The Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals. The Centre's integrated technology ...platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals production. An overview of these capabilities is described.
The UK Synthetic Biology Research Centre, SYNBIOCHEM, hosted by the Manchester Institute of Biotechnology at the University of Manchester is delivering innovative technology platforms to facilitate ...the predictable engineering of microbial bio-factories for fine and speciality chemicals production. We provide an overview of our foundry activities that are being applied to grand challenge projects to deliver innovation in bio-based chemicals production for industrial biotechnology.
The x-ray crystal structure of the thiostrepton resistance RNA methyltransferase (Tsr)· S-adenosyl - l -methionine (AdoMet) complex was determined at 2.45-à resolution. Tsr is definitively ...confirmed as a Class IV methyltransferase
of the SpoU family with an N-terminal âL30-likeâ putative target recognition domain. The structure and our in vitro analysis of the interaction of Tsr with its target domain from 23 S ribosomal RNA (rRNA) demonstrate that the active biological
unit is a Tsr homodimer. In vitro methylation assays show that Tsr activity is optimal against a 29-nucleotide hairpin rRNA though the full 58-nucleotide L11-binding
domain and intact 23 S rRNA are also effective substrates. Molecular docking experiments predict that Tsr·rRNA binding is
dictated entirely by the sequence and structure of the rRNA hairpin containing the A1067 target nucleotide and is most likely
driven primarily by large complementary electrostatic surfaces. One L30-like domain is predicted to bind the target loop and
the other is near an internal loop more distant from the target site where a nucleotide change (U1061 to A) also decreases
methylation by Tsr. Furthermore, a predicted interaction with this internal loop by Tsr amino acid Phe-88 was confirmed by
mutagenesis and RNA binding experiments. We therefore propose that Tsr achieves its absolute target specificity using the
N-terminal domains of each monomer in combination to recognize the two distinct structural elements of the target rRNA hairpin
such that both Tsr subunits contribute directly to the positioning of the target nucleotide on the enzyme.
The x-ray crystal structure of the thiostrepton resistance RNA methyltransferase (Tsr).S-adenosyl-L-methionine (AdoMet) complex was determined at 2.45-A resolution. Tsr is definitively confirmed as a ...Class IV methyltransferase of the SpoU family with an N-terminal "L30-like" putative target recognition domain. The structure and our in vitro analysis of the interaction of Tsr with its target domain from 23 S ribosomal RNA (rRNA) demonstrate that the active biological unit is a Tsr homodimer. In vitro methylation assays show that Tsr activity is optimal against a 29-nucleotide hairpin rRNA though the full 58-nucleotide L11-binding domain and intact 23 S rRNA are also effective substrates. Molecular docking experiments predict that Tsr.rRNA binding is dictated entirely by the sequence and structure of the rRNA hairpin containing the A1067 target nucleotide and is most likely driven primarily by large complementary electrostatic surfaces. One L30-like domain is predicted to bind the target loop and the other is near an internal loop more distant from the target site where a nucleotide change (U1061 to A) also decreases methylation by Tsr. Furthermore, a predicted interaction with this internal loop by Tsr amino acid Phe-88 was confirmed by mutagenesis and RNA binding experiments. We therefore propose that Tsr achieves its absolute target specificity using the N-terminal domains of each monomer in combination to recognize the two distinct structural elements of the target rRNA hairpin such that both Tsr subunits contribute directly to the positioning of the target nucleotide on the enzyme.
The X-ray crystal structure of a ribosomal L11-rRNA complex with chloroplast-like mutations in both protein and rRNA is presented. The global structure is almost identical to that of the wild-type ...(bacterial) complex, with only a small movement of the protein α helix away from the surface of the RNA required to accommodate the altered protein residue. In contrast, the specific hydrogen bonding pattern of the mutated residues is substantially different, and now includes a direct interaction between the protein side chain and an RNA base edge and a water-mediated contact. Comparison of the two structures allows the observations of sequence variation and relative affinities of wild-type and mutant complexes to be clearly rationalized, but reinforces the concept that there is no single simple code for protein-RNA recognition.
A key functional component of the ribosome is a 58 nt rRNA region that is recognised by the ribosomal protein L11. One of the key contacts made in this complex involves the highly conserved residue ...69 of L11 and RNA base pair 1062-1076. The chloroplast like (Ch-like) structure (Asn69/U1062-A1076) of the L11-rRNA complex along with two hybrid structures were solved by X-ray crystallography. The comparison of these structures allowed previous sequence variations and relative binding affinities to be fully rationalised. The L11 and rRNA structures have maintained this important interaction that is essential for ribosome function by the co-evolution of both RNA and protein structures. These structures have also increased our understanding of protein-RNA interaction and how it can adapt to sequence modifications e.g. though water mediated contacts. This complex is the target for several naturally occurring (e.g. thiostrepton) and synthetic ligands that bind and inhibit ribosomal function. An X-ray crystal structure of one of these synthetic compounds bound to this complex revealed a potential mode of antibiotic interaction and may point to a general mechanism for the interaction of naturally occurring ligands at this key ribosomal site.
Neural mass models (NMMs) are important for helping us interpret observations of brain dynamics. They provide a means to understand data in terms of mechanisms such as synaptic interactions between ...excitatory and inhibitory neuronal populations. To interpret data using NMMs we need to quantitatively compare the output of NMMs with data, and thereby find parameter values for which the model can produce the observed dynamics. Mapping dynamics to NMM parameter values in this way has the potential to improve our understanding of the brain in health and disease. Though abstract, NMMs still comprise of many parameters that are difficult to constrain a priori. This makes it challenging to explore the dynamics of NMMs and elucidate regions of parameter space in which their dynamics best approximate data. Existing approaches to overcome this challenge use a combination of linearising models, constraining the values they can take and exploring restricted subspaces by fixing the values of many parameters a priori. As such, we have little knowledge of the extent to which different regions of parameter space of NMMs can yield dynamics that approximate data, how nonlinearities in models can affect parameter mapping or how best to quantify similarities between model output and data. These issues need to be addressed in order to fully understand the potential and limitations of NMMs, and to aid the development of new models of brain dynamics in the future. To begin to overcome these issues, we present a global nonlinear approach to recovering parameters of NMMs from data. We use global optimisation to explore all parameters of nonlinear NMMs simultaneously, in a minimally constrained way. We do this using multi-objective optimisation (multi-objective evolutionary algorithm, MOEA) so that multiple data features can be quantified. In particular, we use the weighted horizontal visibility graph (wHVG), which is a flexible framework for quantifying different aspects of time series, by converting them into networks. We study EEG alpha activity recorded during the eyes closed resting state from 20 healthy individuals and demonstrate that the MOEA performs favourably compared to single objective approaches. The addition of the wHVG objective allows us to better constrain the model output, which leads to the recovered parameter values being restricted to smaller regions of parameter space, thus improving the practical identifiability of the model. We then use the MOEA to study differences in the alpha rhythm observed in EEG recorded from 20 people with epilepsy. We find that a small number of parameters can explain this difference and that, counterintuitively, the mean excitatory synaptic gain parameter is reduced in people with epilepsy compared to control. In addition, we propose that the MOEA could be used to mine for the presence of pathological rhythms, and demonstrate the application of this to epileptiform spike-wave discharges.
The aim of this study was to examine the independent relationships of television viewing or other screen-based entertainment ("screen time") with all-cause mortality and clinically confirmed ...cardiovascular disease (CVD) events. A secondary objective was to examine the extent to which metabolic (body mass index, high-density lipoprotein and total cholesterol) and inflammatory (C-reactive protein) markers mediate the relationship between screen time and CVD events.
Although some evidence suggests that prolonged sitting is linked to CVD risk factor development regardless of physical activity participation, studies with hard outcomes are scarce.
A population sample of 4,512 (1,945 men) Scottish Health Survey 2003 respondents (≥35 years) were followed up to 2007 for all-cause mortality and CVD events (fatal and nonfatal combined). Main exposures were interviewer-assessed screen time (<2 h/day; 2 to <4 h/day; and ≥4 h/day) and moderate to vigorous intensity physical activity.
Two hundred fifteen CVD events and 325 any-cause deaths occurred during 19,364 follow-up person-years. The covariable (age, sex, ethnicity, obesity, smoking, social class, long-standing illness, marital status, diabetes, hypertension)-adjusted hazard ratio (HR) for all-cause mortality was 1.52 (95% confidence interval CI: 1.06 to 2.16) and for CVD events was 2.30 (95% CI: 1.33 to 3.96) for participants engaging in ≥4 h/day of screen time relative to <2 h/day. Adjusting for physical activity attenuated these associations only slightly (all-cause mortality: HR: 1.48, 95% CI: 1.04 to 2.13; CVD events: HR: 2.25, 95% CI: 1.30 to 3.89). Exclusion of participants with CVD events in the first 2 years of follow-up and previous cancer registrations did not change these results appreciably. Approximately 25% of the association between screen time and CVD events was explained collectively by C-reactive protein, body mass index, and high-density lipoprotein cholesterol.
Recreational sitting, as reflected by television/screen viewing time, is related to raised mortality and CVD risk regardless of physical activity participation. Inflammatory and metabolic risk factors partly explain this relationship.
An international group of experts convened to provide guidance for employers to promote the avoidance of prolonged periods of sedentary work. The set of recommendations was developed from the ...totality of the current evidence, including long-term epidemiological studies and interventional studies of getting workers to stand and/or move more frequently. The evidence was ranked in quality using the four levels of the American College of Sports Medicine. The derived guidance is as follows: for those occupations which are predominantly desk based, workers should aim to initially progress towards accumulating 2 h/day of standing and light activity (light walking) during working hours, eventually progressing to a total accumulation of 4 h/day (prorated to part-time hours). To achieve this, seated-based work should be regularly broken up with standing-based work, the use of sit-stand desks, or the taking of short active standing breaks. Along with other health promotion goals (improved nutrition, reducing alcohol, smoking and stress), companies should also promote among their staff that prolonged sitting, aggregated from work and in leisure time, may significantly and independently increase the risk of cardiometabolic diseases and premature mortality. It is appreciated that these recommendations should be interpreted in relation to the evidence from which they were derived, largely observational and retrospective studies, or short-term interventional studies showing acute cardiometabolic changes. While longer term intervention studies are required, the level of consistent evidence accumulated to date, and the public health context of rising chronic diseases, suggest initial guidelines are justified. We hope these guidelines stimulate future research, and that greater precision will be possible within future iterations.
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