium, oesophageal gland and vitelline lobules, respectively, of adult worms. Transcripts of the molecules SGTP4, GP18-22 and cathepsin L were localized to tegument cell bodies and embryonic gut, respectively, of lung schistosomula. We also showed that Fast Red TR fluorescent substrate can refine the pattern of localization permitting use of confocal microscopy. We believe that method of WISH will find broad application, in synergy with other emerging post-genomic techniques, such as RNA interference, to studies focused at increasing our molecular understanding of schistosomes

Potential and realized nutrient resorption in serpentine and non-serpentine chaparral shrubs and trees

Low-nutrient adapted species have numerous mechanisms that aid in nutrient conservation. Hypothetically, species adapted to nutrient-poor soils should have tighter internal nutrient recycling, as evidenced by greater resorption. However, literature results are mixed. We suggest methodological factors may limit our understanding of this process. We hypothesized that plants adapted to serpentine soils would be more proficient in resorbing N and P than plants adapted to non-serpentine soils, although there would be differences among functional groups within each soil type. For six growing seasons, we sampled senescent leaf tissue from the dominant and co-dominant shrubs and trees found in serpentine and non-serpentine chaparral communities in the California Coast Range. Our study also explicitly included congener pairs found on both soil types. Most species were highly N proficient, but species adapted to serpentine soils were more P proficient. Surprisingly, two of the three potential N-fixing species were also highly N proficient. Evergreen Quercus congeners were more N proficient than their deciduous congener pairs, although there was no difference in P resorption proficiency. Overall, large inter-annual variation was observed among most species sampled, but at least in some years, maximum potential resorption likely was reached. However, climate (temperature and precipitation) was not strongly correlated with either N or P resorption proficiency. Our data suggest that controlling for phylogeny can aid in interpretation of resorption patterns. More importantly, our study clearly shows that resorption patterns can only be discerned through long-term datasets, of which few exist in the literature

Computer recommendations for an automatic approach and landing system for V/STOL aircraft. Volume 2 - Equations

Automatic approach and landing system for V/STOL aircraf

Transcriptional regulation by complex interplay between posttranslational modifications

Transcriptional reprogramming in response to developmental changes or environmental inputs is regulated by a wide variety of transcription factors and cofactors. In plants, the stability of many transcriptional regulators is mediated by the ubiquitin-mediated proteasome. Recent reports suggest that additional post-translational modifications modulate the ubiquitination and thus stability of transcriptional regulators. In addition to well-recognized phosphorylative control, particularly conjugation to the ubiquitin-like protein SUMO as well as thiol modification by nitric oxide to yield S-nitrosothiols, are emerging as key regulatory steps for governing protein ubiquitination in the nucleus. Complex interplay between these different post-translational modifications may provide robust control mechanisms to fine tune developmental and stress-responsive transcriptional programs

Delay Discounting is Associated with Treatment Response among Cocaine-Dependent Outpatients

Rationale—Delay discounting (DD) describes the rate at which reinforcers lose value as the temporal delay to their receipt increases. Steeper discounting has been positively associated with vulnerability to substance use disorders, including cocaine use disorders. Objectives—In the present study, we examined whether DD of hypothetical monetary reinforcers is associated with the duration of cocaine abstinence achieved among cocainedependent outpatients. Methods—Participants were 36 adults who were participating in a randomized controlled trial examining the efficacy of voucher-based contingency management (CM) using low-magnitude (N = 18) or high-magnitude (N = 18) voucher monetary values. Results—DD was associated with the number of continuous weeks of cocaine abstinence achieved, even after adjusting for treatment condition during the initial 12-week (t(33) = 2.48, p = .045) and entire recommended 24-week of treatment (t(33) = 2.40, p = .022). Participants who exhibited steeper discounting functions achieved shorter periods of abstinence in the Lowmagnitude voucher condition (12-week: t(16) = 2.48, p = .025; 24-week: t(16) = 2.68, p = .017), but not in the High-magnitude voucher condition (12-week: t(16) = 0.51, p = .618; 24-week: t(16) = 1.08, p = .298), although the interaction between DD and treatment condition was not significant (12-week: t(32) = −1.12, p = .271; 24-week: t(32) = −0.37, p = .712). Conclusions—These results provide further evidence on associations between DD and treatment response and extend those observations to a new clinical population (i.e., cocainedependent outpatients), while also suggesting that a more intensive intervention like the Highmagnitude CM condition may diminish this negative relationship between DD and treatment response

Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections

Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future

Accretion dynamics in the classical T Tauri star V2129 Oph

We analyze the photometric and spectroscopic variability of the classical T Tauri star V2129 Oph over several rotational cycles to test the dynamical predictions of magnetospheric accretion models. The photometric variability and the radial velocity variations in the photospheric lines can be explained by rotational modulation due to cold spots, while the radial velocity variations of the He I (5876 \AA) line and the veiling variability are due to hot spot rotational modulation. The hot and cold spots are located at high latitudes and about the same phase, but the hot spot is expected to sit at the chromospheric level, while the cold spot is at the photospheric level. Using the dipole+octupole magnetic-field configuration previously proposed in the literature for the system, we compute 3D MHD magnetospheric simulations of the star-disk system. We use the simulation's density, velocity and scaled temperature structures as input to a radiative transfer code, from which we calculate theoretical line profiles at all rotational phases. The theoretical profiles tend to be narrower than the observed ones, but the qualitative behavior and the observed rotational modulation of the H\alpha and H\beta emission lines are well reproduced by the theoretical profiles. The spectroscopic and photometric variability observed in V2129 Oph support the general predictions of complex magnetospheric accretion models with non-axisymmetric, multipolar fields.Comment: Accepted by Astronomy and Astrophysic

Controlled Trial of Nursing Interventions to Improve Health Outcomes of Older African American Women With Type 2 Diabetes

Type 2 diabetes affects one in five African American women over the age of 60 years. These women face distinct challenges in managing diabetes self-care. Therefore, tailored self-care interventions for this population need to be developed and tested