Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction

The invasive signal amplification reaction has been previously developed for quantitative detection of nucleic acids and discrimination of single-nucleotide polymorphisms. Here we describe a method that couples two invasive reactions into a serial isothermal homogeneous assay using fluorescence resonance energy transfer detection. The serial version of the assay generates more than 107 reporter molecules for each molecule of target DNA in a 4-h reaction; this sensitivity, coupled with the exquisite specificity of the reaction, is sufficient for direct detection of less than 1,000 target molecules with no prior target amplification. Here we present a kinetic analysis of the parameters affecting signal and background generation in the serial invasive signal amplification reaction and describe a simple kinetic model of the assay. We demonstrate the ability of the assay to detect as few as 600 copies of the methylene tetrahydrofolate reductase gene in samples of human genomic DNA. We also demonstrate the ability of the assay to discriminate single base differences in this gene by using 20 ng of human genomic DNA.

Genetic drift and within-host metapopulation dynamics of HIV-1 infection

Most HIV replication occurs in solid lymphoid tissue, which has prominent architecture at the histological level, which separates groups of productively infected CD4+ cells. Nevertheless, current population models of HIV assume panmixis within lymphoid tissue. We present a simple “metapopulation” model of HIV replication, where the population of infected cells is comprised of a large number of small populations, each of which is established by a few founder viruses and undergoes turnover. To test this model, we analyzed viral genetic variation of infected cell subpopulations within the spleen and demonstrated the action of founder effects as well as significant variation in the extent of genetic differentiation between subpopulations among patients. The combination of founder effects and subpopulation turnover can result in an effective population size much lower than the actual population size and may contribute to the importance of genetic drift in HIV evolution despite a large number of infected cells.

The design of an agent to bend DNA.

An artificial DNA bending agent has been designed to assess helix flexibility over regions as small as a protein binding site. Bending was obtained by linking a pair of 15-base-long triple helix forming oligonucleotides (TFOs) by an adjustable polymeric linker. By design, DNA bending was introduced into the double helix within a 10-bp spacer region positioned between the two sites of 15-base triple helix formation. The existence of this bend has been confirmed by circular permutation and phase-sensitive electrophoresis, and the directionality of the bend has been determined as a compression of the minor helix groove. The magnitude of the resulting duplex bend was found to be dependent on the length of the polymeric linker in a fashion consistent with a simple geometric model. Data suggested that a 50-70 degrees bend was achieved by binding of the TFO chimera with the shortest linker span (18 rotatable bonds). Equilibrium analysis showed that, relative to a chimera which did not bend the duplex, the stability of the triple helix possessing a 50-70 degrees bend was reduced by less than 1 kcal/mol of that of the unbent complex. Based upon this similarity, it is proposed that duplex DNA may be much more flexible with respect to minor groove compression than previously assumed. It is shown that this unusual flexibility is consistent with recent quantitation of protein-induced minor groove bending.

Trypanosome U-deletional RNA editing involves guide RNA-directed endonuclease cleavage, terminal U exonuclease, and RNA ligase activities.

We have studied the mechanism of accurate in vitro RNA editing of Trypanosoma brucei ATPase 6 mRNA, using four mRNA-guide RNA (gRNA) pairs that specify deletion of 2, 3, or 4 U residues at editing site 1 and mitochondrial extract. This extract not only catalyzes deletion of the specified number of U residues but also exhibits a novel endonuclease activity that cleaves the input pre-mRNA in a gRNA-directed manner, precisely at the phosphodiester bond predicted in a simple enzymatic model of RNA editing. This cleavage site is inconsistent with a chimera-based editing mechanism. The U residues to be deleted, present at the 3' end of the upstream cleavage product, are then removed evidently by a 3' U-specific exonuclease and not by a reverse reaction of terminal U transferase. RNA ligase can then join the mRNA halves through their newly formed 5' P and 3' OH termini, generating mRNA faithfully edited at the first editing site. This resultant, partially edited mRNA can then undergo accurate, gRNA-directed cleavage at editing site 2, again precisely as predicted by the enzymatic editing model. All of these enzymatic activities cofractionate with the U-deletion activity and may reside in a single complex. The data imply that each round of editing is a four-step process, involving (i) gRNA-directed cleavage of the pre-mRNA at the bond immediately 5' of the region base paired to the gRNA, (ii) U deletion from or U addition to the 3' OH of the upstream mRNA half, (iii) ligation of the mRNA halves, and (iv) formation of additional base pairing between the correctly edited site and the gRNA that directs subsequent nuclease cleavage at the next editing site.

Evolution as a self-organized critical phenomenon.

We present a simple mathematical model of biological macroevolution. The model describes an ecology of adapting, interacting species. The environment of any given species is affected by other evolving species; hence, it is not constant in time. The ecology as a whole evolves to a "self-organized critical" state where periods of stasis alternate with avalanches of causally connected evolutionary changes. This characteristic behavior of natural history, known as "punctuated equilibrium," thus finds a theoretical explanation as a self-organized critical phenomenon. The evolutionary behavior of single species is intermittent. Also, large bursts of apparently simultaneous evolutionary activity require no external cause. Extinctions of all sizes, including mass extinctions, may be a simple consequence of ecosystem dynamics. Our results are compared with data from the fossil record.

In vivo estimates of division and death rates of human T lymphocytes.

We present data on the decay, after radiotherapy, of naive and memory human T lymphocytes with stable chromosome damage. These data are analyzed in conjunction with existing data on the decay of naive and memory T lymphocytes with unstable chromosome damage and older data on unsorted lymphocytes. The analyses yield in vivo estimates for some life-history parameters of human T lymphocytes. Best estimates of proliferation rates have naive lymphocytes dividing once every 3.5 years and memory lymphocytes dividing once every 22 weeks. It appears that memory lymphocytes can revert to the naive phenotype, but only, on average, after 3.5 years in the memory class. The lymphocytes with stable chromosome damage decay very slowly, yielding surprisingly low estimates of their death rate. The estimated parameters are used in a simple mathematical model of the population dynamics of undamaged naive and memory lymphocytes. We use this model to illustrate that it is possible for the unprimed subset of a constantly stimulated clone to stay small, even when there is a large population of specific primed cells reverting to the unprimed state.

Theory of orientation tuning in visual cortex.

The role of intrinsic cortical connections in processing sensory input and in generating behavioral output is poorly understood. We have examined this issue in the context of the tuning of neuronal responses in cortex to the orientation of a visual stimulus. We analytically study a simple network model that incorporates both orientation-selective input from the lateral geniculate nucleus and orientation-specific cortical interactions. Depending on the model parameters, the network exhibits orientation selectivity that originates from within the cortex, by a symmetry-breaking mechanism. In this case, the width of the orientation tuning can be sharp even if the lateral geniculate nucleus inputs are only weakly anisotropic. By using our model, several experimental consequences of this cortical mechanism of orientation tuning are derived. The tuning width is relatively independent of the contrast and angular anisotropy of the visual stimulus. The transient population response to changing of the stimulus orientation exhibits a slow "virtual rotation." Neuronal cross-correlations exhibit long time tails, the sign of which depends on the preferred orientations of the cells and the stimulus orientation.

Anisotropic magnetoresistance in single electron transport

We study the effect of magnetic anisotropy in a single electron transistor with ferromagnetic electrodes and a non-magnetic island. We identify the variation δμ of the chemical potential of the electrodes as a function of the magnetization orientation as a key quantity that permits to tune the electrical properties of the device. Different effects occur depending on the relative size of δμ and the charging energy. We provide preliminary quantitative estimates of δμ using a very simple toy model for the electrodes.

Guidelines for the design of efficient sono-microreactors

Possible drawbacks of microreactors are inefficient reactant mixing and the clogging of microchannels when solid-forming reactions are carried out or solid (catalysts) suspensions are used. Ultrasonic irradiation has been successfully implemented for solving these problems in microreactor configurations ranging from capillaries immersed in ultrasonic baths to devices with miniaturized piezoelectric transducers. Moving forward in process intensification and sustainable development, the acoustic energy implementation requires a strategy to optimize the microreactor from an ultrasound viewpoint during its design. In this work, we present a simple analytical model that can be used as a guide to achieving a proper acoustic design of stacked microreactors. An example of this methodology was demonstrated through finite element analysis and it was compared with an experimental study found in the literature.

Acoustic properties of porous concrete made from arlite and vermiculite lightweight aggregates

The use of sustainable materials is becoming a common practice for noise abatement in building and civil engineering industries. In this context, many applications have been found for porous concrete made from lightweight aggregates. This work investigates the acoustic properties of porous concrete made from arlite and vermiculite lightweight aggregates. These natural resources can still be regarded as sustainable since they can be recycled and do not generate environmentally hazardous waste. The experimental basis used consists of different type specimens whose acoustic performance is assessed in an impedance tube. Additionally, a simple theoretical model for granular porous media, based on parameters measurable with basic experimental procedures, is adopted to predict the acoustic properties of the prepared mixes. The theoretical predictions compare well with the absorption measurements. Preliminary results show the good absorption capability of these materials, making them a promising alternative to traditional porous concrete solutions.

Discretion and Accountability: The ESMA Judgment and the Meroni Doctrine. Bruges European Economic Research (BEER) Papers 30/2014

This paper assesses the effectiveness of the Meroni doctrine in the light of the recent judgment in the ESMA case. The first part explains in detail the problem of delegation of powers in the EU from the perspective of the principal-agent theory and complements it with the analysis of the trade-off between different levels of independence and accountability of agencies. A simple economic model is developed to illustrated the relationship between the independence and accountability of an agency. It shows that it is the accountability mechanism that induces the agent to act, rather than the extent of his independence. The paper also explains the inter-temporal interactions between the principal and the agent on the basis of the incentives in place for the different players. The second part is devoted to analysis of the functioning of ESMA in the context of its delegated powers. After the presentation of main aspects of the regulatory framework establishing ESMA, the paper continuous with an analysis and interpretation of the discretionary powers of ESMA. The rather rigid position of the Court of Justice in relation to the Meroni doctrine seems to be unsuitable to delegation of complex regulatory tasks. This is particularly evident in the case of financial markets. Finally, the judgment does not examine in any detail whether and how the principals - i.e. the EU and Member States - are best able to evaluate the quality of ESMA decisions and regulations and whether there are different but more effective accountability mechanisms.

On Incentives in Technology Policymaking: What the EU Can Learn from U.S. Developments. CES Germany & Europe Working Papers, No. 07.7, 1997

This paper explores the incentives political and bureaucratic actors face in the institutional setting of EU technology policy. In examining the implications and assumptions of neoclassical and evolutionary theories of technological change, it tries to answer why certain theories do not obtain importance in the political wor1d. By focusing on the positive approach to policymaking, the paper examines why policy learning does not occur m certain institutional settings. In referring to EU technology programs, I show which conceptual and functional shortcomings limit the policies in question. As evaluation and oversight mechanisms have not been sufficiently developed and accepted within the institutional setting, there is much room for inefficiency. I discuss this setting within a simple agency model using two political actors and two firms performing R&D. It is easy to show that when asymmetric information applies, the firms receive positive rents and the political agent gains reputation. The outcome suggests changing the evaluation practices and embedding results in political decision making. Regarding this point, recent U.S. developments seem to have led to more efficiency. Moreover, the paper suggests delegating technology policy to other actors and discussing the empowerment of different principals on the political plane.

Modeling and validation of the thermal behavior of buildings for the development of demand response methods

The representation of the thermal behaviour of the building is achieved through a relatively simple dynamic model that takes into account the effects due to the thermal mass of the building components. The model of a intra-floor apartment has been built in the Matlab-Simulink environment and considers the heat transmission through the external envelope, wall and windows, the internal thermal masses, (i.e. furniture, internal wall and floor slabs) and the sun gain due to opaque and see-through surfaces of the external envelope. The simulations results for the entire year have been compared and the model validated, with the one obtained with the dynamic building simulation software Energyplus.

Constraining porewater chemistry in a 250m thick argillaceous rock sequence

The geochemistry of an argillaceous rock sequence from a deep borehole in NE-Switzerland was investigated. The focus was to constrain the porewater chemistry in low permeability Jurassic rocks comprising the Liassic, the Opalinus Clay formation, the 'Brown Dogger' unit and the Effingen Member (Malm). A multi-method approach including mineralogical analysis, aqueous and Ni-ethylenediamine extraction, squeezing tests and pCO(2) measurements as well as geochemical modelling was applied for this purpose. A consistent dataset was obtained with regard to the main solutes in the porewaters. A fairly constant anion-accessible porosity of similar to 50% of the total porosity was deduced for all analysed samples which displayed variable clay-mineral contents. Sulphate concentrations were shown to be constrained by a sulphate-bearing phase, presumably by celestite or a Sr-Ba sulphate. Application of a simple equilibrium model, including cation exchange reactions, calcite and celestite equilibrium showed good agreement with squeezing data, indicating the suitability of the modelling approach to simulate porewater chemistry in the studied argillaceous rocks. The modelling highlighted the importance of correct determination of the exchangeable cation population. The analysis corroborates that squeezing of the studied rocks is a viable and efficient way to sample porewater.

Pliocene-Pleistocene stack of globally distributed benthic stable oxygen isotope records

We present a 5.3-Myr stack (the ''LR04'' stack) of benthic d18O records from 57 globally distributed sites aligned by an automated graphic correlation algorithm. This is the first benthic delta18O stack composed of more than three records to extend beyond 850 ka, and we use its improved signal quality to identify 24 new marine isotope stages in the early Pliocene. We also present a new LR04 age model for the Pliocene-Pleistocene derived from tuning the delta18O stack to a simple ice model based on 21 June insolation at 65 N. Stacked sedimentation rates provide additional age model constraints to prevent overtuning. Despite a conservative tuning strategy, the LR04 benthic stack exhibits significant coherency with insolation in the obliquity band throughout the entire 5.3 Myr and in the precession band for more than half of the record. The LR04 stack contains significantly more variance in benthic delta18O than previously published stacks of the late Pleistocene as the result of higher resolution records, a better alignment technique, and a greater percentage of records from the Atlantic. Finally, the relative phases of the stack's 41- and 23-kyr components suggest that the precession component of delta18O from 2.7-1.6 Ma is primarily a deep-water temperature signal and that the phase of d18O precession response changed suddenly at 1.6 Ma.