Leu628 of the KIX domain of CBP is a key residue for the interaction with the MLL transactivation domain

AbstractPhysical interaction between the transactivation domain (TAD) of the mixed-lineage leukemia protein (MLL) and the KIX domain of the cyclic-AMP response element binding protein (CREB) binding protein (CBP) is necessary for MLL-mediated transcriptional activation. We show by alanine-scanning mutagenesis that hydrophobic surface residues of KIX, especially L628, are energetically important for binding the MLL TAD. NMR studies of the KIX-L628A mutant suggest that L628 plays a crucial role in conformational transitions at the MLL binding site, necessary for high affinity interactions with MLL. Unexpectedly, MLL also binds to the c-Myb/phosphorylated kinase-inducible domain of CREB (pKID) site of KIX, highlighting the complex nature of interactions involving intrinsically disordered transcriptional activators.Structured summaryMINT-8044564, MINT-8044580, MINT-8044598, MINT-8044616, MINT-8044634, MINT-8044656:Cbp (uniprotkb:P45481) and MLL (uniprotkb:Q03164) bind (MI:0407) by isothermal titration calorimetry (MI:0065)MINT-8044696:Cbp (uniprotkb:P45481) and MLL (uniprotkb:Q03164) bind (MI:0407) by nuclear magnetic resonance (MI:0077

Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance.

Inhibition of nuclear factor kappaB (NF-kappaB) is mainly accomplished by IkappaB alpha, which consists of a signal response sequence at the N-terminus, a six-ankyrin repeat domain (ARD) that binds NF-kappaB, and a C-terminal PEST sequence. Previous studies with the ARD revealed that the fifth and sixth repeats are only partially folded in the absence of NF-kappaB. Here we report NMR studies of a truncated version of IkappaB alpha, containing only the first four ankyrin repeats, IkappaB alpha(67-206). This four-repeat segment is well-structured in the free state, enabling full resonance assignments to be made. H-D exchange, backbone dynamics, and residual dipolar coupling (RDC) experiments reveal regions of flexibility. In addition, regions consistent with the presence of micro- to millisecond motions occur periodically throughout the repeat structure. Comparison of the RDCs with the crystal structure gave only moderate agreement, but an ensemble of structures generated by accelerated molecular dynamics gave much better agreement with the measured RDCs. The regions showing flexibility correspond to those implicated in entropic compensation for the loss of flexibility in ankyrin repeats 5 and 6 upon binding to NF-kappaB. The regions showing micro- to millisecond motions in the free protein are the ends of the beta-hairpins that directly interact with NF-kappaB in the complex

Novel matched stimuli for assessment of lexical semantics

Background: Diagnosis of semantic impairment in stroke and progressive neuro-cognitive conditions is typically facilitated using tests of word comprehension, such as word-picture matching. Many of these tests are not controlled for psycholinguistic variables or the semantic relationships between competitor stimuli and involve pictures which are not controlled for ease of access. Semantic assessment also demands additional cognitive resources, such as explicit decision-making and suppression of semantic competitors. These factors may all confound test performance and subsequent diagnosis. Aims: To develop novel semantic test stimuli for three new semantic processing assessments, which are controlled for psycholinguistic variables, semantic relationship between stimuli, and visual similarity between images presented simultaneously. An additional aim included matching stimuli for these variables across three tests: semantic priming, word-picture verification, and word-picture matching, to allow direct comparison of performance on tests that differ in terms of the additional cognitive demands involved, with priming entailing implicit semantic processing. Methods & Procedures: In phase one, novel stimuli were developed for the three semantic processing tests. Existing databases were searched for values to match stimuli psycholinguistic variables. In phase two, new data were collected from control participants regarding the semantic and visual similarity of stimuli presented simultaneously. Outcomes & Results: Data for three sets of target and distractor stimuli are presented, which are psycholinguistically matched within and between the three semantic tests for concreteness, imageability, age of acquisition, frequency, word length, and emotional valence. “Semantic” relationships between pairs of stimuli are differentiated by semantic similarity (dog-cat) or association (dog-lead). Visual similarity is controlled between images presented in an array. Conclusions: The data provided ensure that test performance across three semantic tasks, differing in additional cognitive demands, can be directly compared in people with potential semantic deficits. This is the first such study to provide control of stimuli within and across a range of semantic tests. Patterns of performance via test reaction time and accuracy data may reveal semantic deficit or competence, contributing to more accurate diagnosis and appropriate therapy choice

Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the evolution of protein function, but little is known about the evolution of functional mechanisms, protein dynamics and conformational plasticity essential for activity. We characterized the atomic-level motions across divergent members of the dihydrofolate reductase (DHFR) family. Despite structural similarity, Escherichia coli and human DHFRs use different dynamic mechanisms to perform the same function, and human DHFR cannot complement DHFR-deficient E. coli cells. Identification of the primary-sequence determinants of flexibility in DHFRs from several species allowed us to propose a likely scenario for the evolution of functionally important DHFR dynamics following a pattern of divergent evolution that is tuned by cellular environment

The influence of the lower stratosphere on ridging Atlantic Ocean anticyclones over South Africa

The link between Rossby wave breaking and ridging Atlantic Ocean anticyclones in the South African domain is examined using NCEP–DOE AMIP-II reanalysis data. A simple composite analysis, which used the duration of ridging events as a basis of averaging, reveals that ridging anticyclones are coupled with Rossby wave breaking at levels higher than the dynamical tropopause. Lower-stratospheric PV anomalies extend to the surface, thus coupling the ridging highs with the lower stratosphere. The anomaly extending from the 70-hPa level to the surface contributes to a southward extension of the surface negative anomaly over the Namibian coast, which induces a cyclonic flow, causing the ridging anticyclone to take a bean-like shape. The surface positive anomaly induces the internal anticyclonic flow within the large-scale pressure system, causing the ridging end to break off and amalgamate with the Indian Ocean high pressure system. Lower-stratospheric Rossby wave breaking lasts for as long as the ridging process, suggesting that the former is critical to the longevity of the latter by maintaining and keeping the vertical coupling intact.This research was partially funded by the Water Research Commission of South Africa.http://www2.ametsoc.org/ams/index.cfm/publications/journals/journal-of-climate/2019-08-01am2019Geography, Geoinformatics and Meteorolog

Maternal Fructose Intake Causes Developmental Reprogramming of Hepatic Mitochondrial Catalytic Activity and Lipid Metabolism in Weanling and Young Adult Offspring

Excess dietary fructose is a major public health concern, yet little is known about its influence on offspring development and later-life disease when consumed in excess during pregnancy. To determine whether increased maternal fructose intake could have long-term consequences on offspring health, we investigated the effects of 10% w/v fructose water intake during preconception and pregnancy in guinea pigs. Female Dunkin Hartley guinea pigs were fed a control diet (CD) or fructose diet (FD; providing 16% of total daily caloric intake) ad libitum 60 days prior to mating and throughout gestation. Dietary interventions ceased at day of delivery. Offspring were culled at day 21 (D21) (weaning) and at 4 months (4 M) (young adult). Fetal exposure to excess maternal fructose intake significantly increased male and female triglycerides at D21 and 4 M and circulating palmitoleic acid and total omega-7 through day 0 (D0) to 4 M. Proteomic and functional analysis of significantly differentially expressed proteins revealed that FD offspring (D21 and 4 M) had significantly increased mitochondrial metabolic activities of β-oxidation, electron transport chain (ETC) and oxidative phosphorylation and reactive oxygen species production compared to the CD offspring. Western blotting analysis of both FD offspring validated the increased protein abundances of mitochondrial ETC complex II and IV, SREBP-1c and FAS, whereas VDAC1 expression was higher at D21 but lower at 4 M. We provide evidence demonstrating offspring programmed hepatic mitochondrial metabolism and de novo lipogenesis following excess maternal fructose exposure. These underlying asymptomatic programmed pathways may lead to a predisposition to metabolic dysfunction later in life

Power and resistance: Reflections on the rhetoric and reality of using participatory methods to promote student voice and engagement in higher education

The focus of this article is methods for facilitating student voice and engagement in higher education, specifically participatory methods. Across the student voice and engagement literature there is a growing emphasis on promoting collaborative partnerships between staff and students. However, there is a lack of detail and criticality with regards to (1) exactly how genuine partnerships can be achieved and (2) comparing the vision for and the reality of positioning ‘students as partners’ in the current higher education climate. In this article, we evaluate the potential of participatory methods to facilitate quality partnerships between staff and students. Drawing on our experiences of being involved in a participatory project in one higher education institution, we offer reflective narratives from three different partners who participated in the project: student, lecturer and researcher. We use these narratives to explore the nature of the partnerships between lecturers and students, focusing specifically on issues of resistance and power. We conclude by considering the implications for how we conceptualise and implement student voice and engagement projects in higher education

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

BACKGROUND: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, where the phylogenetic tree and evolutionary timescale are estimated first using maximum likelihood. Under this hybrid approach, demographic parameters are inferred from estimated trees instead of the sequence data, using maximum likelihood, Bayesian inference, or approximate Bayesian computation. This can vastly reduce the computational burden, but has the disadvantage of ignoring the uncertainty in the phylogenetic tree and evolutionary timescale. RESULTS: We compared the performance of a fully Bayesian and a hybrid method by analysing six whole-genome SNP data sets from a range of bacteria and simulations. The estimates from the two methods were very similar, suggesting that the hybrid method is a valid alternative for very large datasets. However, we also found that congruence between these methods is contingent on the presence of strong temporal structure in the data (i.e. clocklike behaviour), which is typically verified using a date-randomisation test in a Bayesian framework. To reduce the computational burden of this Bayesian test we implemented a date-randomisation test using a rapid maximum likelihood method, which has similar performance to its Bayesian counterpart. CONCLUSIONS: Hybrid approaches can produce reliable inferences of evolutionary timescales and phylodynamic parameters in a fraction of the time required for fully Bayesian analyses. As such, they are a valuable alternative in outbreak studies involving a large number of isolates

Understanding barriers to involving community midwives in identifying research participants; experience of the first Steps randomised controlled trial

- Objective: To explore barriers to the involvement of community midwives in identifying women in early pregnancy as potential participants in the XX, a randomised controlled trial of a new intervention to provide health and parenting support to potentially vulnerable women. - Design: Descriptive qualitative investigation using semi-structured audio-recoded interviews. - Setting: Community midwifery offices. - Participants: Volunteer sample of 13 community midwives. - Measurement: Themes derived from content analysis. - Findings: Understanding of their role in the research process was unclear to many midwives. Confusion arose about the difference between potential participant identification and trial recruitment. There were concerns about the eligibility criteria and it was suggested that there was insufficient time during booking appointments, and sometimes insufficient information, to determine potential eligibility. Midwives had concerns about some aspects of the intervention, which incorporated routine midwifery care, and had expectations that women may not like a group programme. This may have led some not to mention the trial. They were, however positive about the programme's potential for beneficial impacts on mothers and infants. - Key conclusions: Dedicated research midwives may be the best option if research studies need to identify potential participants early in pregnancy, so that they can communicate with all their colleagues. - Implications for practice: If community midwives are asked to be involved in time-critical research they are likely to need additional local resources and support