Gene duplication: a drive for phenotypic diversity and cause of human disease

Gene duplication is one of the key factors driving genetic innovation, i.e., producing novel genetic variants. Although the contribution of whole-genome and segmental duplications to phenotypic diversity across species is widely appreciated, the phenotypic spectrum and potential pathogenicity of small-scale duplications in individual genomes are less well explored. This review discusses the nature of small-scale duplications and the phenotypes produced by such duplications. Phenotypic variation and disease phenotypes induced by duplications are more diverse and widespread than previously anticipated, and duplications are a major class of disease-related genomic variation. Pathogenic duplications particularly involve dosage-sensitive genes with both similar and dissimilar over- and underexpression phenotypes, and genes encoding proteins with a propensity to aggregate. Phenotypes related to human-specific copy number variation in genes regulating environmental responses and immunity are increasingly recognized. Small genomic duplications containing defense-related genes also contribute to complex common phenotypes.

Female-biased dispersal and patrilocal kin groups in a mammal with resource-defence polygyny

In most mammals, dispersal rates are higher in males than in females. Using behavioural and genetic data of individually marked bats, we show that this general pattern is reversed in the greater sac-winged bat (Saccopteryx bilineata). Dispersal is significantly female biased and male philopatry in combination with rare male immigration causes a patrilineal colony structure. Female dispersal helps avoid father-daughter inbreeding, as male tenure exceeds female age at first breeding in this bat species. Furthermore, our data suggest that females may engage in extra-harem copulations to mate with genetically dissimilar males, and thus avoid their male descendants as mating partners. Acquaintance with the natal colony might facilitate territory takeover since male sac-winged bats queue for harem access. Given the virtual absence of male immigration and the possible lower reproductive success of dispersing males, we argue that enhancing the likelihood of settlement of male descendants could be adaptive despite local mate competition. We conclude that resource defence by males is important in promoting male philopatry, and argue that the potential overlap of male tenure and female first conception is the driving force for females to disperse.

Localized annealing of polysilicon microstructures by inductively heated ferromagnetic films

The monolithic integration of dissimilar microsystems is often limited by conflicts in thermal budget. One of the most prevalent examples is the fabrication of active micro-electromechanical systems (MEMS), as structural films utilized for surface micromachining such as polysilicon typically require processing at temperatures unsuitable for microelectronic circuitry. A localized annealing process could provide for the post-deposition heat treatment of integrated structures without compromising active devices. This dissertation presents a new microfabrication technology based on the inductive heating of ferromagnetic films patterned to define regions for heat treatment. Support is provided through theory, finite-element modeling, and experimentation, concluding with the demonstration of inductive annealing on polysilicon inertial sensing structures. Though still in its infancy, the results confirm the technology to be a viable option for integrated MEMS as well as any microsystem fabrication process requiring a thermal gradient.

Evaluation and comparison of cartilage repair tissue of the patella and medial femoral condyle by using morphological MRI and biochemical zonal T2 mapping

The objective of this study was to use advanced MR techniques to evaluate and compare cartilage repair tissue after matrix-associated autologous chondrocyte transplantation (MACT) in the patella and medial femoral condyle (MFC). Thirty-four patients treated with MACT underwent 3-T MRI of the knee. Patients were treated on either patella (n = 17) or MFC (n = 17) cartilage and were matched by age and postoperative interval. For morphological evaluation, the MR observation of cartilage repair tissue (MOCART) score was used, with a 3D-True-FISP sequence. For biochemical assessment, T2 mapping was prepared by using a multiecho spin-echo approach with particular attention to the cartilage zonal structure. Statistical evaluation was done by analyses of variance. The MOCART score showed no significant differences between the patella and MFC (p > or = 0.05). With regard to biochemical T2 relaxation, higher T2 values were found throughout the MFC (p < 0.05). The zonal increase in T2 values from deep to superficial was significant for control cartilage (p < 0.001) and cartilage repair tissue (p < 0.05), with an earlier onset in the repair tissue of the patella. The assessment of cartilage repair tissue of the patella and MFC afforded comparable morphological results, whereas biochemical T2 values showed differences, possibly due to dissimilar biomechanical loading conditions.

TERPENE AND TERPENOID EMISSIONS AND SECONDARY ORGANIC AEROSOL PRODUCTION

Approximately 90% of fine aerosol in the Midwestern United States has a regional component with a sizable fraction attributed to secondary production of organic aerosol (SOA). The Ozark Forest is an important source of biogenic SOA precursors like isoprene (> 150 mg m-2 d-1), monoterpenes (10-40 mg m-2 d-1), and sesquiterpenes (10-40 mg m-2d-1). Anthropogenic sources include secondary sulfate and nitrate and biomass burning (51-60%), vehicle emissions (17-26%), and industrial emissions (16-18%). Vehicle emissions are an important source of volatile and vapor-phase, semivolatile aliphatic and aromatic hydrocarbons that are important anthropogenic sources of SOA precursors. The short lifetime of SOA precursors and the complex mixture of functionalized oxidation products make rapid sampling, quantitative processing methods, and comprehensive organic molecular analysis essential elements of a comprehensive strategy to advance understanding of SOA formation pathways. Uncertainties in forecasting SOA production on regional scales are large and related to uncertainties in biogenic emission inventories and measurement of SOA yields under ambient conditions. This work presents a bottom-up approach to develop a conifer emission inventory based on foliar and cortical oleoresin composition, development of a model to estimate terpene and terpenoid signatures of foliar and bole emissions from conifers, development of processing and analytic techniques for comprehensive organic molecular characterization of SOA precursors and oxidation products, implementation of the high-volume sampling technique to measure OA and vapor-phase organic matter, and results from a 5 day field experiment conducted to evaluate temporal and diurnal trends in SOA precursors and oxidation products. A total of 98, 115, and 87 terpene and terpenoid species were identified and quantified in commercially available essential oils of Pinus sylvestris, Picea mariana, and Thuja occidentalis, respectively, by comprehensive, two-dimensional gas chromatography with time-of-flight mass spectrometric detection (GC × GC-ToF-MS). Analysis of the literature showed that cortical oleoresin composition was similar to foliar composition of the oldest branches. Our proposed conceptual model for estimation of signatures of terpene and terpenoid emissions from foliar and cortical oleoresin showed that emission potentials of the foliar and bole release pathways are dissimilar and should be considered for conifer species that develop resin blisters or are infested with herbivores or pathogens. Average derivatization efficiencies for Methods 1 and 2 were 87.9 and 114%, respectively. Despite the lower average derivatization efficiency of Method 1, distinct advantages included a greater certainty of derivatization yield for the entire suite of multi- and poly-functional species and fewer processing steps for sequential derivatization. Detection limits for Method 1 using GC × GC- ToF-MS were 0.09-1.89 ng μL-1. A theoretical retention index diagram was developed for a hypothetical GC × 2GC analysis of the complex mixture of SOA precursors and derivatized oxidation products. In general, species eluted (relative to the alkyl diester reference compounds) from the primary column (DB-210) in bands according to n and from the secondary columns (BPX90, SolGel-WAX) according to functionality, essentially making the GC × 2GC retention diagram a Carbon number-functionality grid. The species clustered into 35 groups by functionality and species within each group exhibited good separation by n. Average recoveries of n-alkanes and polyaromatic hydrocarbons (PAHs) by Soxhlet extraction of XAD-2 resin with dichloromethane were 80.1 ± 16.1 and 76.1 ± 17.5%, respectively. Vehicle emissions were the common source for HSVOCs [i.e., resolved alkanes, the unresolved complex mixture (UCM), alkylbenzenes, and 2- and 3-ring PAHs]. An absence of monoterpenes at 0600-1000 and high concentrations of monoterpenoids during the same period was indicative of substantial losses of monoterpenes overnight and the early morning hours. Post-collection, comprehensive organic molecular characterization of SOA precursors and products by GC × GC-ToFMS in ambient air collected with ~2 hr resolution is a promising method for determining biogenic and anthropogenic SOA yields that can be used to evaluate SOA formation models.

LOCAL DIGITAL CONTROL OF POWER ELECTRONIC CONVERTERS IN A DC MICROGRID BASED ON A-PRIORI DERIVATION OF SWITCHING SURFACES

In power electronic basedmicrogrids, the computational requirements needed to implement an optimized online control strategy can be prohibitive. The work presented in this dissertation proposes a generalized method of derivation of geometric manifolds in a dc microgrid that is based on the a-priori computation of the optimal reactions and trajectories for classes of events in a dc microgrid. The proposed states are the stored energies in all the energy storage elements of the dc microgrid and power flowing into them. It is anticipated that calculating a large enough set of dissimilar transient scenarios will also span many scenarios not specifically used to develop the surface. These geometric manifolds will then be used as reference surfaces in any type of controller, such as a sliding mode hysteretic controller. The presence of switched power converters in microgrids involve different control actions for different system events. The control of the switch states of the converters is essential for steady state and transient operations. A digital memory look-up based controller that uses a hysteretic sliding mode control strategy is an effective technique to generate the proper switch states for the converters. An example dcmicrogrid with three dc-dc boost converters and resistive loads is considered for this work. The geometric manifolds are successfully generated for transient events, such as step changes in the loads and the sources. The surfaces corresponding to a specific case of step change in the loads are then used as reference surfaces in an EEPROM for experimentally validating the control strategy. The required switch states corresponding to this specific transient scenario are programmed in the EEPROM as a memory table. This controls the switching of the dc-dc boost converters and drives the system states to the reference manifold. In this work, it is shown that this strategy effectively controls the system for a transient condition such as step changes in the loads for the example case.

Say on Pay: ein Überblick über Gestaltungsoptionen, ökonomische Konsequenzen und Erkenntnisse aus Empirie und Laborexperimenten

Unter dem Stichwort Say on Pay (SoP) haben in den letzen Jahren die meisten Länder der EU und die USA den Aktionären Abstimmungsrechte im Zusammenhang mit der Vergütung des Top-Managements eingeräumt. Zwischen den einzelnen Ländern bestehen jedoch erhebliche Unterschiede hinsichtlich der konkreten Ausgestaltung des SoP. Dieser Beitrag diskutiert die Wirkungen unterschiedlicher Gestaltungsoptionen des SoP auf die Anreizgestaltung und den Nutzen des Managements und der Aktionäre im Rahmen eines einfachen linearen Agency Modells. Dabei erweisen sich das vorvertragliche bindende SoP und das bedingt verpflichtende, nachvertragliche bindende SoP gegenüber den anderen untersuchten Varianten als überlegen. Während das konsultative SoP an seiner mangelnden Durchsetzbarkeit leidet, bietet das nachvertragliche bindende SoP Anreize für opportunistisches Verhalten auf Seiten der Aktionäre und führt deshalb zu Wohlfahrtsverlusten. In Ergänzung der Modellanalyse wird ein Überblick über die wichtigsten empirischen und experimentellen Studien zum Thema SoP gegeben und deren Inhalt im Lichte der Modellergebnisse diskutiert. Most countries of the European Union as well as the US recently introduced shareholder votes on the remuneration of executives, also referred to as “Say on Pay” (SoP). Interestingly, legislators in different jurisdictions opted for quite dissimilar voting right regimes. We provide an overview of the main regulatory approaches and discuss the potential impact of variations in SoP design on the structure of compensation contracts and the utility of shareholders and executives. We find that pre-contractual SoP and conditional post-contractual SoP with binding consequences are in the best interest of shareholders. By contrast, advisory SoP typically suffers from lacking enforceability. We also find that post-contractual SoP with binding consequences results in efficiency losses because it fuels moral hazard on the part of shareholders. We complement the theoretical analysis with a discussion of recent empirical and experimental studies on Say on Pay.

Schul-, Praxis- und habituelles Herrschaftswissen. Bildung ländlicher Eliten mit Blick auf die korporative Selbstverwaltung in der frühmodernen Schweiz (18. und 19. Jahrhundert)

Knowledge taught at schools, everyday skills and practical know-how. The relevancy of formation for local elites and the corporative self-government of Early Modern Switzerland Daniel Schläppi, Bern There were different kinds of rural elites in Early Modern Switzerland. The diverse parts of the country developed in very dissimilar ways politically and economically. Some regions were dominated by traditional types of agriculture. Some territories were ruled by major cities. In some of the rural Cantons like Uri, Schwyz, Unterwalden, Glarus and Zug a political elite took control over generations and practiced a cultural lifestyle comparable to the famous aristocracies in cities like Bern, Basel, Freiburg, Luzern, Solothurn and Zurich. Intense proto-industrialization formed a completely different sort of elite with strong affinities to industry and trade in other regions. Meanwhile the habitants of the valley close-by stayed farmers like their ancestors (like in Appenzell). In the most conservative parts of the country mercenary business played an important role till the very end of the Ancien Regime and even furthermore. In summery the variety of historical circumstances caused heterogeneous elites all over. Such socio-political diversity provoked a variety of educational backgrounds. I an academic understanding of the term we know only little about literacy in local rural elites. But there is strong evidence that a lively culture of reading and story-telling existed. This means that even simple countrymen seem to have been in possession of some books. The organisation and capacity of the school system is subject of controversial discussions among up to date researchers. The state of research makes us suppose that the people designed to political careers learned their essential skills not only in school but also in everyday life or on the job. Based on the fact that every community and countless public corporations managed their affairs by their own it’s evident that the local elite’s key-players had a large repertoire of techniques and skills like writing, calculating, strategic thinking or knowledge of oral tradition, old usage or important rituals. Unfortunately the historical actors left not that many sources that would tell us precisely how knowledge and know-how were transferred in former times. Hardly any private account books or common correspondence have been conserved. But a huge bunch of sources that originate from corporative self-administration shows us that most local elites were well-educated and had the necessary skills anyway. Above all other sources like for instance the «Topographische Beschreibungen» (topographic descriptions) that were initiated by the «Ökonomische Gesellschaft» of Berne since the sixties of the 18th century provide an insight into pre-modern classrooms. More important information on the historical formation-reality can be gained by the autobiography of the famous poor peasant Ulrich Bräker (1735‒1798) or some of the novels by Albert Bitzius (1797‒1854, better known as Jeremias Gotthelf). The pedagogic writings by Johann Heinrich Pestalozzi (1746‒1827) and the influences by his mentors Johann Rudolf Tschiffeli (1716‒1780) or Philipp Emanuel von Fellenberg (1771‒1884) are quite illustrative as well.

Clostridium perfringens beta-toxin induces necrostatin-inhibitable, calpain-dependent necrosis in primary porcine endothelial cells

Clostridium perfringens β-toxin (CPB) is a β-barrel pore-forming toxin and an essential virulence factor of C. perfringens type C strains, which cause fatal hemorrhagic enteritis in animals and humans. We have previously shown that CPB is bound to endothelial cells within the intestine of affected pigs and humans, and that CPB is highly toxic to primary porcine endothelial cells (pEC) in vitro. The objective of the present study was to investigate the type of cell death induced by CPB in these cells, and to study potential host cell mechanisms involved in this process. CPB rapidly induced lactate dehydrogenase (LDH) release, propidium iodide uptake, ATP depletion, potassium efflux, a marked rise in intracellular calcium [Ca(2+)]i, release of high-mobility group protein B1 (HMGB1), and caused ultrastructural changes characteristic of necrotic cell death. Despite a certain level of caspase-3 activation, no appreciable DNA fragmentation was detected. CPB-induced LDH release and propidium iodide uptake were inhibited by necrostatin-1 and the two dissimilar calpain inhibitors PD150606 and calpeptin. Likewise, inhibition of potassium efflux, chelation of intracellular calcium and treatment of pEC with cyclosporin A also significantly inhibited CPB-induced LDH release. Our results demonstrate that rCPB primarily induces necrotic cell death in pEC, and that necrotic cell death is not merely a passive event caused by toxin-induced membrane disruption, but is propagated by host cell-dependent biochemical pathways activated by the rise in intracellular calcium and inhibitable by necrostatin-1, consistent with the emerging concept of programmed necrosis ("necroptosis").

Aminoacyl-tRNA synthetases: Probing the molecular basis of catalysis and discrimination

Aminoacyl-tRNA synthetases (RSs) are responsible for the essential connection of amino acids with trinucleotide sequences of tRNA's. The RS family constitutes two structurally dissimilar groups of proteins, class I and class II. Methionyl-tRNA synthetase (MetRS) and isoleucyl-tRNA synthetase (IleRS), both members of class I, were the focus of this work. Both enzymes are zinc-containing proteins; show a high degree of amino acid specificity; and edit activated noncognate amino acids, thereby ensuring the fidelity of the genetic code. The goals of this work were to further delineate the molecular basis of catalysis and discrimination in these enzymes by mapping active site geometries using high-resolution nuclear magnetic resonance spectroscopy (NMR).^ Internuclear distances obtained from transferred nuclear Overhauser effects were used to define the conformations of Mg($\alpha$,$\beta$-methylene)ATP bound to E. coli MetRS and E. coli IleRS in multiple complexes. Identical conformations were found for the bound ATP. Thus, the predicted structural homology between IleRS and MetRS is supported by consensus enzyme-bound nucleotide conformations. The conformation of the bound nucleotide is not sensitive to occupation of the amino acid site of MetRS or IleRS. Therefore, conformational changes known to occur in the synthetases upon ligand binding appear not to alter the bound conformation of the adenosine portion of the nucleotide. Nuclear Overhauser effects on the substrate amino acid L-selenomethionine were also used to evaluate the enzyme-bound conformation of the cognate amino acid. The amino acid assumes a conformation which is consistent with a proposed editing mechanism.^ The E. coli MetRS was shown to catalyze amino acid $\alpha$-proton exchange in the presence of deuterium oxide of all cognate amino acids. It is proposed that the enzyme-bound zinc coordinates the $\alpha$-carboxylate of the amino acid, rendering the $\alpha$-proton more acidic. An enzymic base is responsible for exchange of the $\alpha$-proton. This proposal suggests that the enzyme-bound zinc may have a role in amino acid discrimination in MetRS. However, the role of this exchange reaction in catalysis remains unknown. ^

ANALYTICAL MODELS OF EXOPLANETARY ATMOSPHERES. I. ATMOSPHERIC DYNAMICS VIA THE SHALLOW WATER SYSTEM

Within the context of exoplanetary atmospheres, we present a comprehensive linear analysis of forced, damped, magnetized shallow water systems, exploring the effects of dimensionality, geometry (Cartesian, pseudo-spherical, and spherical), rotation, magnetic tension, and hydrodynamic and magnetic sources of friction. Across a broad range of conditions, we find that the key governing equation for atmospheres and quantum harmonic oscillators are identical, even when forcing (stellar irradiation), sources of friction (molecular viscosity, Rayleigh drag, and magnetic drag), and magnetic tension are included. The global atmospheric structure is largely controlled by a single key parameter that involves the Rossby and Prandtl numbers. This near-universality breaks down when either molecular viscosity or magnetic drag acts non-uniformly across latitude or a poloidal magnetic field is present, suggesting that these effects will introduce qualitative changes to the familiar chevron-shaped feature witnessed in simulations of atmospheric circulation. We also find that hydrodynamic and magnetic sources of friction have dissimilar phase signatures and affect the flow in fundamentally different ways, implying that using Rayleigh drag to mimic magnetic drag is inaccurate. We exhaustively lay down the theoretical formalism (dispersion relations, governing equations, and time-dependent wave solutions) for a broad suite of models. In all situations, we derive the steady state of an atmosphere, which is relevant to interpreting infrared phase and eclipse maps of exoplanetary atmospheres. We elucidate a pinching effect that confines the atmospheric structure to be near the equator. Our suite of analytical models may be used to develop decisively physical intuition and as a reference point for three-dimensional magnetohydrodynamic simulations of atmospheric circulation.

Fire ecology north and south of the Alps since the last ice age

Wildfires are very rare in central Europe, which is probably why fire effects on vegetation have been neglected by most central European ecologists and palaeoecologists. Presently, reconstructions of fire history and fire ecology are almost absent. We analysed sediment cores from lakes on the Swiss Plateau (Lobsigensee and Soppensee) for pollen and charcoal to investigate the relationship between vegetation and fire. Microscopic charcoal evidence suggests increasing regional fire frequencies during the Neolithic (7350-4150 cal. BP, 5400-2200 BC) and the subsequent prehistoric epochs at Lobsigensee, whereas at Soppensee burnings remained rather rare until modern times. Neolithic peaks of charcoal at 6200 and 5500 cal. BP (4250 and 3550 BC) coincided with declines of pollen of fire-sensitive taxa at both sites (e.g., Ulmus, Tilia, Hedera, Fagus), suggesting synchronous vegetational responses to fire at regional scales. However, correlation analysis between charcoal and pollen for the period 6600-4400 cal. BP (4650-2650 BC) revealed no significant link between fire and vegetation at Soppensee, whereas at Lobsigensee increases of Corylus and decreases of Fagus were related to fire events. Fire impact on vegetation increased during the subsequent epochs at both sites. Correlation analyses of charcoal and pollen data for the period 4250-1150 cal. BP (2300 BC -AD 800) suggest that fires were intentionally set to disrupt forests and to provide open areas for arable and pastoral farming (e.g., significant positive correlations between charcoal and Cerealia, Plantago lanceolata, Asteroideae). These results are compared with southern European records (Lago di Origlio, Lago di Muzzano), which are situated in particularly fire-prone environments. After the Mesolithic period (I1 200-7350 cal. BP, 9250-5400 BC), charcoal influx was higher by an order of magnitude in the south, suggesting more frequent fires. Neolithic fires caused similar though more pronounced responses of vegetation in the south (e.g., expansions of Corylus). Post-Neolithic land-use practices involving (controlled) burning culminated in both regions at about 2550 cal. BP (c. 600 BC). However, fire-caused disappearances of entire forest communities were confined to the southern sites. Such differences in fire effects among the sites are explained by the dissimilar importance of fire as a result of different climatic conditions and cultural activities. Our results imply that the remaining (fire-sensitive) fragments of central European vegetation north of the Alps are especially endangered by increasing fire frequencies resulting from predicted climatic change.

STUDIES ON THE PATTERNS OF NUCLEOTIDE AND AMINO ACID SUBSTITUTION (ELECTROPHORESIS, MUTATION RATE, SELECTION, BASE, COMPOSITION)

Theoretical and empirical studies were conducted on the pattern of nucleotide and amino acid substitution in evolution, taking into account the effects of mutation at the nucleotide level and purifying selection at the amino acid level. A theoretical model for predicting the evolutionary change in electrophoretic mobility of a protein was also developed by using information on the pattern of amino acid substitution. The specific problems studied and the main results obtained are as follows: (1) Estimation of the pattern of nucleotide substitution in DNA nuclear genomes. The pattern of point mutations and nucleotide substitutions among the four different nucleotides are inferred from the evolutionary changes of pseudogenes and functional genes, respectively. Both patterns are non-random, the rate of change varying considerably with nucleotide pair, and that in both cases transitions occur somewhat more frequently than transversions. In protein evolution, substitution occurs more often between amino acids with similar physico-chemical properties than between dissimilar amino acids. (2) Estimation of the pattern of nucleotide substitution in RNA genomes. The majority of mutations in retroviruses accumulate at the reverse transcription stage. Selection at the amino acid level is very weak, and almost non-existent between synonymous codons. The pattern of mutation is very different from that in DNA genomes. Nevertheless, the pattern of purifying selection at the amino acid level is similar to that in DNA genomes, although selection intensity is much weaker. (3) Evaluation of the determinants of molecular evolutionary rates in protein-coding genes. Based on rates of nucleotide substitution for mammalian genes, the rate of amino acid substitution of a protein is determined by its amino acid composition. The content of glycine is shown to correlate strongly and negatively with the rate of substitution. Empirical formulae, called indices of mutability, are developed in order to predict the rate of molecular evolution of a protein from data on its amino acid sequence. (4) Studies on the evolutionary patterns of electrophoretic mobility of proteins. A theoretical model was constructed that predicts the electric charge of a protein at any given pH and its isoelectric point from data on its primary and quaternary structures. Using this model, the evolutionary change in electrophoretic mobilities of different proteins and the expected amount of electrophoretically hidden genetic variation were studied. In the absence of selection for the pI value, proteins will on the average evolve toward a mildly basic pI. (Abstract shortened with permission of author.) ^

Dielectrophoresis-based analyte separation and analysis

Dielectrophoresis—the tendency of a material of high dielectric permittivity to migrate in an electrical field gradient to a region of maximum field strength—provides an ideal motive force for manipulating small volumes of biological analytes in microfluidic microsystems. The work described in this thesis was based on the hypothesis that dielectrophoresis could be exploited to provide high-resolution cell separations in microsystems as well as a means for the electrically-controllable manipulation of solid supports for molecular analysis. To this end, a dielectrophoretic/gravitational field-flow-fractionation (DEP/G-FFF) system was developed and the separation performance evaluated using various types and sizes of polystyrene microspheres as model particles. It was shown that separation of the polystyrene beads was based on the differences in their effective dielectrophoretic properties. The ability of an improved DEP/G-FFF system to separate genetically identical, but phenotypically dissimilar cell types was demonstrated using mixtures of 6m2 mutant rat kidney cells grown under transforming and non-transforming culture conditions. Additionally, a panel of engineered dielectric microspheres was designed with specific, predetermined dielectrophoretic properties such that their dielectrophoretic behaviors would be controllable and predictable. The fabrication method involved the use of gold-coated polystyrene microsphere cores coated with a self-assembled monolayer of alkanethiol and, optionally, a self-assembled monolayer of phospholipid to form a thin-insulating-shell-over-conductive-interior structure. The successful development of the DEP/G-FFF separation system and the dielectrically engineered microspheres provides proof-of-principle demonstrations of enabling dielectrophoresis-based microsystem technology that should provide powerful new methods for the manipulation, separation and identification of analytes in many diverse fields. ^

Regulation of the heat shock response by thiol-reactive compounds in the yeast Saccharomyces cerevisiae

Cells govern their activities and modulate their interactions with the environment to achieve homeostasis. The heat shock response (HSR) is one of the most well studied fundamental cellular responses to environmental and physiological challenges, resulting in rapid synthesis of heat shock proteins (HSPs), which serve to protect cellular constituents from the deleterious effects of stress. In addition to its role in cytoprotection, the HSR also influences lifespan and is associated with a variety of human diseases including cancer, aging and neurodegenerative disorders. In most eukaryotes, the HSR is primarily mediated by the highly conserved transcription factor HSF1, which recognizes target hsp genes by binding to heat shock elements (HSEs) in their promoters. In recent years, significant efforts have been made to identify small molecules as potential pharmacological activators of HSF1 that could be used for therapeutic benefit in the treatment of human diseases relevant to protein conformation. However, the detailed mechanisms through which these molecules drive HSR activation remain unclear. In this work, I utilized the baker's yeast Saccharomyces cerevisiae as a model system to identify a group of thiol-reactive molecules including oxidants, transition metals and metalloids, and electrophiles, as potent activators of yeast Hsf1. Using an artificial HSE-lacZ reporter and the glucocorticoid receptor system (GR), these diverse thiol-reactive compounds are shown to activate Hsf1 and inhibit Hsp90 chaperone complex activity in a reciprocal, dose-dependent manner. To further understand whether cells sense these reactive compounds through accumulation of unfolded proteins, the proline analog azetidine-2-carboxylic acid (AZC) and protein cross-linker dithiobis(succinimidyl propionate) (DSP) were used to force misfolding of nascent polypeptides and existing cytosolic proteins, respectively. Both unfolding reagents display kinetic HSP induction profiles dissimilar to those generated by thiol-reactive compounds. Moreover, AZC treatment leads to significant cytotoxicity, which is not observed in the presence of the thiol-reactive compounds at the concentrations sufficient to induce Hsf1. Additionally, DSP treatment has little to no effect on Hsp90 functions. Together with the ultracentrifugation analysis of cell lysates that detected no insoluble protein aggregates, my data suggest that at concentrations sufficient to induce Hsf1, thiol-reactive compounds do not induce the HSR via a mechanism based on accumulation of unfolded cytosolic proteins. Another possibility is that thiol-reactive compounds may influence aspects of the protein quality control system such as the ubiquitin-proteasome system (UPS). To address this hypothesis, β-galactosidase reporter fusions were used as model substrates to demonstrate that thiol-reactive compounds do not inhibit ubiquitin activating enzymes (E1) or proteasome activity. Therefore, thiol-reactive compounds do not activate the HSR by inhibiting UPS-dependent protein degradation. I therefore hypothesized that these molecules may directly inactivate protein chaperones, known as repressors of Hsf1. To address this possibility, a thiol-reactive biotin probe was used to demonstrate in vitro that the yeast cytosolic Hsp70 Ssa1, which partners with Hsp90 to repress Hsf1, is specifically modified. Strikingly, mutation of conserved cysteine residues in Ssa1 renders cells insensitive to Hsf1 activation by cadmium and celastrol but not by heat shock. Conversely, substitution with the sulfinic acid and steric bulk mimic aspartic acid led to constitutive activation of Hsf1. Cysteine 303, located in the nucleotide-binding/ATPase domain of Ssa1, was shown to be modified in vivo by a model organic electrophile using Click chemistry technology, verifying that Ssa1 is a direct target for thiol-reactive compounds through adduct formation. Consistently, cadmium pretreatment promoted cells thermotolerance, which is abolished in cells carrying SSA1 cysteine mutant alleles. Taken together, these findings demonstrate that Hsp70 acts as a sensor to induce the cytoprotective heat shock response in response to environmental or endogenously produced thiol-reactive molecules and can discriminate between two distinct environmental stressors.