Sequence-function relationships in E. coli transcriptional regulation

Understanding how transcriptional regulatory sequence maps to regulatory function remains a difficult problem in regulatory biology. Given a particular DNA sequence for a bacterial promoter region, we would like to be able to say which transcription factors bind there, how strongly they bind, and whether they interact with each other and/or RNA polymerase, with the ultimate objective of integrating knowledge of these parameters into a prediction of gene expression levels. The theoretical framework of statistical thermodynamics provides a useful framework for doing so, enabling us to predict how gene expression levels depend on transcription factor binding energies and concentrations. We used thermodynamic models, coupled with models of the sequence-dependent binding energies of transcription factors and RNAP, to construct a genotype to phenotype map for the level of repression exhibited by the lac promoter, and tested it experimentally using a set of promoter variants from E. coli strains isolated from different natural environments. For this work, we sought to ``reverse engineer'' naturally occurring promoter sequences to understand how variations in promoter sequence affects gene expression. The natural inverse of this approach is to ``forward engineer'' promoter sequences to obtain targeted levels of gene expression. We used a high precision model of RNAP-DNA sequence dependent binding energy, coupled with a thermodynamic model relating binding energy to gene expression, to predictively design and verify a suite of synthetic E. coli promoters whose expression varied over nearly three orders of magnitude.

However, although thermodynamic models enable predictions of mean levels of gene expression, it has become evident that cell-to-cell variability or ``noise'' in gene expression can also play a biologically important role. In order to address this aspect of gene regulation, we developed models based on the chemical master equation framework and used them to explore the noise properties of a number of common E. coli regulatory motifs; these properties included the dependence of the noise on parameters such as transcription factor binding strength and copy number. We then performed experiments in which these parameters were systematically varied and measured the level of variability using mRNA FISH. The results showed a clear dependence of the noise on these parameters, in accord with model predictions.

Finally, one shortcoming of the preceding modeling frameworks is that their applicability is largely limited to systems that are already well-characterized, such as the lac promoter. Motivated by this fact, we used a high throughput promoter mutagenesis assay called Sort-Seq to explore the completely uncharacterized transcriptional regulatory DNA of the E. coli mechanosensitive channel of large conductance (MscL). We identified several candidate transcription factor binding sites, and work is continuing to identify the associated proteins.

Hydrogen-Atom Transfer Photochemistry of Tetrakis(µ-pyrophosphito)diplatinate(II)

In many senses, the hydrogen-atom transfer reactions observed with the triplet excited state of pyrophosphito-bridged platinum(II) dimers resemble the reactions of organic ketone nπ* states. The first two chapters describe our attempts to understand the reactivity differences between these two chromophores. Reactivity of the metal dimers is strongly regulated by the detailed nature of the ligands that ring the axial site, the hydrogen-abstraction center. A hydrogen-bonded network linking the ligands facilitates H-atom transfer quenching with alcohols through the formation of a hydrogen-bonded complex between the alcohol and a dimer. For substrates of equal C-H bond strength that lack a hydroxyl group (e.g., benzyl hydrocarbons), the quenching rate is several orders of magnitude slower.

The shape and size of the axial site, as determined by the ligands, also discriminate among quenchers by their steric characteristics. Very small quenchers quench slowly because of high entropies of activation, while very large ones have large enthalpic barriers. The two effects find a balance with quenchers of "just the right size."

The third chapter discusses the design of a mass spectrometer that uses positron annihilation to ionize neutral molecules. The mass spectrometer creates positron-molecule adducts whose annihilation produces fragmentation products that may yield information on the bonding of positrons in such complexes.

Fishes of the Lagunas Encadenadas (Province of Buenos Aires, Argentina), a wetland of international importance

The Lagunas Encadenadas form a large endorheic wetland. The system comprises a chain of five main lagoons (Alsina, Chochico, Del Monte, Del Venado, and Epecuen). During two recent collection trips, 13 species of fish were caught. From the collected material and available data in the literature the following points can be made: The fish fauna of this wetland comprises 18 species from 11 families and six orders. Four species (Cyprinus carpio, Hoplias malabaricus, Loricariichthys anus and Parapimelodus valenciennis) are new records for these water bodies. Fish species diversity decreases from east to west, ie from the most freshwater lagoon (Alsina, with 15 species) to the most saline (Epecuen, 1 species). A similar diversity pattern has been found in zooplankton species.

A Responsabilidade Civil do Advogado sob a perspectiva civil-constitucional

A responsabilidade civil do advogado é um tema que merece destaque sob a perspectiva civil constitucional. A abrangência dessa relação jurídica pelo Código de Defesa do Consumidor e a natureza negocial multiforme da relação estabelecida entre o advogado e o cliente, cuja normativa deve ser estabecida tendo em vista o caso concreto, são pontos de destaque desse trabalho, assim como a aplicabilidade do consentimento informado. Nessa toada, pretende-se conferir o enfoque funcional a partir da releitura das classificações tradicionais da responsabilidade civil em contratual, extracontratual, subjetiva, objetiva e entre as obrigações de meio e resultado para em seguida, analisarmos das hipóteses mais frequentes de responsabilização, quais sejam: a perda de uma chance, o abuso do direito processual e a reversão de liminares revertidas ao final do processo. Por fim, dentre as tendências de prevenção e precaução de danos da responsabilidade civil, revela-se a formalização de seguros de responsabilidade profissional para advogados.

Subspecies, morphs and clines in the amphipod Gammarus duebeni from fresh and saline waters

The nature and extent of morphological variation within populations of Gammarus duebeni are examined. The exceptional tolerance of G. duebeni to salinities that encompass three orders of magnitude was known in the 19th Century, and has attracted considerable attention from physiologists and ecologists in the 20th Century, including the likelihood that populations in freshwater are distinct from those living in more saline environments. It is concluded that gradual evolution into discrete and readily distinguished subspecies is currently underway, eventually producing several new species in freshwater and saline habitats.

Panpinan egindako bihotz-biriketako berpizte maniobran bularra bere onera bueltatzearen analisia

[EU]Dokumentu honek "Panpinan Egindako Bihotz-Biriketako Berpizte Maniobran Bularra Bere Onera Bueltatzearen Analisia" izena duen Gradu Amaierako Lanaren memoria eta eranskinak biltzen ditu. Bertan, lan horren bitartez lorturiko helburuak, horiek nola lortu diren eta burutu ahal izateko egin beharreko pausuak aurkezten dira. Bihotz-biriketako berpizterako berrelikadura gailuek berpizte maniobren kalitateari buruzko informazioa momentuan ematen dute. Proiektua berrelikadurarako laguntza gailuen parametroen kalitatea hobetzeko ikerlan bat egitera bideratuta dago, zehazki bularra bere onera bueltatzen den jakiteko metodoen azterketan sakontzen duelarik interesa duelarik. Alde batetik, benetako sakoneraren kalkulu zehatzari buruzko ikerketa bat egiten da, horretarako aukera ezberdinak aztertuz, metodo desberdinen analisia eginez. Bestetik, berrelikaduran zehar bularra bere onera bueltatzen den ohartarazteko (esate baterako, alarma sistema baten bitartez) parametroan egiten da ikerketa, horretarako indar sentsore gehigarri bat erabiliz.

Bihotz-biriketako berpizte masajeak EKG-an eta bular-inpedantzian eragindako interferentziaren azterketa

[EU]Proiektu honetan bihotz-biriketako berpizte masajearen bular-sakadek elektrokardiograman eta bular-inpedantziaren seinaleetan eragindako interferentziaren azterketa egiten da. Helburu nagusia bi interferentzia hauen arteko erlazioa aztertzea da, horretarako tresna garatuz. Erlazio hau definitzeak interferentziaren eragina txikitzeko modua aurkitzen lagunduko luke, eta honek berpizteko aukerak handituko lituzke. Proiektua gauzatzeko ospitalez kanpoko geldialdien erregistro multzo batetik abiatuta datu-base propioa garatu da ezarritako irizpide batzuk jarraituz. Datu-base berri hau 37 pazienteren 237 mozketak osatzen dute, 10 segundotako luzera minimoarekin non pazienteek asistolia bitarteko kanpoko bular masajea jasotzen duten. Bestalde, interferentzia ezaugarritzeko interfaze grafiko bat garatu da, elektrokardiograma eta bular-inpedantziaren seinaleak denboran eta maiztasunean erakutsi eta hauen parametro esanguratsuak automatikoki zein eskuz ateratzeko aukera ematen duena. Parametroak seinaleen sakada bakoitzeko maximo eta minimoak, beraien kokapenak eta oinarrizko maiztasuna, bere harmonikoak eta hauen anplitudeak dira. Tresna hau erabiliz aipatutako datu-baseko episodioen prozesaketa egin da. Bukatzeko, lortutako emaitzak tratatzeko bigarren interfaze grafiko bat garatu da, non emaitzen banaketa estatistikoa eta hauen arteko erlazio lineala aztertzen diren. Proiektuaren ekarpen nagusia, beraz, bihotz-biriketako berpizte masajeak eragindako interferentzia aztertzeko tresna ahaltsuaren garapena da, jatorri desberdineko bestelako berpizte episodioak aztertzeko ere balio duena.

Manipulating spectral anomalies of focused pulses in a medium with electromagnetically induced transparency

We study the possibility of manipulating the focusing properties of a medium with electromagnetically induced transparency. In the focal region of focused ultraslow light pulses, the spectral anomalous behaviors can be actively modified by varying the control field intensity. Unlike the case in free space, we find in slow light focusing that the spectrum bandwidth of the incident field needed to produce observable spectral changes can be reduced by several orders. Numerical simulations with accessible parameters clearly show that spectral anomalies of focused mu s pulses are observable.

Plataforma de investigación en el ámbito de la resucitación cardio-pulmonar basada en un maniquí de entrenamiento sensorizado

[ES]Hoy en día las muertes por parada cardiorrespiratoria superan en número a otras más mediáticas como aquellas que se producen por incendios o en accidentes de tráfico, y sin embargo su repercusión es mucho menor. Este hecho debe ser motivo de preocupación ya que, con una correcta formación de la población en materia de resucitación cardíaca, muchas de estas muertes podrían ser evitadas. Con el objetivo de reducir estas estadísticas han surgido multitud de estudios y proyectos de investigación consistentes en tratar de mejorar las herramientas disponibles tanto para personal sanitario como no sanitario. En este marco se encuadra el proyecto presentado en este documento, consistente en la sensorización de un maniquí de entrenamiento para episodios de parada cardiorrespiratoria, el cual ofrecerá la posibilidad de analizar con detalle el artifact o interferencia generada por el rescatador sobre el paciente en el momento de efectuar la maniobra de resucitación, así como la interferencia causada por el contacto electrodo-piel. Paralelamente podrá ser utilizado como mero instrumento de entrenamiento para posibles situaciones reales. El porqué de la utilización de este tipo de maniquíes reside principalmente en la imposibilidad de emplear personas debido a las posibles lesiones torácicas que pueden ocurrir por las compresiones realizadas. Finalmente debe citarse el hecho de que no es imprescindible tener conocimientos médicos para poder aplicar las técnicas básicas de resucitación cardíaca, acción que incrementa las posibilidades de supervivencia de un paciente de manera excepcional, ya que cada minuto que pasa desde la parada cardiorrespiratoria la probabilidad de supervivencia disminuye en un porcentaje significativamente elevado. Tomando como base lo descrito hasta ahora, en este documento se detalla la solución técnica de la sensorización de un maniquí genérico para la adquisición de las señales de fuerza de compresión, aceleración sufrida por el pecho en tres ejes ortogonales, profundidad de compresión, impedancia entre los dos electrodos colocados sobre el pecho del paciente y señal electrocardiográfica emitida por el corazón; además, se incluye la posibilidad de inyectar una señal electrocardiográfica previamente grabada. La base de registros obtenida de estos ensayos podrá ser utilizada posteriormente para su análisis, ya que su similitud con señales extraídas en un caso real es máxima.

Ferromagnetic Resonance Force Microscopy

A new approach to magnetic resonance was introduced in 1992 based upon detection of spin-induced forces by J. Sidles [1]. This technique, now called magnetic resonance force microscopy (MRFM), was first demonstrated that same year via electron paramagnetic resonance (EPR) by D. Rugar et al. [2]. This new method combines principles of magnetic resonance with those of scanned probe technology to detect spin resonance through mechanical, rather than inductive, means. In this thesis the development and use of ferromagnetic resonance force microscopy (FMRFM) is described. This variant of MRFM, which allows investigation of ferromagnetic samples, was first demonstrated in 1996 by Z. Zhang et al. [3]. FMRFM enables characterization of (a) the dynamic magnetic properties of microscale magnetic devices, and (b) the spatial dependence of ferromagnetic resonance within a sample. Both are impossible with conventional ferromagnetic resonance techniques.

Ferromagnetically coupled systems, however, pose unique challenges for force detection. In this thesis the attainable spatial resolution - and the underlying physical mechanisms that determine it - are established. We analyze the dependence of the magnetostatic modes upon sample dimensions using a series of microscale yttrium iron garnet (YIG) samples. Mapping of mode amplitudes within these sample is attained with an unprecedented spatial resolution of 15μm. The modes, never before analyzed on this scale, fit simple models developed in this thesis for samples of micron dimensions. The application of stronger gradient fields induces localized perturbation of the ferromagnetic resonance modes. The first demonstrations of this effect are presented in this study, and a simple theoretical model is developed to explain our observations. The results indicate that the characteristics of the locally-detected ferromagnetic modes are still largely determined by the external fields and dimensions of the entire sample, rather than by the localized interaction volume (i.e., the locale most strongly affected by the local gradient field). Establishing this is a crucial first step toward understanding FMRFM in the high gradient field limit where the dispersion relations become locally determined. In this high gradient field regime, FMRFM imaging becomes analogous with that of EPR MRFM.

FMRFM has also been employed to characterize magnetic multilayers, similar to those utilized in giant magnetoresistance (GMR) devices, on a lateral scale 40 x 40μm. This is orders of magnitude smaller than possible via conventional methods. Anisotropy energies, thickness, and interface qualities of individual layers have been resolved.

This initial work clearly demonstrates the immense and unique potential that FMRFM offers for characterizing advanced magnetic nanostructures and magnetic devices.

以慢原子束方式进行原子转移的双磁光阱系统

建立了一套用于玻色．爱因斯坦凝聚实验的铷原子双磁光阱装置．从低速强源中获得慢原子柬，向超高真空磁光阱进行原子转移．低速强源磁光阱与超高真空磁光阱之间可维持3个量级的压强差，超高真空磁光阱的真空度最高可达1×10^-9Pa．慢原子束的束流通量达1×10^9／s．约4×10^8个^17Rb原子被装载到超高真空磁光阱中．还讨论了两种典型情况下磁光阱中装载的最大原子数．

Bihotz biriketako berpiztea simulatzeko panpin baten kudeaketarako tresna

[EU]Lan honen helburua, sentsorizatutako panpina kontrolatzeko software bat garatzea da, bihotz biriketako berpiztearen inguruko ikerkuntza sustatzeko helburuarekin. Kontrol hau aurrera eramateko bihotz biriketako berpiztearen inguruko kalitate parametro garrantzitsuenak jasotzen dituzten sentsoreekin hornitutako panpina bat erabili da, softwarearen eta panpinaren sentsoreen arteko interfaze gisa NI-DAQ National Instruments-eko txartela erabili delarik. Eskema honi jarraituz, software honek eskaintzen dituen funtzionalitate garrantzitsuenak hurrengoak dira: panpinaren bihotza simulatuko duen elektrokardiograma seinale bat panpinara transferitzea, sentsoreetatik lortutako informazioa biltegiratzea eta denbora errealean bistaratzea eta aurretiaz grabatutako erregistroen erreprodukzioa. Software hau garatzearen arrazoi nagusiak, bihotz biriketako berpiztearen kalitatea hobetzea eta elektrodoen eta pazientearen azalaren arteko kontaktuak elektrokardiograman sortzen duen interferentzia ezaugarritzea dira, bihotz-geldiunea pairatzen duen pazientearen bizi-iraupena handituko duten tresnen garapena sustatuz. Izan ere, bihotz-heriotza da herrialde garatuenen lehen heriotza-arrazoia.

Acceleration Sensing, Feedback Cooling, and Nonlinear Dynamics with Nanoscale Cavity-Optomechanical Devices

Light has long been used for the precise measurement of moving bodies, but the burgeoning field of optomechanics is concerned with the interaction of light and matter in a regime where the typically weak radiation pressure force of light is able to push back on the moving object. This field began with the realization in the late 1960's that the momentum imparted by a recoiling photon on a mirror would place fundamental limits on the smallest measurable displacement of that mirror. This coupling between the frequency of light and the motion of a mechanical object does much more than simply add noise, however. It has been used to cool objects to their quantum ground state, demonstrate electromagnetically-induced-transparency, and modify the damping and spring constant of the resonator. Amazingly, these radiation pressure effects have now been demonstrated in systems ranging 18 orders of magnitude in mass (kg to fg).

In this work we will focus on three diverse experiments in three different optomechanical devices which span the fields of inertial sensors, closed-loop feedback, and nonlinear dynamics. The mechanical elements presented cover 6 orders of magnitude in mass (ng to fg), but they all employ nano-scale photonic crystals to trap light and resonantly enhance the light-matter interaction. In the first experiment we take advantage of the sub-femtometer displacement resolution of our photonic crystals to demonstrate a sensitive chip-scale optical accelerometer with a kHz-frequency mechanical resonator. This sensor has a noise density of approximately 10 micro-g/rt-Hz over a useable bandwidth of approximately 20 kHz and we demonstrate at least 50 dB of linear dynamic sensor range. We also discuss methods to further improve performance of this device by a factor of 10.

In the second experiment, we used a closed-loop measurement and feedback system to damp and cool a room-temperature MHz-frequency mechanical oscillator from a phonon occupation of 6.5 million down to just 66. At the time of the experiment, this represented a world-record result for the laser cooling of a macroscopic mechanical element without the aid of cryogenic pre-cooling. Furthermore, this closed-loop damping yields a high-resolution force sensor with a practical bandwidth of 200 kHZ and the method has applications to other optomechanical sensors.

The final experiment contains results from a GHz-frequency mechanical resonator in a regime where the nonlinearity of the radiation-pressure interaction dominates the system dynamics. In this device we show self-oscillations of the mechanical element that are driven by multi-photon-phonon scattering. Control of the system allows us to initialize the mechanical oscillator into a stable high-amplitude attractor which would otherwise be inaccessible. To provide context, we begin this work by first presenting an intuitive overview of optomechanical systems and then providing an extended discussion of the principles underlying the design and fabrication of our optomechanical devices.

General-domain compressible Navier-Stokes solvers exhibiting quasi-unconditional stability and high-order accuracy in space and time

This thesis presents a new class of solvers for the subsonic compressible Navier-Stokes equations in general two- and three-dimensional spatial domains. The proposed methodology incorporates: 1) A novel linear-cost implicit solver based on use of higher-order backward differentiation formulae (BDF) and the alternating direction implicit approach (ADI); 2) A fast explicit solver; 3) Dispersionless spectral spatial discretizations; and 4) A domain decomposition strategy that negotiates the interactions between the implicit and explicit domains. In particular, the implicit methodology is quasi-unconditionally stable (it does not suffer from CFL constraints for adequately resolved flows), and it can deliver orders of time accuracy between two and six in the presence of general boundary conditions. In fact this thesis presents, for the first time in the literature, high-order time-convergence curves for Navier-Stokes solvers based on the ADI strategy---previous ADI solvers for the Navier-Stokes equations have not demonstrated orders of temporal accuracy higher than one. An extended discussion is presented in this thesis which places on a solid theoretical basis the observed quasi-unconditional stability of the methods of orders two through six. The performance of the proposed solvers is favorable. For example, a two-dimensional rough-surface configuration including boundary layer effects at Reynolds number equal to one million and Mach number 0.85 (with a well-resolved boundary layer, run up to a sufficiently long time that single vortices travel the entire spatial extent of the domain, and with spatial mesh sizes near the wall of the order of one hundred-thousandth the length of the domain) was successfully tackled in a relatively short (approximately thirty-hour) single-core run; for such discretizations an explicit solver would require truly prohibitive computing times. As demonstrated via a variety of numerical experiments in two- and three-dimensions, further, the proposed multi-domain parallel implicit-explicit implementations exhibit high-order convergence in space and time, useful stability properties, limited dispersion, and high parallel efficiency.

二次光栅在波前测量中的应用

采用一种特殊的二次光栅用于激光波前测量, 它对非零级衍射光束具有不同的聚焦效应, 其光栅线为圆弧型而非直线。导出了在会聚光束情况下的两平面成像在单一像平面上的距离关系, 实验上实现了二次光栅用于会聚光束的波前测量, 测量得到会聚光束具有较大的散焦(-2.93λ)和球差(1.34λ), 与该透镜引起波前的离焦像差理论理想值(-2.695λ)基本符合。该技术可以实现波前的高空间分辨力和高精度实时测量, 大大减少光学元件数量, 降低装置成本。由于大功率激光束的不稳定性, 其波前变化非常快, 所以该方法的实时性非