An evolutionary computing approach for parameter estimation investigation of a model for cholera

We consider the problem of using time-series data to inform a corresponding deterministic model and introduce the concept of genetic algorithms (GA) as a tool for parameter estimation, providing instructions for an implementation of the method that does not require access to special toolboxes or software. We give as an example a model for cholera, a disease for which there is much mechanistic uncertainty in the literature. We use GA to find parameter sets using available time-series data from the introduction of cholera in Haiti and we discuss the value of comparing multiple parameter sets with similar performances in describing the data.     

An SEI model for sarcoptic mange among chamois

We consider a simple model to study the dynamics of sarcoptic mange in a population of chamois. The epidemiological patterns observed during an epidemic in Italy are reconstructed and key parameters of the model are estimated from field data. In particular, we calculate the basic reproductive ratio R ₀, a threshold value for chamois density for the occurrence of an epidemic and the speed of propagation of the epidemic wave. The model is then used to obtain indications on the effect of culling as a possible control measure in a closed population and extended to analyse the spatial diffusion of the epidemic. Our results are in agreement with mange epidemiology and observations, and suggest that intervention could be efficacious in reducing the impact of an epidemic.     

Fabrication of Polymeric Visual Decoys for the Male Emerald Ash Borer (Agrilus planipennis)

Through a bioreplication approach, we have fabricated artificial visual decoys for the invasive species Agrilus planipennis—commonly known as the Emerald Ash Borer (EAB). The mating behavior of this species involves an overflying EAB male pouncing on an EAB female at rest on an ash leaflet before copulating. The male spots the female on the leaflet by visually detecting the iridescent green color of the female's elytra. As rearing EAB and then deploying dead females as decoys for trapping is both arduous and inconvenient, we decided to fabricate artificial decoys. We used a dead female to make a negative die of nickel and a positive die of epoxy. Decoys were then made by first depositing a quarter-wave-stack Bragg reflector on a polymer sheet and then stamping it with a pair of matched negative and positive dies to take the shape of the upper surface of an EAB female. As nearly 100 artificial decoys were fabricated from just one EAB female, this bioreplication process is industrially scalable. Preliminary results from a field trapping test are indicative of success.     

Impact of the invasion of the imported fire ant

The impact of the imported fire ant (IFA) is complex, in large part, because several very different species of “Fire Ants” have invaded and one of these has two forms, all of which are hard to separate by the public, as well as, some investigators not focused on the ant. Each of these different “IFA” species and forms differ in their impact. Further, these ants impact a number of “things” ranging from the environment and wildlife (plants and animals) as well as people, their environment and infrastructure. In addition, they can not only lead to death of living things (including people), but they can destroy many aspects of our environment and infrastructure at the cost of millions of dollars. But there are some beneficial aspects and some people can make many thousands of dollars due to their presence. This is an attempt to look at these issues.     

Adaptation changes in dynamic postural control and contingent negative variation during repeated transient forward translation in the elderly

Background

Adaptation changes in postural control and contingent negative variation (CNV) for the elderly were investigated during repeated forward floor translation.

Methods

Fifteen healthy elderly persons, living in the suburban area of Kanazawa City, Japan, underwent backward postural disturbance by a forward-floor translation (S2) 2 s after an auditory warning signal (S1). A set with 20 trials was repeated until a negative peak of late CNV was recognized in the 600-ms period before S2, and the last set was defined as the final set. Electroencephalograms, center of foot pressure in the anteroposterior direction (CoPap), and electromyograms of postural muscles were analyzed.

Results

CoPap displacement generated by the floor translation was significantly decreased until the twelfth trial in the first set, and mean CoPap displacement was smaller in the second and final sets than in the first set. The mean displacement was significantly smaller in the final set than the previous set. A late CNV with a negative peak was not recognized in the first and second sets. However, most subjects (13/15) showed a negative peak by the fourth set, when the late CNV started to increase negatively from about 1,000 ms after S1 and peaked at about 300 ms before S2. At about 160 ms before the CNV peak, the CoPap forward shift started. The increase in timing of the gastrocnemius activity related to the CoPap shift was significantly correlated with the CNV peak timing (r = 0.64). After S2, peak amplitudes of the anterior postural muscles were significantly decreased in the final set compared to the first set.

Conclusions

It was demonstrated that even for the elderly, with so many repetitions of postural disturbance, a late CNV with a negative peak was recognized, leading to accurate postural preparation. This suggests the improvement of frontal lobe function (e.g., anticipatory attention and motor preparation) in the elderly.     

GAP promoter‐based fed‐batch production of highly bioactive core streptavidin by Pichia pastoris

Streptavidin is a homotetrameric protein binding the vitamin biotin and peptide analogues with an extremely high affinity, which leads to a large variety of applications. The biotin‐auxotrophic yeast Pichia pastoris has recently been identified as a suitable host for the expression of the streptavidin gene, allowing both high product concentrations and productivities. However, so far only methanol‐based expression systems have been applied, bringing about increased oxygen demand, strong heat evolution and high requirements for process safety, causing increased cost. Moreover, common methanol‐based processes lead to large proportions of biotin‐blocked binding sites of streptavidin due to biotin‐supplemented media. Targeting these problems, this paper provides strategies for the methanol‐free production of highly bioactive core streptavidin by P. pastoris under control of the constitutive GAP promoter. Complex were superior to synthetic production media regarding the proportion of biotin‐blocked streptavidin. The optimized, easily scalable fed‐batch process led to a tetrameric product concentration of up to 4.16 ± 0.11 µM of biotin‐free streptavidin and a productivity of 57.8 nM h^?1 based on constant glucose feeding and a successive shift of temperature and pH throughout the cultivation, surpassing the concentration in un‐optimized conditions by a factor of 3.4. Parameter estimation indicates that the optimized conditions caused a strongly increased accumulation of product at diminishing specific growth rates (μ ≈ D < 0.01 h^?1), supporting the strategy of feeding. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:855–864, 2016     

A comparison of four different conformations adopted by human telomeric G‐quadruplex using computer simulations

The telomeric G‐quadruplexes for their unique structural features are considered as potential anticancer drug targets. These, however, exhibit structural polymorphism as different topology types for the intra‐molecular G‐quadruplexes from human telomeric G‐rich sequences have been reported based on NMR spectroscopy and X‐ray crystallography. These techniques provide detailed atomic‐level information about the molecule but relative conformational stability of the different topologies remains unsolved. Therefore, to understand the conformational preference, we have carried out quantum chemical calculations on G‐quartets; used all‐atom molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations to characterize the four human telomeric G‐quadruplex topologies based on its G‐tetrad core‐types, viz., parallel, anti‐parallel, mixed‐(3 + 1)‐form1 and mixed‐(3 + 1)‐form2. We have also studied a non‐telomeric sequence along with these telomeric forms giving a comparison between the two G‐rich forms. The structural properties such as base pairing, stacking geometry and backbone conformations have been analyzed. The quantum calculations indicate that presence of a sodium ion inside the G‐tetrad plane or two potassium ions on both sides of the plane give it an overall planarity which is much needed for good stacking to form a helix. MD simulations indicate that capping of the G‐tetrad core by the TTA loops keep the terminal guanine bases away from water. The SMD simulations along with equilibrium MD studies indicate that the parallel and non‐telomeric forms are comparatively less stable. We could come to the conclusion that the anti‐parallel form and also the mixed‐(3 + 1)‐form1 topology are most likely to represent the major conformation., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 83–99, 2016