The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms

Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying,that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian radiation and those seen after major extinction events.

Analysis of acousto-ultrasonic characteristics for contact-type transducers coupled to composite laminated plates

The acousto-ultrasonic (AU) input-output characteristics for contact-type transmitting and receiving transducers coupled to composite laminated plates are considered in this paper. Combining a multiple integral transform method, an ordinary discrete layer theory for the laminates and some simplifying assumptions for the electro-mechanical transduction behaviour of the transducers, an analytical solution is developed which can deal with all the wave processes involved in the AU measurement system, i.e, wave generation, wave propagation and wave reception. The spectral response of the normal contact pressure sensed by the receiving transducer due to an arbitrary input pulse excited by the transmitting transducer is obtained. To validate the new analytical-numerical spectral technique in the low-frequency regime, the results are compared with Mindlin plate theory solutions. Based on the analytical results, numerical calculations are carried out to investigate the influence of various external parameters such as frequency content of the input pulse, transmitter/receiver spacing and transducer aperture on the output of the measurement system. The results show that the presented analytical-numerical procedure is an effective tool for understanding the input-output characteristics of the AU technique for laminated plates. (C) 2001 Elsevier Science Ltd. All rights reserved.

Continuous quantum measurement of two coupled quantum dots using a point contact: A quantum trajectory approach

We obtain the finite-temperature unconditional master equation of the density matrix for two coupled quantum dots (CQD's) when one dot is subjected to a measurement of its electron occupation number using a point contact (PC). To determine how the CQD system state depends on the actual current through the PC device, we use the so-called quantum trajectory method to derive the zero-temperature conditional master equation. We first treat the electron tunneling through the PC barrier as a classical stochastic point process (a quantum-jump model). Then we show explicitly that our results can be extended to the quantum-diffusive limit when the average electron tunneling rate is very large compared to the extra change of the tunneling rate due to the presence of the electron in the dot closer to the PC. We find that in both quantum-jump and quantum-diffusive cases, the conditional dynamics of the CQD system can be described by the stochastic Schrodinger equations for its conditioned state vector if and only if the information carried away from the CQD system by the PC reservoirs can be recovered by the perfect detection of the measurements.

Time-dependent master equation simulation of complex elementary reactions in combustion: Application to the reaction of (CH2)-C-1 with C2H2 from 300-2000 K

Computational simulations of the title reaction are presented, covering a temperature range from 300 to 2000 K. At lower temperatures we find that initial formation of the cyclopropene complex by addition of methylene to acetylene is irreversible, as is the stabilisation process via collisional energy transfer. Product branching between propargyl and the stable isomers is predicted at 300 K as a function of pressure for the first time. At intermediate temperatures (1200 K), complex temporal evolution involving multiple steady states begins to emerge. At high temperatures (2000 K) the timescale for subsequent unimolecular decay of thermalized intermediates begins to impinge on the timescale for reaction of methylene, such that the rate of formation of propargyl product does not admit a simple analysis in terms of a single time-independent rate constant until the methylene supply becomes depleted. Likewise, at the elevated temperatures the thermalized intermediates cannot be regarded as irreversible product channels. Our solution algorithm involves spectral propagation of a symmetrised version of the discretized master equation matrix, and is implemented in a high precision environment which makes hitherto unachievable low-temperature modelling a reality.

Complex natural resonances of conducting planar objects buried in a dielectric half-space

A scheme is presented to incorporate a mixed potential integral equation (MPIE) using Michalski's formulation C with the method of moments (MoM) for analyzing the scattering of a plane wave from conducting planar objects buried in a dielectric half-space. The robust complex image method with a two-level approximation is used for the calculation of the Green's functions for the half-space. To further speed up the computation, an interpolation technique for filling the matrix is employed. While the induced current distributions on the object's surface are obtained in the frequency domain, the corresponding time domain responses are calculated via the inverse fast Fourier transform (FFT), The complex natural resonances of targets are then extracted from the late time response using the generalized pencil-of-function (GPOF) method. We investigate the pole trajectories as we vary the distance between strips and the depth and orientation of single, buried strips, The variation from the pole position of a single strip in a homogeneous dielectric medium was only a few percent for most of these parameter variations.

Human pigmentation genes: identification, structure and consequences of polymorphic variation

The synthesis of the visible pigment melanin by the melanocyte cell is the basis of the human pigmentary system, those genes directing the formation, transport and distribution of the specialised melanosome organelle in which melanin accumulates can legitimately be called pigmentation genes. The genes involved in this process have been identified through comparative genomic studies of mouse coat colour mutations and by the molecular characterisation of human hypopigmentary genetic diseases such as OCA1 and OCA2. The melanocyte responds to the peptide hormones a-MSH or ACTH through the MC1R G-protein coupled receptor to stimulate melanin production through induced maturation or switching of melanin type. The pheomelanosome, containing the key enzyme of the pathway tyrosinase, produces light red/yellowish melanin, whereas the eumelanosome produces darker melanins via induction of additional TYRP1, TYRP2, SILV enzymes, and the P-protein. Intramelanosomal pH governed by the P-protein may act as a critical determinant of tyrosinase enzyme activity to control the initial step in melanin synthesis or TYRP complex formation to facilitate melanogenesis and melanosomal maturation. The search for genetic variation in these candidate human pigmentation genes in various human populations has revealed high levels of polymorphism in the MC1R locus, with over 30 variant alleles so far identified. Functional correlation of MC1R alleles with skin and hair colour provides evidence that this receptor molecule is a principle component underlying normal human pigment variation. (C) 2001 Elsevier Science B.V. All rights reserved.

Xmds: eXtensible multi-dimensional simulator

A software package that efficiently solves a comprehensive range of problems based on coupled complex nonlinear stochastic ODEs and PDEs is outlined. Its input and output syntax is formulated as a subset of XML, thus making a step towards a standard for specifying numerical simulations.

Coupled experimental and thermodynamic study of the Zn-Fe-Si-O system

Experimental and thermodynamic modeling studies have been carried out on the Zn-Fe-Si-O system. This research is part of a wider program to characterize zinc/lead industrial slags and sinters in the PbO-ZnO-SiO2-CaO-FeO-Fe2O3 system. Experimental investigations involve high-temperature equilibration and quenching techniques followed by electron probe X-ray microanalysis (EPMA). Liquidus temperatures and solid solubilities of the crystalline phases were measured in the temperature range from 1200 °C to 1450 °C (1473 to 1723 K) in the zinc ferrite, zincite, willemite, and tridymite primary-phase fields in the Zn-Fe-Si-O system in air. These equilibrium data for the Zn-Fe-Si-O system in air, combined with previously reported data for this system, were used to obtain an optimized self-consistent set of parameters of thermodynamic models for all phases.

Functional roles of abdominal and back muscles during isometric axial rotation of the trunk

Electromyographic (EMG) studies have shown that a large number of trunk muscles are recruited during axial rotation. The functional roles of these trunk muscles in axial rotation are multiple and have not been well investigated. In addition, there is no information on the coupling torque at different exertion levels during axial rotation. The aim of the study was to investigate the functional roles of rectus abdominis. external oblique. internal oblique, latissimus dorsi, iliocostalis lumborum and multifidus during isometric right and left axial rotation at 100%, 70%, 50% and 30% maximum voluntary contractions (MVC) in a standing position. The coupling torques in sagittal and coronal planes were measured during axial rotation to examine the coupling nature of torque at different levels of exertions. Results showed that the coupled sagittal torque switches from nil to flexion at maximum exertion of axial rotation. Generally, higher EMG activities were shown at higher exertion levels for all the trunk muscles. Significant differences in activity between the right and left axial rotation exertions were demonstrated in external oblique, internal oblique, latissimus dorsi and iliocostalis lumborum while no difference was shown in rectus abdominis and multifidus. These results demonstrated the different functional roles of trunk muscles during axial rotation. This is important considering that the abdominal and back muscles not only produce torque but also maintain the spinal posture and stability during axial rotation exertions. The changing coupling torque direction in the sagittal plane when submaximal to maximal exertions were compared may indicate the complex nature of the kinetic coupling of trunk muscles. (C) 2001 Orthopaedic Research Society. Published by Elsevier Science Ltd. All rights reserved.

Descriptions of the Anopheles (Cellia) farauti complex of sibling species (Diptera : Culicidae) in Australia

Descriptions of the three sibling species of the Anopheles farauti complex in Australia, A. farauti Laveran (formerly A. farauti No. 1), A. hinesorum Schmidt sp.n. (formerly A. farauti No. 2) and A. torresiensis Schmidt sp.n. (formerly A. farauti No. 3) are provided. These species form a part of the punctulatus group, which contains the major malaria vectors in the southwest Pacific. Morphological markers are described for adult females, fourth instar larvae and pupae which identify most specimens, and are presented in keys.

Congenital thyrotoxicosis in premature infants

OBJECTIVES Graves' disease (GD) complicates 0.1% to 0.2% of pregnancies, but congenital thyrotoxicosis is rare occurring in one in 70 of these pregnancies independent of maternal disease status. Antenatal prediction of affected infants is imprecise; however, maternal history, coupled with a high maternal serum TSH receptor binding immunoglobulin index (TBII) predict adverse neonatal outcome. Mortality is reported to be as high as 25% in affected infants and would therefore be expected to be higher in premature infants. This study illustrates that in sick, premature, extreme low birth weight (ELBW) or intrauterine growth retarded (IUGR) infants, the diagnosis maybe overlooked especially in the absence of antenatal risk assessment and management of thyrotoxicosis in this setting is complex. DESIGN and PATIENTS The records of premature neonates born at the three main maternity units in Brisbane, between January 1996 and July 1998 diagnosed with congenital thyrotoxicosis were reviewed. Data were recorded on gestational age, birth weight (B Wt), maternal thyroid history and current status, and neonatal course. Thyroid function and TBII status was assessed using standard biochemical assays. RESULTS Seven neonates from five pregnancies were identified (four female, three male). Mean gestational age was 30 week (25-36 week) and median B Wt was 1.96 kg (0.50-2.62 kg). Only one mother received formal antenatal counselling by a paediatric endocrine service and had a TBII (54%) measured prior to delivery. Three of five mothers had elevated TBII measured after diagnosis in their offspring (57%, 65%, 83%) and in one mother, a TBII was not performed. All mothers were biochemically euthyroid at delivery. Mean age at diagnosis was 9 days (1-16 days) and mean age at commencement of treatment was 12 days (7-26 days). Two infants received propylthiouracil and five received a combination of carbimazole and propranolol. Pour became biochemically hypothyroid, in three this resolved with cessation of the antithyroid drug (ATD), and one required ongoing T4 supplementation. Only one infant required treatment for cardiac failure and there were no deaths in this cohort. CONCLUSIONS This is a large series of extremely small and premature infants with neonatal thyrotoxicosis. Presentation was nonspecific. The diagnosis was delayed because of low birth weight, prematurity, multiple birth and/or an unrecognized maternal history of Graves' disease. The treatment of neonatal thyrotoxicosis was difficult in these extreme law birth weight infants yet no infant died and significant morbidity was confined to high output cardiac failure in one infant. With antenatal recognition of past or active Graves' disease, assessment of maternal TSH receptor binding immunoglobulin index prior to delivery and postnatal monitoring of cord TSH and venous fT4 and TSH on days 4 and 7 rapid treatment of affected infants may have further reduced neonatal morbidity.

Vps45p stabilizes the syntaxin homologue Tlg2p and positively regulates SNARE complex formation

Sec1p-like/Munc-18 (SM) proteins bind to t-SNAREs and inhibit ternary complex formation. Paradoxically, the absence of SM proteins does not result in constitutive membrane fusion, Here, we show that in yeast cells lacking the SM protein Vps45p, the t-SNARE Tlg2p is down-regulated, to undetectable levels, by rapid proteasomal degradation. In the absence of Vps45p, Tlg2p can be stabilized through abolition of proteasome activity. Surprisingly, the stabilized Tlg2p was targeted to the correct intracellular location. However, the stabilized Tlg2p is non-functional and unable to bind its cognate SNARE binding partners, Tlg1p and Vti1p, in the absence of Vps45p, A truncation mutant lacking the first 230 residues of Tlg2p no longer bound Vps45p but was able to form complexes with Tlg1p and Vti1p in the absence of the SM protein. These data provide us with two valuable insights into the function of SM proteins. First, SM proteins act as chaperone-like molecules for their cognate t-SNAREs, Secondly, SM proteins play an essential role in the activation process allowing their cognate t-SNARE to participate in ternary complex formation.

Mouse Sox8 is located between, not within, the t-complex deletions t(w18) and t(h20) on chromosome 17

The SOX family of developmental transcription factors is known to play critical roles in cell lineage specification, fate determination and differentiation during development in diverse phyla. Their importance is underscored by their involvement in a number of human diseases and mouse mutants, and by targeted mutation in mice. SOX8 is broadly expressed during development and is located on human chromosome 16p and within the t-complex on mouse chromosome 17, in the vicinity of two mutations t(w18) and t(h20). Here we analyse mutant genomic DNA to show that the Sox8 gene locus lies outside the deletion regions of both t(w18) and t(h20) and between these deletions. These data exclude Sox8 from contributing to the t(w18) and t(h20) phenotypes, and provide an additional marker for structural characterization of this complex genomic region. Copyright (C) 2001 S. Karger AG, Basel.

Exact form factors for the Josephson tunneling current and relative particle number fluctuations in a model of two coupled Bose-Einstein condensates

Form factors are derived for a model describing the coherent Josephson tunneling between two coupled Bose-Einstein condensates. This is achieved by studying the exact solution of the model within the framework of the algebraic Bethe ansatz. In this approach the form factors are expressed through determinant representations which are functions of the roots of the Bethe ansatz equations.