592 research outputs found
Exploring adaptation with evolutionary activity plots
No full textEvolutionary activity statistics and their visualization are introduced, and their motivation is explained. Examples of their use are described, and their strengths and limitations are discussed. References to more extensive or general accounts of these techniques are provided
LIM Domain Kinase 1 (LIMK1), Human Kinase Domain; A Target Enabling Package
No full textLoss of the translational repressor FMRP in fragile X syndrome causes upregulation of the type II BMP receptor BMPR2 and its non-canonical signalling via the kinase LIMK1. LIMK1 performs inhibitory phosphorylation on cofilin proteins blocking their actin-severing activity. Excessive BMPR2-LIMK1 activation was associated with dendritic spine and behavioural defects in animal models that could be rescued by BMPR2 knockdown or LIMK1 inhibition. Here we present a target enabling package for the therapeutic target LIMK1. We include crystal structures of BMPR2, LIMK1, LIMK2 and the LIMK1-cofilin complex, as well as multiple assays for small molecule inhibitor screening. Finally, we identify a series of allosteric LIMK1 inhibitors with promising potency and selectivity that may potentially allow the development of a safe drug for this chronic indication
With No Lysine Kinase 3 (WNK3); A Target Enabling Package
No full textKinases WNK1-4 regulate cation-chloride cotransporters via phosphorylation of SPAK and OSR1 and thereby control salt homeostasis, cell volume and blood pressure. Gain of function mutations in WNK kinases are found in Gordonâs hypertension syndrome suggesting the WNK pathway as a therapeutic target. WNK3 inhibition in particular has also been shown to reduce cerebral injury after Ischemic stroke. Here we present assays and crystal structures that define (i) the molecular basis for disease mutations; (ii) the multiple functional domains of WNK kinases and their protein interactions; (iii) the binding of small molecule kinase inhibitors and a potential allosteric pocket
Secondary Literacy Across the Curriculum
No full textThis paper discusses the challenges and possibilities attendant upon successfully implementing literacy across the curriculum initiatives – or ‘school language policies’ as they have come to be known – particularly at the secondary or high school level. It provides a theoretical background to these issues, exploring previous academic discussions of school language policies, and highlights key areas of concern as well as opportunity with respect to school implementation of such policies. As such, it provides a necessary conceptual background to the subsequent papers in this special issue, which focus upon the Secondary Schools’ Literacy Initiative (SSLI) – a New Zealand funded programme that aims to establish cross-curricular language and literacy policies in secondary schools
Exosomal microRNAs (exomiRs): small molecules with a big role in cancer
No full textExosomes are secreted vesicles which can transmit molecular cargo between cells. Exosomal microRNAs (exomiRs) have drawn much attention in recent years because there is increasing evidence to suggest that loading of microRNAs into exosomes is not a random process. Preclinical studies have identified functional roles for exomiRs in influencing many hallmarks of cancer. Mechanisms underpinning their actions, such as exomiR receptors ("miRceptors"), are now becoming apparent. Even more exciting is the fact that exomiRs are highly suitable candidates for use as non-invasive biomarkers in an era of personalized cancer medicine.</p
The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation.
No full textThe positive transcription elongation factor b (P-TEFb) (CDK9/cyclin T (CycT)) promotes mRNA transcriptional elongation through phosphorylation of elongation repressors and RNA polymerase II. To understand the regulation of a transcriptional CDK by its cognate cyclin, we have determined the structures of the CDK9/CycT1 and free cyclin T2. There are distinct differences between CDK9/CycT1 and the cell cycle CDK CDK2/CycA manifested by a relative rotation of 26 degrees of CycT1 with respect to the CDK, showing for the first time plasticity in CDK cyclin interactions. The CDK9/CycT1 interface is relatively sparse but retains some core CDK-cyclin interactions. The CycT1 C-terminal helix shows flexibility that may be important for the interaction of this region with HIV TAT and HEXIM. Flavopiridol, an anticancer drug in phase II clinical trials, binds to the ATP site of CDK9 inducing unanticipated structural changes that bury the inhibitor. CDK9 activity and recognition of regulatory proteins are governed by autophosphorylation. We show that CDK9/CycT1 autophosphorylates on Thr186 in the activation segment and three C-terminal phosphorylation sites. Autophosphorylation on all sites occurs in cis
Timescale and stability in adaptive behaviour
No full textRecently, in both the neuroscience and adaptive behaviour
communities, there has been growing interest in the interplay of multiple
timescales within neural systems. In particular, the phenomenon
of neuromodulation has received a great deal of interest within neuroscience
and a growing amount of attention within adaptive behaviour
research. This interest has been driven by hypotheses and evidence that
have linked neuromodulatory chemicals to a wide range of important
adaptive processes such as regulation, reconfiguration, and plasticity.
Here, we first demonstrate that manipulating timescales can qualitatively
alter the dynamics of a simple system of coupled model neurons.
We go on to explore this effect in larger systems within the framework
employed by Gardner, Ashby and May in their seminal studies of stability
in complex networks. On the basis of linear stability analysis, we
conclude that, despite evidence that timescale is important for stability,
the presence of multiple timescales within a single system has, in
general, no appreciable effect on the May-Wigner stability/connectance
relationship. Finally we address some of the shortcomings of linear stability
analysis and conclude that more sophisticated analytical approaches
are required in order to explore the impact of multiple timescales on the
temporally extended dynamics of adaptive systems
A top-down view of the tumor microenvironment: structure, cells and signaling
No full textIt is well established that the tumor microenvironment (TME) contributes to cancer progression. Stromal cells can be divided into mesenchymal, vascular, and immune. Signaling molecules secreted by the tumor corrupts these cells to create "activated" stroma. Equally, the extracellular matrix (ECM) contributes to tumor development and invasion by forming a biologically active scaffold. In this review we describe the key structural, cellular and signaling components of the TME with a perspective on stromal soluble factors and microRNAs (miRNAs)
Structural mechanisms of multimeric BTB E3 ligases and interactors
No full textIn recent years, E3 ligases and ubiquitination biology have garnered increased attention due to their critical role in emerging field targeted protein degradation field (TPD). However, many E3 ligases associate with multiple interactors and are often implicated in several diverse cellular processes. The ability to utilise these E3 ligases relies on complete characterisation of their structural mechanisms and interactor partners.
This thesis presents investigations into three distinct multimeric cullin-RING ligases. KCTD9 is a unique member of an unusual set of E3 ligases that typically assemble into higher-order assemblies. Newly generated structural data has provided insights into its function, while affinity mass spectrometry has identified a shortlist of potential interactors that may elucidate KCTD9’s role in natural killer cell development.
Dimeric KLHL12 is a rare example of an E3 ligase that can engage multiple types of interactors through a shared recognition motif. Structural data confirm, that despite some variation in protein sequence among interactors, they adopt a common binding mode.
Finally, attempts were made to setup a reproducible crystal system and establish biophysical assays for the E3 ligase FBXO31, in order to screen compounds selected by virtual ligand screening. However, these experiments were waylaid by previous studies of FBXO31, in which its interactions with Cyclin D1 were poorly characterised.
Overall, these findings contribute to the growing understanding of E3 ligases, and this will aid in TPD developments
Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation
No full textMedulloblastoma is the most common malignant brain tumour in children. Genomic studies have identified distinct disease subgroups: wnt/wingless (WNT), sonic hedgehog (SHH), and non-WNT/non-SHH, comprising group 3 and group 4. Alterations in WNT and SHH signalling form the pathogenetic basis for their subgroups, whereas those for non-WNT/non-SHH tumours remain largely elusive. Recent analyses have revealed recurrent in-frame insertions in the E3 ubiquitin ligase adaptor Kelch Repeat and BTB Domain Containing 4 (KBTBD4) in cases of group 3/4 medulloblastoma. Critically, group 3/4 tumours with KBTBD4 mutations typically lack other gene-specific alterations, such as MYC amplification, indicating KBTBD4 insertion mutations as the primary genetic driver. Delineating the role of KBTBD4 mutations thus offers significant opportunities to understand tumour pathogenesis and to exploit the underpinning mechanisms therapeutically. Here, we show a novel mechanism in cancer pathogenesis whereby indel mutations in KBTBD4 drive its recognition of neo-substrates for degradation. We observe that KBTBD4 mutants promote the recruitment and ubiquitylation of the REST Corepressor (CoREST), which forms a complex to modulate chromatin accessibility and transcriptional programmes. The degradation of CoREST promoted by KBTBD4 mutation diverts epigenetic programmes inducing significant alterations in transcription to promote increased stemness of cancer cells. Transcriptional analysis of >200 human group 3 and 4 medulloblastomas by RNA-seq, highlights the presence of CoREST and stem-like signatures in tumours with KBTBD4 mutations, which extend to a further sub-set of non-mutant tumours, suggesting CoREST alterations as a novel pathogenetic mechanism of wide relevance in group 3 and 4. Our findings uncover KBTBD4 mutation as a novel driver of epigenetic reprogramming in non-WNT/non-SHH medulloblastoma, establish a novel mode of tumorigenesis through gain-of-function mutations in ubiquitin ligases (neo-substrate recruitment) and identify both mutant KBTBD4 and CoREST complexes as new druggable targets for improved tumour-specific therapies
- …
