Stochastic model of transcription factor-regulated gene expression

We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes: Gene A and Gene B which synthesize the TFs and the target gene proteins respectively. We show through analytic calculations that the TF fluctuations have a significant effect on the distribution of the target gene protein levels when the mean TF level falls in the highest sensitive region of the dose-response curve. We further study the effect of reducing the copy number of Gene A from two to one. The enhanced TF fluctuations yield results different from those in the deterministic case. The probability that the target gene protein level exceeds a threshold value is calculated with a knowledge of the probability density functions associated with the TF and target gene protein levels. Numerical simulation results for a more detailed stochastic model are shown to be in agreement with those obtained through analytic calculations. The relevance of these results in the context of the genetic disorder haploinsufficiency is pointed out. Some experimental observations on the haploinsufficiency of the tumour suppressor gene, Nkx3.1, are explained with the help of the stochastic model of TF-regulated gene expression.Comment: 17 pages, 11 figures. Accepted for publication in Physical Biolog

Coastal oceanography and sedimentology in New Zealand, 1967-91.

This paper reviews research that has taken place on physical oceanography and sedimentology on New Zealand's estuaries and the inner shelf since c. 1967. It includes estuarine sedimentation, tidal inlets, beach morphodynamics, nearshore and inner shelf sedimentation, tides and coastal currents, numerical modelling, short-period waves, tsunamis, and storm surges. An extensive reference list covering both published and unpublished material is included. Formal teaching and research programmes dealing with coastal landforms and the processes that shape them were only introduced to New Zealand universities in 1964; the history of the New Zealand Journal of Marine and Freshwater Research parallels and chronicles the development of physical coastal science in New Zealand, most of which has been accomplished in last 25 years

Colour Relations in Form

The orthodox monadic determination thesis holds that we represent colour relations by virtue of representing colours. Against this orthodoxy, I argue that it is possible to represent colour relations without representing any colours. I present a model of iconic perceptual content that allows for such primitive relational colour representation, and provide four empirical arguments in its support. I close by surveying alternative views of the relationship between monadic and relational colour representation

Decontamination of a \u3cem\u3eHistoplasma capsulatum\u3c/em\u3e-Infested Blackbird Roost: Use of a Sprinkler System to Apply Formalin

When disturbed, blackbird/starling roost sites can be sources of locally severe outbreaks of histoplasmosis; therefore decontamination with formalin is sometimes prudent. We describe the use of a $5000 sprinkler system for spraying formalin on a Histoplasma capsulatum-infested roost site. This system precludes direct worker involvement in the application of this hazardous chemical to the area. Analysis of soil samples collected and cultured both before and after formalin treatment confirmed the eradication of H. capsulatum from the 1.3 ha site. Cost was approximately$17,000 with sprinkler system provided at no charge

Petrogenesis of diachronous mixed siliciclastic-carbonate megafacies in the cool-water Oligocene Tikorangi Formation, Taranaki Basin, New Zealand

The Oligocene (Whaingaroan-Waitakian) Tikorangi Formation is a totally subsurface, lithostratigraphically complex, mixed siliciclastic-limestone-rich sequence forming an important fracture reservoir within Taranaki Basin, New Zealand. Petrographically the formation comprises a spectrum of interbedded rock types ranging from calcareous mudstone to wackestone to packstone to clean sparry grainstone. Skeletal and textural varieties within these rock types have aided in the identification of three environmentally distinctive megafacies for the Tikorangi Formation rocks-shelfal, foredeep, and basinal. Data from these megafacies have been used to detail previous conclusions on the petrogenesis and to further refine depositional paleoenvironmental models for the Tikorangi Formation in the central eastern Taranaki Basin margin.Shelfal Megafacies 1 rocks (reference well Hu Road-1A) are latest Oligocene (early Waitakian) in age and formed on or proximal to the Patea-Tongaporutu-Herangi basement high. They are characterised by coarse, skeletal-rich, pure sparry grainstone comprising shallow water, high energy taxa (bryozoans, barnacles, red algae) and admixtures of coarse well-rounded lithic sand derived from Mesozoic basement greywacke. This facies type has previously gone unrecorded in the Tikorangi Formation. Megafacies 2 is a latest Oligocene (early Waitakian) foredeep megafacies (formerly named shelfal facies) formed immediately basinward and west of the shelfal basement platform. It accumulated relatively rapidly (>20 cm/ka) from redeposition of shelfal megafacies biota that became intermixed with bathyal taxa to produce a spectrum of typically mudstone through to sparry grainstone. The resulting skeletal mix (bivalve, echinoderm, planktic and benthic foraminiferal, red algal, bryozoan, nannofossil) is unlike that in any of the age-equivalent limestone units in neighbouring onland King Country Basin. Megafacies 3 is an Oligocene (Whaingaroan-Waitakian) offshore basinal megafacies (formerly termed bathyal facies) of planktic foraminiferal-nannofossil-siliciclastic wackestone and mudstone formed away from redepositional influences. The siliciclastic input in this distal basinal setting (sedimentation rates <7 mm/ka) was probably sourced mainly from oceanic currents carrying suspended sediment from South Island provenances exposed at this time.Tikorangi Formation rocks record the Taranaki Basin’s only period of carbonate-dominated sedimentation across a full range of shelfal, foredeep, and basinal settings. Depositional controls on the three contrasting megafacies were fundamentally the interplay of an evolving and complex plate tectonic setting, including development of a carbonate foredeep, changes in relative sea level within an overall transgressive regime, and changing availability, sources, and modes of deposition of both bioclastic and siliciclastic sediments. The mixed siliciclastic-carbonate nature of the formation, and its skeletal assemblages, low-Mg calcite mineralogy, and delayed deep burial diagenetic history, are features consistent with formation in temperate-latitude cool waters

Long-lived qubit memory using atomic ions

We demonstrate experimentally a robust quantum memory using a magnetic-field-independent hyperfine transition in 9Be+ atomic ion qubits at a magnetic field B ~= 0.01194 T. We observe that the single physical qubit memory coherence time is greater than 10 seconds, an improvement of approximately five orders of magnitude from previous experiments with 9Be+. We also observe long coherence times of decoherence-free subspace logical qubits comprising two entangled physical qubits and discuss the merits of each type of qubit.Comment: 5 pages, 4 figure

Hyperfine Coherence in the Presence of Spontaneous Photon Scattering

The coherence of a hyperfine-state superposition of a trapped $^{9}$Be$^+$ ion in the presence of off-resonant light is experimentally studied. It is shown that Rayleigh elastic scattering of photons that does not change state populations also does not affect coherence. Coherence times exceeding the average scattering time of 19 photons are observed. This result implies that, with sufficient control over its parameters, laser light can be used to manipulate hyperfine-state superpositions with very little decoherence.Comment: Letter, 4 figure

Quantum control, quantum information processing, and quantum-limited metrology with trapped ions

We briefly discuss recent experiments on quantum information processing using trapped ions at NIST. A central theme of this work has been to increase our capabilities in terms of quantum computing protocols, but we have also applied the same concepts to improved metrology, particularly in the area of frequency standards and atomic clocks. Such work may eventually shed light on more fundamental issues, such as the quantum measurement problem.Comment: Proceedings of the International Conference on Laser Spectroscopy (ICOLS), 10 pages, 5 figure