Synthesis of Hybrid Cyclopeptides through Enzymatic Macrocyclization

Acknowledgements We thank Dr. G. Mann and Dr. A. Bent for supplying the enzymes and the useful discussions, and Dr. T. Lebl for the useful NMR discussions. This work was supported by the European Research Council (339367), UK Biotechnology and Biological Sciences Research Council (K015508/1), the Wellcome Trust [TripleTOF 5600 mass spectrometer (094476), the MALDI TOF-TOF Analyzer (079272AIA), 700 NMR], and the EPSRC UK National Mass Spectrometry Facility at Swansea University. J.H.N., M.A.J., and N.J.W. are named on patents that have been filed by St. Andrews and Aberdeen Universities to commercialize the enzymes (PatG) and (LynD) used in the study. No income derives from the patent.Peer reviewedPublisher PD

Computer algebra based assessment of mathematics online

In this paper, we investigate computer algebra based assessment of mathematics online, with a focus on undergraduate students. Introducing a computer algebra system to assist in marking allows a paradigm shift from teacher-provided answers to student-provided answers. The Computer Algebra Based Learning and Evaluation (CABLE) system is presented as an open source infrastructure for mathematical learning objects. Features of the CABLE system, including the modular design, database structure, learning object specification and learning object contextualisation are described and areas for future work are identified

Neuropsychological and functional outcomes in recent-onset major depression, bipolar disorder and schizophrenia-spectrum disorders: a longitudinal cohort study

Functional disability is the lead contributor to burden of mental illness. Cognitive deficits frequently limit functional recovery, although whether changes in cognition and disability are longitudinally associated in recent-onset individuals remains unclear. Using a prospective, cohort design, 311 patients were recruited and assessed at baseline. One hundred and sixty-seven patients met eligibility criteria (M = 21.5 years old, s.d. = 4.8) and returned for follow-up (M = 20.6 months later, s.d. = 7.8). Two-hundred and thirty participants were included in the final analysis, comprising clinically stable patients with major depression (n = 71), bipolar disorder (BD; n = 61), schizophrenia-spectrum disorders (n = 35) and 63 healthy controls. Neuropsychological functioning and self-rated functional disability were examined using mixed-design, repeated-measures analysis, across diagnoses and cognitive clusters, covarying for relevant confounds. Clinical, neuropsychological and functional changes did not differ between diagnoses (all P40.05). Three reliable neuropsychological subgroups emerged through cluster analysis, characterized by psychomotor slowing, improved sustained attention, and improved verbal memory. Controlling for diagnosis and changes in residual symptoms, clusters with improved neuropsychological functioning observed greater reductions in functional disability than the psychomotor slowing cluster, which instead demonstrated a worsening in disability (Po0.01). Improved sustained attention was independently associated with greater likelihood of follow-up employment (Po0.01). Diagnosis of BD uniquely predicted both follow-up employment and independent living. Neuropsychological course appears to be independently predictive of subjective and objective functional outcomes. Importantly, cognitive phenotypes may reflect distinct pathophysiologies shared across major psychiatric conditions, and be ideal targets for personalized early intervention

The NTPase activity of the double FYVE domain-containing protein 1 regulates lipid droplet metabolism.

Lipid droplets (LDs) are transient lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks and therefore play a central role in cellular metabolism. However, the molecular factors and underlying mechanisms that regulate the growth and degradation of LDs are poorly understood. It has emerged that proteins that establish contacts between LDs and the endoplasmic reticulum play a critical role in regulating LD metabolism. Recently, the autophagy-related protein, double FYVE domain-containing protein 1 (DFCP1/ZFYVE1) was shown to reside at the interface of the endoplasmic reticulum and LDs, however, little is known about the involvement of DFCP1 in autophagy and LD metabolism. Here, we show that DFCP1 is a novel NTPase that regulates free fatty acid metabolism. Specifically, we show that DFPC1-knockdown, particularly during starvation, increases cellular free fatty acids and decreases the levels of cellular TAGs, resulting in accumulated small LDs. Using selective truncations, we demonstrate that DFCP1 accumulation on LDs in cells and in vitro is regulated by a previously unknown NTPase domain. Using spectroscopic approaches, we show that this NTPase domain can dimerize and can hydrolyze both ATP and GTP. Furthermore, mutations in DFCP1 that either impact nucleotide hydrolysis or dimerization result in changes in the accumulation of DFCP1 on LDs, changes in LD density and size, and colocalization of LDs to autophagosomes. Collectively, our findings suggest that DFCP1 is an NTPase that modulates the metabolism of LDs in cells

Interrelationships between carbohydrate, fat and protein metabolism

This thesis is primarily concerned with the relationship of energy metabolism to protein metabolism. The field of enquiry was subsequently extended to the metabolism of liver phospholipids and ribonucleic acid, since both of these display certain metabolic features in common with liver protein. The influence of energy intake on protein metabolism in the rat was explored in a study of nitrogen-balance and the protein content of the liver. Rats were fed diets, either adequate in protein content or free from protein, in combination with various levels of energy intake provided by carbohydrate or fat. At the adequate level of protein intake, nitrogen-balance and the protein content of the liver were affected in a strictly linear fashion by variations in energy supply, whereas on the protein-free diet energy intake appeared to have no considerable effect on these. A study was made of the bodily distribution of the changes in nitrogen balance produced by varying the energy content of the diet containing protein. As an extension of these experiments, measurements were made, under the same nutritional conditions, of the rate of incorporation of an isotopically labelled amino acid (glycine-2-14G) into the mixed proteins of the liver. In the post-absorptive state, the rate of glycine incorporation was essentially the same, at any given plane of energy intake, for animals previously fed the protein-containing and protein-free diets. At each level of protein intake, however, the influence of the energy content of the preceding diet was apparent, the effect being considerably more marked when the preceding diet contained protein. This difference in the response of protein metabolism to energy Intake at the two protein levels accounts for the fact that energy intake affected the amount of protein in the liver on one diet, but not on the other. On feeding protein, the pattern of protein metabolism was completely changed. The influx of amino, acids into the liver promoted a rapid increase in the rate of Incorporation of labelled glycine, independent of both the protein and energy content of the previous diet. These observations suggest that synthesis of liver protein proceeds in intermittent bursts, following the ingestion of protein, while the effect of energy Intake on the rate of protein synthesis is a prolonged one exerted between meals on the so-called "endogenous" metabolism of protein. The picture obtained in studying phospholipid metabolism in the liver showed some resemblance to that of liver protein. Only when the diet did the synthesis of phospholid in the liver increase in response to increments in response to increments in energy intake. It is suggested that the feeding of a protein-free diet so reduces the concentration of some precursor or essential component in phospholipid formation that it becomes the limiting factor in the rate of synthesis. Choline was eliminated as the missing factor. No such factor restricts the response of ribonucleic acid metabolism to changes in the energy level of the protein-free diet; the rate of synthesis of ribonucleic acid, as measured by combined quantitative and isotopic studies (32P and glycine-2A4C), appears to be determined, by the energy content of the diet, rather than by its protein content, a fact of particular interest in view of the alleged relationship between ribonucleic acid and protein synthesis. The stimulating effect of an increased energy intake on ribonucleic acid synthesis has been shown to result from the improvement in energy balance rather than from direct involvement in energy balance rather than from direct involvement of ribonucleic acid in energy metabolism. Vitamin B12 was eliminated as a dietary factor affecting the synthesis of ribonucleic acid under the conditions of these experiments. As an hypothesis consistent with these observations on the metabolism of protein, phospholipids and ribonucleic acid in the liver, the availability of energy may be pictured as the factor governing their rates of synthesis. Provided no other component of the synthetic mechanism limits the response to a change in available energy, an improvement in energy balance is associated with an augmented rate of synthesis, It would, however, seem that the increased protein synthesis following the ingestion of protein is independent of energy intake. The findings of these experiments are discussed in the light of current views on the biosynthesis of proteins

Bypassing the proline/thiazoline requirement of the macrocyclase PatG

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Salt bridges regulate both dimer formation and monomeric flexibility in HdeB and may have a role in periplasmic chaperone function

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Circadian rhythmicity in emerging mood disorders: state or trait marker?

Background: Circadian rhythm disturbances overlap with the symptoms of mood episodes and may trigger or prolong mood symptoms. There is limited research on the role of circadian disturbances in mood disorders in young people and/or first episode cases of unipolar and bipolar disorders. Methods: Actigraphy was undertaken for about 14 days in 63 post-pubertal individuals aged 13–25 years with a recent onset of a mood disorder meeting recognised diagnostic criteria. We examined associations between three easily interpretable markers of circadian rhythm activity (amplitude, acrophase and rhythmicity index) and demography and clinical characteristics. Then, circadian markers were compared between diagnostic groups, controlling for potential confounders. Results: Longer duration of illness was correlated with reduced circadian rhythmicity and lower levels of activity over 24 h. A delay in the timing of maximum activity was associated with the level of manic but not depressive symptoms. The circadian rhythmicity index differentiated unipolar from bipolar cases, and in bipolar but not unipolar disorder, the rhythmicity was less robust in those with more severe manic or depressive symptoms. Conclusions: Less robust circadian rhythmicity, especially associated with increasing symptom severity, may represent a more specific or a trait marker of young people with mood disorders who are at higher risk of a bipolar course of illness

What is the prevalence, and what are the clinical correlates, of insulin resistance in young people presenting for mental health care? A cross-sectional study

Objectives: To report the distribution and predictors of insulin resistance (IR) in young people presenting to primary care-based mental health services. Design: Cross-sectional. Setting: Headspace-linked clinics operated by the Brain and Mind Centre of the University of Sydney. Participants: 768 young people (66% female, mean age 19.7±3.5, range 12–30 years). Main outcome measures: IR was estimated using the updated homeostatic model assessment (HOMA2-IR). Height and weight were collected from direct measurement or self-report for body mass index (BMI). Results: For BMI, 20.6% of the cohort were overweight and 10.2% were obese. However,6.9 mmol/L). By contrast, 9.9% had a HOMA2-IR score \u3e2.0 (suggesting development of IR) and 11.7% (n=90) had a score between 1.5 and 2. Further, there was a positive correlation between BMI and HOMA2-IR (r=0.44, p Conclusions: Emerging IR is evident in a significant subgroup of young people presenting to primary care based mental health services. While the major modifiable risk factor is BMI, a large proportion of the variance is not accounted for by other demographic, clinical or treatment factors. Given the early emergence of IR, secondary prevention interventions may need to commence prior to the development of full-threshold or major mood or psychotic disorders

TarO : a target optimisation system for structural biology

This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative.Publisher PDFPeer reviewe