Structure and dynamics of the kinase IKK-β – A key regulator of the NF-kappa B transcription factor

'This is the author's version of a work that was accepted for publication in Journal of Structural Biology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Structural Biology, 176 (2) (2011) DOI 10.1016/j.jsb.2011.07.012'The inhibitor κB kinase-β (IKK-β) phosphorylates the NF-κB inhibitor protein IκB leading to the translocation of the transcription factor NF-κB to the nucleus. The transcription factor NF-κB and consequently IKK-β are central to signal transduction pathways of mammalian cells. The purpose of this research was to develop a 3D structural model of the IKK-β kinase domain with its ATP cofactor and investigate its dynamics and ligand binding potential. Through a combination of comparative modelling and simulated heating/annealing molecular dynamics (SAMD) simulation in explicit water the model accuracy could be substantially improved compared to comparative modelling on its own as shown by model validation measures. The structure revealed the details of ATP/Mg2+ binding indicating hydrophobic interactions with the adenine base and a significant contribution of Mg2+ as a bridge between ATP phosphate groups and negatively charged side chains. The molecular dynamics trajectories of the ATP-bound and free enzyme showed two conformations in each case, which contributed to the majority of the trajectory. The ATP-free enzyme revealed a novel binding site distant from the ATP binding site that was not encountered in the ATP bound enzyme. Based on the overall structural flexibility, it is suggested that a truncated version of the kinase domain from Ala14 to Leu265 should be subjected to crystallisation trials. The 3D structure of this enzyme will enable rational design of new ligands and analysis of protein–protein interactions. Furthermore, our results may provide a new impetus for wet-lab based structural investigation focussing on a truncated kinase domain.Peer reviewedFinal Accepted Versio

Molecular Dipolar Crystals as High Fidelity Quantum Memory for Hybrid Quantum Computing

We study collective excitations of rotational and spin states of an ensemble of polar molecules, which are prepared in a dipolar crystalline phase, as a candidate for a high fidelity quantum memory. While dipolar crystals are formed in the high density limit of cold clouds of polar molecules under 1D and 2D trapping conditions, the crystalline structure protects the molecular qubits from detrimental effects of short range collisions. We calculate the lifetime of the quantum memory by identifying the dominant decoherence mechanisms, and estimate their effects on gate operations, when a molecular ensemble qubit is transferred to a superconducting strip line cavity (circuit QED). In the case rotational excitations coupled by dipole-dipole interactions we identify phonons as the main limitation of the life time of qubits. We study specific setups and conditions, where the coupling to the phonon modes is minimized. Detailed results are presented for a 1D dipolar chain

Structural basis of mitochondrial receptor binding and constriction by DRP1.

Mitochondrial inheritance, genome maintenance and metabolic adaptation depend on organelle fission by dynamin-related protein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogues mitochondrial dynamics proteins of 49 and 51 kDa (MID49 and MID51) and mitochondrial fission factor (MFF); however, the mechanisms by which these proteins recruit and regulate DRP1 are unknown. Here we present a cryo-electron microscopy structure of full-length human DRP1 co-assembled with MID49 and an analysis of structure- and disease-based mutations. We report that GTP induces a marked elongation and rotation of the GTPase domain, bundle-signalling element and connecting hinge loops of DRP1. In this conformation, a network of multivalent interactions promotes the polymerization of a linear DRP1 filament with MID49 or MID51. After co-assembly, GTP hydrolysis and exchange lead to MID receptor dissociation, filament shortening and curling of DRP1 oligomers into constricted and closed rings. Together, these views of full-length, receptor- and nucleotide-bound conformations reveal how DRP1 performs mechanical work through nucleotide-driven allostery

Dynamic Transition in the Structure of an Energetic Crystal during Chemical Reactions at Shock Front Prior to Detonation

Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive force-field molecular dynamics (ReaxFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillion-atom ReaxFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front

The GoodNight study—online CBT for insomnia for the indicated prevention of depression: study protocol for a randomised controlled trial

BACKGROUND Cognitive Behaviour Therapy for Insomnia (CBT-I) delivered through the Internet is effective as a treatment in reducing insomnia in individuals seeking help for insomnia. CBT-I also lowers levels of depression in this group. However, it is not known if targeting insomnia using CBT-I will lower depressive symptoms, and thus reduce the risk of major depressive episode onset, in those specifically at risk for depression. Therefore, this study aims to examine whether Internet delivery of fully automated self-help CBT-I designed to reduce insomnia will prevent depression. METHOD/DESIGN A sample of 1,600 community-dwelling adults (aged 18-64), who screen positive for both subclinical levels of depressive symptoms and insomnia, will be recruited via various media and randomised to either a 9-week online insomnia treatment programme, Sleep Healthy Using The internet (SHUTi), or an online attention-matched control group (HealthWatch). The primary outcome variable will be depression symptom levels at the 6-month post-intervention on the Patient Heath Questionnaire-9 (PHQ-9). A secondary outcome will be onset of major depressive episodes assessed at the 6-month post-intervention using 'current' and 'time from intervention' criteria from the Mini International Neuropsychiatric Interview. DISCUSSION This trial is the first randomised controlled trial of an Internet-based insomnia intervention as an indicated preventative programme for depression. If effective, online provision of a depression prevention programme will facilitate dissemination. TRIAL REGISTRATION Australian New Zealand Clinical Trials Registry (ANZCTR), Registration number: ACTRN12611000121965.This study is supported by a grant from the National Health and Medical Research Council, Australia (GNT1005867)

Diagnostic accuracy of laparoscopy following computed tomography (CT) scanning for assessing the resectability with curative intent in pancreatic and periampullary cancer

BACKGROUND: Surgical resection is the only potentially curative treatment for pancreatic and periampullary cancer. A considerable proportion of patients undergo unnecessary laparotomy because of underestimation of the extent of the cancer on computed tomography (CT) scanning. Laparoscopy can detect metastases not visualised on CT scanning, enabling better assessment of the spread of cancer (staging of cancer). This is an update to a previous Cochrane Review published in 2013 evaluating the role of diagnostic laparoscopy in assessing the resectability with curative intent in people with pancreatic and periampullary cancer. OBJECTIVES: To determine the diagnostic accuracy of diagnostic laparoscopy performed as an add-on test to CT scanning in the assessment of curative resectability in pancreatic and periampullary cancer. SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE via PubMed, EMBASE via OvidSP (from inception to 15 May 2016), and Science Citation Index Expanded (from 1980 to 15 May 2016). SELECTION CRITERIA: We included diagnostic accuracy studies of diagnostic laparoscopy in people with potentially resectable pancreatic and periampullary cancer on CT scan, where confirmation of liver or peritoneal involvement was by histopathological examination of suspicious (liver or peritoneal) lesions obtained at diagnostic laparoscopy or laparotomy. We accepted any criteria of resectability used in the studies. We included studies irrespective of language, publication status, or study design (prospective or retrospective). We excluded case-control studies. DATA COLLECTION AND ANALYSIS: Two review authors independently performed data extraction and quality assessment using the QUADAS-2 tool. The specificity of diagnostic laparoscopy in all studies was 1 because there were no false positives since laparoscopy and the reference standard are one and the same if histological examination after diagnostic laparoscopy is positive. The sensitivities were therefore meta-analysed using a univariate random-effects logistic regression model. The probability of unresectability in people who had a negative laparoscopy (post-test probability for people with a negative test result) was calculated using the median probability of unresectability (pre-test probability) from the included studies, and the negative likelihood ratio derived from the model (specificity of 1 assumed). The difference between the pre-test and post-test probabilities gave the overall added value of diagnostic laparoscopy compared to the standard practice of CT scan staging alone. MAIN RESULTS: We included 16 studies with a total of 1146 participants in the meta-analysis. Only one study including 52 participants had a low risk of bias and low applicability concern in the patient selection domain. The median pre-test probability of unresectable disease after CT scanning across studies was 41.4% (that is 41 out of 100 participants who had resectable cancer after CT scan were found to have unresectable disease on laparotomy). The summary sensitivity of diagnostic laparoscopy was 64.4% (95% confidence interval (CI) 50.1% to 76.6%). Assuming a pre-test probability of 41.4%, the post-test probability of unresectable disease for participants with a negative test result was 0.20 (95% CI 0.15 to 0.27). This indicates that if a person is said to have resectable disease after diagnostic laparoscopy and CT scan, there is a 20% probability that their cancer will be unresectable compared to a 41% probability for those receiving CT alone.A subgroup analysis of people with pancreatic cancer gave a summary sensitivity of 67.9% (95% CI 41.1% to 86.5%). The post-test probability of unresectable disease after being considered resectable on both CT and diagnostic laparoscopy was 18% compared to 40.0% for those receiving CT alone. AUTHORS' CONCLUSIONS: Diagnostic laparoscopy may decrease the rate of unnecessary laparotomy in people with pancreatic and periampullary cancer found to have resectable disease on CT scan. On average, using diagnostic laparoscopy with biopsy and histopathological confirmation of suspicious lesions prior to laparotomy would avoid 21 unnecessary laparotomies in 100 people in whom resection of cancer with curative intent is planned

Mesenchymal stem cells with increased stromal cell-derived factor 1 expression enhanced fracture healing

Treatment of critical size bone defects pose a challenge in orthopedics. Stem cell therapy together with cytokines has the potential to improve bone repair as they cause the migration and homing of stem cells to the defect site. However, the engraftment, participation, and recruitment of other cells within the regenerating tissue are important. To enhance stem cell involvement, this study investigated overexpression of stem cells with stromal cell-derived factor 1 (SDF-1) using an adenovirus. We hypothesized that these engineered cells would effectively increase the migration of native cells to the site of fracture, enhancing bone repair. Before implantation, we showed that SDF-1 secreted by transfected cells increased the migration of nontransfected cells. In a rat defect bone model, bone marrow mesenchymal stem cells overexpressing SDF-1 showed significantly (p=0.003) more new bone formation within the gap and less bone mineral loss at the area adjacent to the defect site during the early bone healing stage. In conclusion, SDF-1 was shown to play an important role in accelerating fracture repair and contributing to bone repair in rat models, by recruiting more host stem cells to the defect site and encouraging osteogenic differentiation and production of bone

Wavelet-Galerkin method for numerical solution of partial differential equation

In recent years wavelets are given much attention in many branches of science and technology due to its comprehensive mathematical power and application potential. The advantage of wavelet techniques over finite difference or element method is well known.The objective of this work is to implementing the Wavelet-Galerkin method for approximating solutions of differential equations. In this paper, we elaborate the wavelet techniques and apply the Galerkin method procedure to analyse one dimensional wave equation as a test problem using fictitious boundary approach. The sections of this thesis will include defining wavelets and their scaling functions.This will give the reader valued insight about wavelets.Following this will be a section defining the Daubechies wavelet and its scaling function. This section comprises some subsection about computing the scaling function and its derivative and integral.The purpose of this section will be to give the reader an understanding how scaling function and its derivative are computed. Next will be a section on multiresolution analysis and its properties. The next section give information about the 2-term connection coefficients. The main focus of this work will be to solve the one dimensional wave equation using fictitious boundary approach and made a comparison between the exact and approximate solution which gives the accuracy and efficiency of this method

A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task

A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory