Scientific Publications Library
The IFR along with BBSRC is fully committed to making the outputs from its research publicly available where possible.
As a means of improving access to our scientific outputs we have created this online library. Those outputs with open access are clearly marked as such and will provide the user with either a link to a downloadable PDF or to the publisher’s version of the article.
|Green open access publications are marked by the PDF icon. Click on the publication title, or the PDF icon, and read a pre-print PDF version of the publication.||Gold open access publications have the gold open padlock icon. You can read the full version of these papers on the publishing journal’s website without a subscription.|
The creation of this publications repository was funded by BBSRC.
Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure
Carbohydrate Polymers 152 p441-449
Publisher’s version: 10.1016/j.carbpol.2016.06.016
The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh) < 100 nm; this protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh > 100 nm.
Time series analysis of the Bacillus subtilis sporulation network reveals low dimensional chaotic dynamics
Frontiers in Microbiology 7 p1760
Publisher’s version: 10.3389/fmicb.2016.01760
Chaotic behaviour refers to a behaviour which, albeit irregular, is generated by an underlying deterministic process. Therefore, a chaotic behaviour is potentially controllable. This possibility becomes practically amenable especially when chaos is shown to be low-dimensional, i.e. to be attributable to a small fraction of the total systems components. In this case, including the major drivers of chaos in a system into the modelling approach allows us to improve predictability of the systems dynamics. Here, we analysed the numerical simulations of an accurate ordinary differential equation model of the gene network regulating sporulation initiation in Bacillus subtilis to explore whether the non-linearity underlying time series data is due to low-dimensional chaos. Low-dimensional chaos is expectedly common in systems with few degrees of freedom, but rare in systems with many degrees of freedom such as the B. subtilis sporulation network. The estimation of a number of indices, which reflect the chaotic nature of a system, indicates that the dynamics of this network is affected by deterministic chaos. The neat separation between the indices obtained from the time series simulated from the model and those obtained from time series generated by Gaussian white and coloured noise confirmed that the B. subtilis sporulation network dynamics is affected by low dimensional chaos rather than by noise. Furthermore, our analysis identifies the principal driver of the networks chaotic dynamics to be sporulation initiation phosphotransferase B (Spo0B). As Spo0A is the master regulator of the sequence of the events regulating B. subtilis sporulation, we then analysed a sub-space of the systems phase space phase spanned defined just by Spo0A and Spo0B dynamics. A characterization of the instability points in this sub-space allowed us to identify the ranges of values assumed by Spo0A and Spo0B for which the whole system is highly sensitive to minimal perturbation. In summary, we described an unappreciated source of complexity in the B. subtilis sporulation network by gathering evidence for the chaotic behaviour of the system, and by suggesting candidate molecules driving chaos in the system. The results from this chaos analysis could help to refine theoretical predictions of the behaviour of the system and to advance the control of the mechanisms underlying B. subtilis sporulation.
Frontiers in Microbiology 7 p1702
Publisher’s version: 10.3389/fmicb.2016.01702
Clostridium botulinum is a highly dangerous pathogen that forms very resistant endospores that are ubiquitous in the environment, and which, under favourable conditions germinate to produce vegetative cells that multiply and form the exceptionally potent botulinum neurotoxin. To improve the control of botulinum neurotoxin-forming clostridia, it is important to understand the mechanisms involved in spore germination. Here we present the first models for spore germination in C. botulinum, with similar models proposed for C. botulinum Groups I and III, and similar models proposed for C. botulinum Groups II and IV. All spores germinate in response to amino acids interacting with a germinant receptor, with four types of germinant receptor identified (encoded by various combinations of gerA, gerB and gerC genes (gerX)). There are three gene clusters with an ABC-like configuration; ABC [gerX1], ABABCB [gerX2] and ACxBBB [gerX4], and a single CA-B [gerX3] gene cluster. Subtypes have been identified for most germinant receptors types, and individual subunits of different germinant receptor gene clusters have co-evolved, suggesting different subtypes have arisen through divergence and not by subsequent recombination or insertion. C. botulinum Group I contained the largest variety of gerX subtypes, with three gerX1, three gerX2 and one gerX3 subtypes, while C. botulinum Group III contained two gerX1 types and gerX4. C. botulinum Groups II and IV contained a single germinant receptor, gerX3 and gerX1, respectively. It is likely that all four C. botulinum Groups include a SpoVA channel involved in DPA release. The cortex lytic enzymes present in C. botulinum Groups I and III appear to be CwlJ and SleB, while in C. botulinum Groups II and IV, SleC appears to be important.