Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression. Methodology/Principal Findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation. Conclusions/Significance: Of the,27,000 predicted open reading frames, transcripts homologous to only,5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

INFLUENCE OF THE 90-DEGREES PARTIAL DISLOCATION CORE STRUCTURE IN SILICON ON ENERGY-LEVELS

An LCAO-scheme taking into account 10 atomic orbitals (s-, p-, and d-type) is used to calculate the electronic structure of the reconstructed 90-degrees partial dislocation in Si. Two different valence force fields producing deviating results are used for modelling the core structure. Geometrical data published by another group is also used. The aim is to explore the influence of geometry on energy levels. We find that the band structure depends sensitively on bond angles. Using data determined by the Tersoff potential we obtain two bands of which the upper one penetrates deeply into the indirect band gap while the geometry minimizing the simple Keating potential leaves the gap completely clear of dislocation states. Thus, from a theoretical point of view, the chief difficulty in calculating the electronic structure of the reconstructed 90-degrees partial is the lack of accurate structural information.

CHARACTERIZATION OF HIGH FLUENCE NEUTRON-INDUCED DEFECT LEVELS IN HIGH-RESISTIVITY SILICON DETECTORS USING A LASER DEEP-LEVEL TRANSIENT SPECTROSCOPY (L-DLTS)

Neutron irradiated high resistivity (4-6 kOMEGA-cm) silicon detectors in the neutron fluence (PHI(n)) range of 5 X 10(11) n/cm2 to 1 X 10(14) n/cm2 have been studied using a laser deep level transient spectroscopy (L-DLTS). It has been found that the A-center (oxygen-vacancy, E(c) = 0.17 eV) concentration increases with neutron fluence, reaching a maximum at PHI(n) almost-equal-to 5 X 10(12) n/cm2 before decreasing with PHI(n). A broad peak has been found between 200 K and 300 K, which is the result of the overlap of three single levels: the V-V- (E(c) = 0.38 eV), the E-center (P-V, E(c) = 0.44 eV), and a level at E(c) = 0.56 eV that is probably V-V0. At low neutron fluences (PHI(n) < 5 X 10(12) n/cm2), this broad peak is dominated by V-V- and the E-centers. However, as the fluence increases (PHI(n) greater-than-or-equal-to 5 X 10(12) n/cm2), the peak becomes dominated by the level of E(c) = 0.56 eV.

ANTICROSSING DUE TO RESONANT COUPLING OF HOLE LEVELS IN ASYMMETRIC COUPLED-QUANTUM-WELLS

We present distinct evidence of anticrossing behavior for excitonic transitions due to resonant coupling of heavy-hole ground levels in a biased GaAs/Al0.35Ga0.65As/GaAs (50/40/100 angstrom) asymmetric coupled-double-quantum-wells p-i-n structure by using photoluminescence spectra. The minimum level splitting is about 2.5 meV.

EFFECTS OF AN EXTERNAL MAGNETIC-FIELD ON SHALLOW DONOR LEVELS IN SEMICONDUCTORS

An extension of Faulkner's method for the energy levels of the shallow donor in silicon and germanium at zero field is made in order to investigate the effects of a magnetic field upon the excited states. The effective-mass Hamiltonian matrix elements of an electron bound to a donor center and subjected to a magnetic field B, which involves both the linear and quadratic terms of magnetic field, are expressed analytically and matrices are solved numerically. The photothermal ionization spectroscopy of phosphorus in ultrapure silicon for magnetic fields parallel to the [1,0,0] and [1,1,1] directions and up to 10 T is explained successfully.

HIGH-RESOLUTION DLTS AND ITS APPLICATION TO LATTICE-MISMATCH-INDUCED DEEP LEVELS IN INGAP

A new method of differentiating the deep level transient spectroscopy (DLTS) signal is used to increase the resolution of conventional DLTS. Using this method, more than one single deep level with small differences in activation energy or capture cross section, which are often hard to determine by conventional DLTS, can be distinguished. A series of lattice-mismatched InxGa1-xP samples are measured by improved DLTS to determine accurately the activation energy of a lattice-mismatch-induced deep level. This level cannot be clearly determined using conventional DLTS because the two signals partly overlap each other. Both the signals are thought to originate from a phosophorus vacancy and lattice-mismatch-induced defect.

IDENTIFICATION OF THE ENERGY-LEVELS OF SI-RH

Two thermostable levels E(0.31) and E(0.58) related to Rh in Si were observed using deep level transient spectroscopy and double correlation deep level transient spectroscopy techniques. By means of thermal annealing and electron irradiation, the microscopic natures of these levels were identified for the first time. The levels E(0.31) and E(0.58) arise from by the same impurity center but have different charge states. Their microstructures are not related to a pure substitutional Rh atom, but correspond to a complex. This result is compared to our self-consistent theoretical calculation.

SEMICLASSICAL AND ENVELOPE-FUNCTION TREATMENT OF MAGNETIC LEVELS IN SUPERLATTICES UNDER AN INPLANE MAGNETIC-FIELD

The theoretical treatment of magnetic levels formed in the minibands of superlattices under an in-plane magnetic field is discussed. It is found that the results of semiclassical and envelope-function treatments based on miniband structures are in good agreement with the results calculated strictly by the quantum-mechanical method, so long as the critical parameter 2hc/eBL2 is larger than 1. The wave functions obtained are in the nature of superlattice envelope functions, which are over and above the usual effective-mass envelope functions for bulk materials.