Cutting the Gordian knot : early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation

SAJ would like to thank the University of Aberdeen for an Elphinstone Scholarship. CC-A thanks CONICYT PFCHA/DOCTORADO BECAS CHILE/2016 (#21160585) fellowship and CONICYT Basal Centre Grant for the Centre for Biotechnology and Bioengineering, CeBiB (FB0001). JFC also thanks CONICYT for a National PhD Scholarship (#21110356) and a Visiting Student Scholarship.Peer reviewedPostprin

Antimicrobial antagonists against food pathogens; a bacteriocin perspective

peer-reviewedEfforts are continuing to find novel bacteriocins with enhanced specificity and potency. Traditional plating techniques are still being used for bacteriocin screening studies, however, the availability of ever more bacterial genome sequences and the use of in silico gene mining tools have revealed novel bacteriocin gene clusters that would otherwise have been overlooked. Furthermore, synthetic biology and bioengineering-based approaches are allowing scientists to harness existing and novel bacteriocin gene clusters through expression in different hosts and by enhancing functionalities. The same principles apply to bacteriocin producing probiotic cultures and their application to control pathogens in the gut. We can expect that the recent developments on bacteriocins from Lactic Acid Bacteria (LAB) described here will contribute greatly to increased commercialisation of bacteriocins in food systems.This work was funded by the Alimentary Pharmabiotic Centre, a research centre funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan. The authors and their work were supported by SFI (grant no. 12/RC/2273

Micoteca da Universidade do Minho (MUM): a portuguese culture collection

[Excerpt] Micoteca da Universidade do Minho - MUM is a mycological culture collection that exists since 1996 and is hosted by the Biological Engineering Research Centre (www.deb.uminho.pt), a centre of excellence integrated in the Institute for Biotechnology and Bioengineering (IBB - www.ibb.pt). The mission of MUM is to provide the highest quality services to its customers, collecting, maintaining and supplying fungal strains and their associated information for teaching and research in biotechnology and life sciences, and to be a centre of knowledge, information and training in mycology, operating at a global level and under national and international regulations [1,2]. (...

Saturation Mutagenesis of Lysine 12 Leads to the Identification of Derivatives of Nisin A with Enhanced Antimicrobial Activity

peer-reviewedIt is becoming increasingly apparent that innovations from the “golden age” of antibiotics are becoming ineffective, resulting in a pressing need for novel therapeutics. The bacteriocin family of antimicrobial peptides has attracted much attention in recent years as a source of potential alternatives. The most intensively studied bacteriocin is nisin, a broad spectrum lantibiotic that inhibits Gram-positive bacteria including important food pathogens and clinically relevant antibiotic resistant bacteria. Nisin is gene-encoded and, as such, is amenable to peptide bioengineering, facilitating the generation of novel derivatives that can be screened for desirable properties. It was to this end that we used a site-saturation mutagenesis approach to create a bank of producers of nisin A derivatives that differ with respect to the identity of residue 12 (normally lysine; K12). A number of these producers exhibited enhanced bioactivity and the nisin A K12A producer was deemed of greatest interest. Subsequent investigations with the purified antimicrobial highlighted the enhanced specific activity of this modified nisin against representative target strains from the genera Streptococcus, Bacillus, Lactococcus, Enterococcus and Staphylococcus.This work was supported by the Irish Government under the National Development Plan; by the Irish Research Council for Science Engineering and Technology (IRCSET); by Enterprise Ireland; and by Science Foundation Ireland (SFI), through the Alimentary Pharmabiotic Centre (APC) at University College Cork, Ireland, which is supported by the SFI-funded Centre for Science, Engineering and Technology (SFI-CSET) and provided P.D.C., C.H. and R.P.R. with SFI Principal Investigator funding

Application of the morphological alpha shape method to the extraction of topographical features from engineering surfaces

In contrast to the mean-line based filters, morphological filters are function oriented and more suitable for the functional prediction of component performance. This paper presents a novel morphological method based on the alpha shape for the extraction of topographical features from engineering surfaces. Compared to the traditional implementation of morphological filters, the alpha shape method is more efficient in performance for large structuring element. The resulting envelope follows the form of the surface all over such that the distortions caused the end effects are avoided. A series of measured surfaces from the automotive cylinder liner and the bioengineering femoral heads are analyzed using the morphological alpha shape method. The topographical features are successfully extracted, enabling further analysis to the components

Biomechanical motion analysis in the clinical environment : the dawn of a new era ?

Philip Rowe looks at biomechanical motion analysis and the work the department of Biomedical engineering at the University of Strathclyde, Glasgow, UK (formerly the Bioengineering Unit), has played a key role in these developments over the last 50 years

On the creation of a subject specific finite element model of the wrist joint

Anatomy varies greatly between individuals and therefore it can be inaccurate to derive any clinical conclusions based on a single computer model. It is important to create models which are directly linked to a specific subject who then can be identified as a part of a larger population 1. By these means it is possible to draw conclusions about the discrepancy between two or more subjects or two or more subject groups. Advances have been made to create a subject specific finite element model of the hip, by using automated procedures 2. The hip poses a relatively simple geometry for such robust procedures to be implemented. However when faced with a more geometrically such as the wrist joint or the ankle joint, the procedure becomes more laborious since automatic procedures become impossible to apply. The geometry is the single most important factor for modeling such types of multi-bone systems and there needs to exist a good balance between creation time and level of accuracy and mesh refinement. In previously reported finite element studies of the wrist joint, ad hoc boundary conditions have been applied to the system. In creating a subject specific model it is important to apply boundary conditions that have been measured from the particular subject. Coupling subject specific boundary conditions with accurate application of material properties of the bones and soft tissues allows the creation of models to predict realistic in-vivo stresses on the carpal bones. In this study three subject specific finite element models were created of the wrist joint, ranging from the distal end of the radius and ulna to the proximal third of the metacarpals, a total of 14 bones were included in the model

Noninvasive assessment of inspiratory muscle neuromechanical coupling during inspiratory threshold loading

Diaphragm neuromechanical coupling (NMC), which reflects the efficiency of conversion of neural activation to transdiaphragmatic pressure (Pdi), is increasingly recognized to be a useful clinical index of diaphragm function and respiratory mechanics in neuromuscular weakness and cardiorespiratory disease. However, the current gold standard assessment of diaphragm NMC requires invasive measurements of Pdi and crural diaphragm electromyography (oesEMGdi), which complicates the measurement of diaphragm NMC in clinical practice. This is the first study to compare invasive measurements of diaphragm NMC (iNMC) using the relationship between Pdi and oesEMGdi, with noninvasive assessment of NMC (nNMC) using surface mechanomyography (sMMGlic) and electromyography (sEMGlic) of lower chest wall inspiratory muscles. Both invasive and noninvasive measurements were recorded in twelve healthy adult subjects during an inspiratory threshold loading protocol. A linear relationship between noninvasive sMMGlic and sEMGlic measurements was found, resulting in little change in nNMC with increasing inspiratory load. By contrast, a curvilinear relationship between invasive Pdi and oesEMGdi measurements was observed, such that there was a progressive increase in iNMC with increasing inspiratory threshold load. Progressive recruitment of lower ribcage muscles, serving to enhance the mechanical advantage of the diaphragm, may explain the more linear relationship between sMMGlic and sEMGlic (both representing lower intercostal plus costal diaphragm activity) than between Pdi and crural oesEMGdi. Noninvasive indices of NMC derived from sEMGlic and sMMGlic may prove to be useful indices of lower chest wall inspiratory muscle NMC, particularly in settings that do not have access to invasive measures of diaphragm function.Peer ReviewedPostprint (published version

The Strathclyde Brain Computer Interface (S-BCI) : the road to clinical translation

In this paper, we summarise the state of development of the Strathclyde Brain Computer Interface (S-BCI) and what has been so far achieved. We also briefly discuss our next steps for translation to spinal cord injured patients and the challenges we envisage in this process and how we plan to address some of them. Projections of the S-BCI project for the coming few years are also presented