Hsp90 governs dispersion and drug resistance of fungal biofilms

Fungal biofilms are a major cause of human mortality and are recalcitrant to most treatments due to intrinsic drug resistance. These complex communities of multiple cell types form on indwelling medical devices and their eradication often requires surgical removal of infected devices. Here we implicate the molecular chaperone Hsp90 as a key regulator of biofilm dispersion and drug resistance. We previously established that in the leading human fungal pathogen, Candida albicans, Hsp90 enables the emergence and maintenance of drug resistance in planktonic conditions by stabilizing the protein phosphatase calcineurin and MAPK Mkc1. Hsp90 also regulates temperature-dependent C. albicans morphogenesis through repression of cAMP-PKA signalling. Here we demonstrate that genetic depletion of Hsp90 reduced C. albicans biofilm growth and maturation in vitro and impaired dispersal of biofilm cells. Further, compromising Hsp90 function in vitro abrogated resistance of C. albicans biofilms to the most widely deployed class of antifungal drugs, the azoles. Depletion of Hsp90 led to reduction of calcineurin and Mkc1 in planktonic but not biofilm conditions, suggesting that Hsp90 regulates drug resistance through different mechanisms in these distinct cellular states. Reduction of Hsp90 levels led to a marked decrease in matrix glucan levels, providing a compelling mechanism through which Hsp90 might regulate biofilm azole resistance. Impairment of Hsp90 function genetically or pharmacologically transformed fluconazole from ineffectual to highly effective in eradicating biofilms in a rat venous catheter infection model. Finally, inhibition of Hsp90 reduced resistance of biofilms of the most lethal mould, Aspergillus fumigatus, to the newest class of antifungals to reach the clinic, the echinocandins. Thus, we establish a novel mechanism regulating biofilm drug resistance and dispersion and that targeting Hsp90 provides a much-needed strategy for improving clinical outcome in the treatment of biofilm infections

Dynamic Walking: Toward Agile and Efficient Bipedal Robots

Dynamic walking on bipedal robots has evolved from an idea in science fiction to a practical reality. This is due to continued progress in three key areas: a mathematical understanding of locomotion, the computational ability to encode this mathematics through optimization, and the hardware capable of realizing this understanding in practice. In this context, this review article outlines the end-to-end process of methods which have proven effective in the literature for achieving dynamic walking on bipedal robots. We begin by introducing mathematical models of locomotion, from reduced order models that capture essential walking behaviors to hybrid dynamical systems that encode the full order continuous dynamics along with discrete footstrike dynamics. These models form the basis for gait generation via (nonlinear) optimization problems. Finally, models and their generated gaits merge in the context of real-time control, wherein walking behaviors are translated to hardware. The concepts presented are illustrated throughout in simulation, and experimental instantiation on multiple walking platforms are highlighted to demonstrate the ability to realize dynamic walking on bipedal robots that is agile and efficient

Tools for Nonlinear Control Systems Design

This is a brief statement of the research progress made on Grant NAG2-243 titled "Tools for Nonlinear Control Systems Design", which ran from 1983 till December 1996. The initial set of PIs on the grant were C. A. Desoer, E. L. Polak and myself (for 1983). From 1984 till 1991 Desoer and I were the Pls and finally I was the sole PI from 1991 till the end of 1996. The project has been an unusually longstanding and extremely fruitful partnership, with many technical exchanges, visits, workshops and new avenues of investigation begun on this grant. There were student visits, long term.visitors on the grant and many interesting joint projects. In this final report I will only give a cursory description of the technical work done on the grant, since there was a tradition of annual progress reports and a proposal for the succeeding year. These progress reports cum proposals are attached as Appendix A to this report. Appendix B consists of papers by me and my students as co-authors sorted chronologically. When there are multiple related versions of a paper, such as a conference version and journal version they are listed together. Appendix C consists of papers by Desoer and his students as well as 'solo' publications by other researchers supported on this grant similarly chronologically sorted

G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy

G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing interest. Indeed, G4s have been reported in several viruses, including those involved in recent epidemics, such as the Zika and Ebola viruses. Viral G4s are usually located in regulatory regions of the genome and implicated in the control of key viral processes; in some cases, they have been involved also in viral latency. In this context, G4 ligands have been developed and tested both as tools to study the complexity of G4-mediated mechanisms in the viral life cycle, and as therapeutic agents. In general, G4 ligands showed promising antiviral activity, with G4-mediated mechanisms of action both at the genome and transcript level. This review aims to provide an updated close-up of the literature on G4s in viruses. The current state of the art of G4 ligands in antiviral research is also reported, with particular focus on the structural and physicochemical requirements for optimal biological activity. The achievements and the to-dos in the field are discussed

Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based “conformational selection” of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected residue clusters may be a rather general functional requirement encoded across molecular chaperones. The obtained insights may be useful in guiding discovery of allosteric Hsp90 inhibitors targeting protein interfaces with co-chaperones and protein binding clients

Power quality and electromagnetic compatibility: special report, session 2

The scope of Session 2 (S2) has been defined as follows by the Session Advisory Group and the Technical Committee: Power Quality (PQ), with the more general concept of electromagnetic compatibility (EMC) and with some related safety problems in electricity distribution systems. Special focus is put on voltage continuity (supply reliability, problem of outages) and voltage quality (voltage level, flicker, unbalance, harmonics). This session will also look at electromagnetic compatibility (mains frequency to 150 kHz), electromagnetic interferences and electric and magnetic fields issues. Also addressed in this session are electrical safety and immunity concerns (lightning issues, step, touch and transferred voltages). The aim of this special report is to present a synthesis of the present concerns in PQ&EMC, based on all selected papers of session 2 and related papers from other sessions, (152 papers in total). The report is divided in the following 4 blocks: Block 1: Electric and Magnetic Fields, EMC, Earthing systems Block 2: Harmonics Block 3: Voltage Variation Block 4: Power Quality Monitoring Two Round Tables will be organised: - Power quality and EMC in the Future Grid (CIGRE/CIRED WG C4.24, RT 13) - Reliability Benchmarking - why we should do it? What should be done in future? (RT 15

Autoregulation of c-Fes by intramolecular interaction of the F-BAR and SH2 domains: a novel role for the unique N-terminal region

The c-Fes protein is a structurally unique non-receptor protein-tyrosine kinase encoded by the fes/fps proto-oncogene and is expressed in myeloid hematopoietic, vascular endothelial, and some epithelial and neuronal cell types. Downstream of a number of cytokines and growth factors, c-Fes plays a role in regulation of cell growth, differentiation, and chemotaxis. Dysregulation of c-Fes activity is implicated in a number of cancers, including acute myelogenous leukemia (AML) and some renal carcinomas. Structurally, c-Fes includes an amino-terminal F-BAR region—consisting of a Fes/CIP4 homology (FCH) domain and the first of two coiled-coil motifs (CC1)—followed by CC2 and the carboxy-terminal Src homology 2 (SH2) domain closely linked to a typical bilobate kinase domain (KD). Unlike its oncogenic retroviral orthologs (v-Fes/Fps), c-Fes kinase activity is tightly regulated in vivo, yet lacks known negative regulatory features common to other cytoplasmic tyrosine kinases, such as a SH3 domain or regulatory tail tyrosine. In fact, a c-Fes truncation containing only the SH2 and KD is constitutively active which suggests a possible auto-inhibitory role for the unique N-terminal region. Deletion and mutation experiments reveal that loss of the predicted CC1 structure leads to upregulation similar to the c-Fes SH2-KD truncation. This would be the first case of autoinhibition by the coiled-coil; however, it is still unclear how the F-BAR acts in cis to accomplish autoinhibition. Substitution of the native c-Fes SH2 with that of v-Src (but not homologous v-Fps) displays an uninhibited catalytic activity level analogous to the CC1 mutant, suggesting interdomain interaction between the F-BAR and SH2/KD may contribute to an inactive conformation. I collected evidence for this mechanism and began to develop tools to define the putative F-BAR:SH2 interface utilizing the bimolecular fluorescence complementation (BiFC) technique. Demonstrated by BiFC in 293T cells, the F-BAR interacts with the SH2 domain in a CC1-dependent manner. It may be that CC1 forms a critical interface with αB of the SH2 as preliminary data suggest that v-Src-mimetic mutations in αB weaken CC1-SH2 recognition. Further characterization of the specific intramolecular interactions involved in c-Fes regulation would advance new paradigms in modular domain relationships and could expand cancer drug discovery efforts

Some resonances between Eastern thought and Integral Biomathics in the framework of the WLIMES formalism for modelling living systems

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought