Optimized state feedback regulation of 3DOF helicopter system via extremum seeking

In this paper, an optimized state feedback regulation of a 3 degree of freedom (DOF) helicopter is designed via extremum seeking (ES) technique. Multi-parameter ES is applied to optimize the tracking performance via tuning State Vector Feedback with Integration of the Control Error (SVFBICE). Discrete multivariable version of ES is developed to minimize a cost function that measures the performance of the controller. The cost function is a function of the error between the actual and desired axis positions. The controller parameters are updated online as the optimization takes place. This method significantly decreases the time in obtaining optimal controller parameters. Simulations were conducted for the online optimization under both fixed and varying operating conditions. The results demonstrate the usefulness of using ES for preserving the maximum attainable performance

Inhibition of Penicillin-Binding Protein 2: Toward New Therapeutics for Antimicrobial-Resistant Gonorrhea

Gonorrhea is the second most common sexually transmitted bacterial infection in the United States, with nearly 600,000 cases reported in 2018 by the Centers for Disease Control. Alarmingly, the causative agent Neisseria gonorrhoeae has developed resistance to a number of antimicrobials over the last century. With limited options remaining, the CDC now recommends dual therapy with ceftriaxone and azithromycin to decrease the likelihood of resistance development. However, strains with combined cephalosporin and macrolide resistance have now emerged, raising concerns of a post-antibiotic future in which untreatable gonorrhea would impose enormous human and economic cost. The discovery and development of novel antigonococcal agents is, therefore, necessary to avoid a public health crisis. The pharmacologic receptors for β-lactams are a group of transpeptidases known as penicillin-binding proteins (PBP), which catalyze the cross-linkage of peptidoglycan, an essential component of the bacterial cell wall that plays major roles in cell growth and division. N. gonorrhoeae develops chromosomally mediated β-lactam resistance via alterations of PBPs affecting drug affinity, specifically through the acquisition of mutations in the penA gene encoding PBP2. Resistant strains harbor mosaic penA alleles encoding PBP2 variants containing around 60 amino acid changes compared to wild-type. In this work, we examine inhibition of a mosaic form of N. gonorrhoeae PBP2 from the cephalosporin-resistant strain H041, seeking to understand better which features of ligand structure enhance or diminish PBP2 binding in order to develop more effective PBP2 inhibitors. First, we report structure-activity relationships (SAR) for the cephalosporin class of β-lactams against PBP2 from N. gonorrhoeae H041 with the goal of identifying or designing cephalosporins effective against resistant strains. We find that structural features of the C7 acylamino side chain (R1) correlate highly with the second-order rate of PBP2H041 acylation, including increased size, modest lipophilicity, and two ring systems separated by a single branch point. The C3 side chain (R2) makes lesser, but still important, contributions to inhibition, with electronegative elements and planarity enhancing activity. We also found that many of the features enhancing target inhibition (e.g., lipophilicity, aromaticity) diminish antimicrobial activity against the H041 strain, perhaps due to decreased accumulation in the periplasm. Finally, we identify cefoperazone as highly active against PBP2H041 and similarly active against N. gonorrhoeae H041 both in vitro and in vivo compared to ceftriaxone. Second, we report the in silico discovery of novel noncovalent PBP2 inhibitors possessing a 1,1’-biphenyl system. Arylamide JEK-42 and its isosteric sulfonamide derivative JMT-1 are capable of inhibiting PBP2 from both β-lactam-susceptible and -resistant gonococcal strains. Their cross-inhibition of P. aeruginosa PBP3, predicted binding modes showing interaction with highly conserved residues, and structural similarities to bicyclic β-lactam scaffolds indicate their potential for broader activity against class B PBPs. Using the structural similarities between JEK-42, JMT-1, and bicyclic β-lactam scaffolds (i.e., penam, carbapenem, and cephem), a three-point pharmacophore was generated that can be used to identify additional PBP-inhibitory scaffolds. Third, we report the synthesis of 127 derivatives of JMT-1, showing specific substitutions that enhance the inhibition of PBP2 derived from both β-lactam-susceptible and -resistant strains. In keeping with the cephalosporin SAR, hydrophobic substitutions enhance PBP2 inhibition, likely through increased van der Waals contact with the active site, but they can also result in diminished antimicrobial activity. Together, our efforts yielded 10 compounds that show near full inhibition of PBP2 from susceptible and resistant strains, as well as large zones of gonococcal growth inhibition in disc diffusion assays. These studies lay the groundwork for the development of several structurally diverse antigonococcal chemotypes, thereby increasing the probability of producing a successful preclinical candidate

Adaptive responses of salmonella enterica serovar enteritidis ATCC 4931 biofilms to nutrient laminar flow and benzalkonium chloride treatment

Salmonella enterica serovar Enteritidis is an important biofilm-forming food-borne pathogen. This study examined the adaptive responses of Salmonella serovar Enteritidis biofilms to different environmental conditions such as flow velocity and benzalkonium chloride (BC) treatment. The influence of a 10-fold difference in nutrient laminar flow velocity on the dynamics of biofilm formation and protein expression profiles was compared. The mode of development and architecture of low-flow and high-flow biofilms were distinct. Exopolymer composition of the two biofilms was also different. However, no major shift in protein expression was seen between the biofilms, nor were there any stress response proteins involved. The biofilms altered their architecture in response to flow, presumably assuming a structure that minimized overall biofilm stress. An empirically-determined shear-inducing flow was applied on high-flow biofilms, fractionating the biofilms into shearable and non-shearable regions. Length:width indices of cells from the two biofilm regions, as well as planktonic cells from biofilm effluent and continuous culture were determined to be 3.2, 2.3, 2.2, and 1.7, respectively. Expression of proteins involved in cold-shock response, adaptation, and broad regulatory functions in the shearable region, and expression of protein involved in heat-shock response and chaperonin function in the non-shearable region indicated that the physiological status of cells in two biofilm regions was also distinct. The development of biofilm adaptive resistance to BC was then examined. Adapted biofilms survived a lethal BC challenge and re-grew, whereas unadapted biofilms did not. Proteins up-regulated following adaptation included those involved in energy metabolism, amino acid and protein biosynthesis, nutrient-transportation, adaptation, detoxification, and 1,2-propanediol degradation. A putative universal stress protein was also up-regulated. Cold-shock response, stress response, and detoxification are suggested to play roles in adaptive resistance to BC. Functional differences in adaptive response and survival of plankonic and biofilm cells adapted to BC were also studied. The proportion of BC-adapted biofilm cells that survived a lethal BC exposure and heat-shock was significantly higher than that of BC-adapted planktonic cells. Enhanced biofilm-specific up-regulation of various proteins, coupled with alterations in cell surface roughness and shift in fatty acid composition are proposed to function in the enhanced survival of BC-adapted biofilm cells, relative to BC-adapted planktonic cells.It is concluded that biofilms adapt to the stress conditions by means of community, cellular, and sub-cellular level responses. These adaptive responses help the biofilms to enhance their ability for survival in the nature, especially those formed in critical environments such as healthcare facilities, the food industry, and households

The cyanobacterial rhomboid protease is a regulator of the CCM

Cyanobacteria are aquatic photosynthetic bacteria and useful models for study of the chloroplast and photosynthesis. We are studying a ‘rhomboid’ membrane-located proteases in Synechocystis sp. PCC 6803, which appears to function as a previously undiscovered regulator of the carbon concentrating mechanism (CCM) of this phototroph. Rhomboids are almost ubiquitous across evolution, and are known to activate diverse cellular processes via proteolysis of their specific, membrane-sequestered substrates. Although this well-conserved family has solved crystal structures of bacterial enzymes such as Escherichia coli GlpG, ironically, most work has been carried out on eukaryotic representatives. Following our study of the Arabidopsis thaliana chloroplast RBL10 protease, we identified cyanobacterial orthologues with the aim of discovering if roles might be conserved between these and organellar rhomboids. Molecular biology and reverse-genetics studies were made on slr1461, a mutant in the single rhomboid protease of Synechocystis. When photosynthetic parameters were investigated, it could be seen that inactivation of slr1461 did not affect nonphotochemical quenching, unlike the chloroplast rbl10 mutant, but Slr1461 was required for reduction of photosynthetic activity in mixotrophic conditions. This reduction allows cyanobacteria to avoid expending energy on the uptake of CO2 when an organic carbon source can be utilised: as might be expected, therefore, Slr1461 transcription was linked with downregulation of genes encoding proteins facilitating high-affinity CO2 import under high CO2 and mixotrophic conditions. Quantitative RT-PCR of CCM network genes suggested that Slr1461 is located upstream of known regulators, including another membrane protease, the Slr0228 FtsH, and a central, controlling transcription factor NdhR

Imaging polyphenolic therapeutic compounds in a eukaryotic model microbe

Flavonoids are polyphenolic metabolites that have a range of physiological and developmental functions in plants. They are the focus of much work as potential therapeutics, although investigation of specific mode of action remains a notably under-researched area. Monitoring transport and location of flavonoids in cells is difficult because, despite a role in UV-absorption in plants, they emit only low levels of fluorescence. Visualising them in plants is possible using the Naturstoff reagent (NA), reported historically to be a polyphenol-fluorescence-enhancing stain. We explored therefore whether this agent was effective during preclinical assessment of polyphenolic therapeutics in a microbial-model. The eukaryote Dictyostelium discoideum has been shown to be a useful model when identifying novel drug targets for treating various diseases. For example, in the case of polycystic kidney disease, naringenin decreased Dictyostelium cell division whereas a polycystin-2-null Dictyostelium line was resistant to the flavonoid, and, subsequently, naringenin treatment proved to reduce cyst-formation in mammalian-kidney model cell lines1. To monitor transport and site of action of the drugs investigated in such studies, we developed a method using NA-staining in this model organism. A range of polyphenolics were assayed in cells, cell-extracts and the cell-washes, and NA-enhanced imaging was evaluated in parallel with LCMS-quantification. NA-enhanced fluorescence of compounds at therapeutically relevant concentrations proved an effective and qualitative measure of transport and localisation in Dictyostelium, and could be used in concert with localisation dyes. Fluorescence-enhancement is limited to a subset of flavonoids, however, and not more widely applicable in our studies to date

Physics of Ionic Conduction in Narrow Biological and Artificial Channels

The book reprints a set of important scientific papers applying physics and mathematics to address the problem of selective ionic conduction in narrow water-filled channels and pores. It is a long-standing problem, and an extremely important one. Life in all its forms depends on ion channels and, furthermore, the technological applications of artificial ion channels are already widespread and growing rapidly. They include desalination, DNA sequencing, energy harvesting, molecular sensors, fuel cells, batteries, personalised medicine, and drug design. Further applications are to be anticipated.The book will be helpful to researchers and technologists already working in the area, or planning to enter it. It gives detailed descriptions of a diversity of modern approaches, and shows how they can be particularly effective and mutually reinforcing when used together. It not only provides a snapshot of current cutting-edge scientific activity in the area, but also offers indications of how the subject is likely to evolve in the future

Physics of Ionic Conduction in Narrow Biological and Artificial Channels

This is a book about ion channels. It has been written mostly by physical scientists and mathematicians, even though the most widespread and important manifestation of ion channels is in biology, where they are essential to life in all its forms. How do non-biologists get involved in such investigations? Everyone will have their own particular story but, for ourselves, it was the heady combination of scientific curiosity, a wish to contribute to the fundamental understanding of natural phenomena that clearly have crucially important applications, and the realisation that some of our physics knowledge and expertise might be relevant