Molecular cloning and expression pattern of a Cubitus interruptus homologue from the mulberry silkworm Bombyx mori

A homologue of the segment polarity gene Cubitus interruptus from Bombyx Mori, (BmCi) has been cloned and characterized. This region harbouring Zn2+ finger motif is highly conserved across species. In B. Mori, BmCi RNA expression was first detected at stage 6 of embryogenesis, which reached maximum levels at stage 21C and was maintained until larval hatching. The segmentally reiterated striped pattern of transcript distribution in stage 21C embryos was in conformity with its predicted segment polarity nature. BmCi was expressed in the fore- and hind-wing discs, ovaries, testes and gut during fifth larval intermolt, reminiscent of its expression domains in Drosophila. Besides, BmCi expression was seen in the. anterior part of the middle silkglands in late embryonic stages, and this pattern was maintained during larval development. The transition from third to fourth and fifth larval intermolts was accompanied by an increase in the transcript levels in the middle silkglands. Our results demonstrate the presence of a novel expression domain for Ci in Bombyx. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.

Scheduling expression trees for delayed-load architectures

In this paper we consider the problem of scheduling expression trees on delayed-load architectures. The problem tackled here takes root from the one considered in [Proceedings of the ACM SIGPLAN '91 Conf. on Programming Language Design and Implementation, 1991. p. 256] in which the leaves of the expression trees all refer to memory locations. A generalization of this involves the situation in which the trees may contain register variables, with the registers being used only at the leaves. Solutions to this generalization are given in [ACM Trans. Prog. Lang. Syst. 17 (1995) 740, Microproc. Microprog. 40 (1994) 577]. This paper considers the most general case in which the registers are reusable. This problem is tackled in [Comput. Lang, 21 (1995) 49] which gives an approximate solution to the problem under certain assumptions about the contiguity of the evaluation order: Here we propose an optimal solution (which may involve even a non-contiguous evaluation of the tree). The schedule generated by the algorithm given in this paper is optimal in the sense that it is an interlock-free schedule which uses the minimum number of registers required. An extension to the algorithm incorporates spilling. The problem as stated in this paper is an instruction scheduling problem. However, the problem could also be rephrased as an operations research problem with a difference in terminology. (C) 2002 Elsevier Science B.V. All rights reserved.

Cloning, expression, purification and preliminary X-ray diffraction studies of a putative Mycobacterium smegmatis thiolase

Thiolases are important in fatty-acid degradation and biosynthetic pathways. Analysis of the genomic sequence of Mycobacterium smegmatis suggests the presence of several putative thiolase genes. One of these genes appears to code for an SCP-x protein. Human SCP-x consists of an N-terminal domain (referred to as SCP2 thiolase) and a C-terminal domain (referred as sterol carrier protein 2). Here, the cloning, expression, purification and crystallization of this putative SCP-x protein from M. smegmatis are reported. The crystals diffracted X-rays to 2.5 angstrom resolution and belonged to the triclinic space group P1. Calculation of rotation functions using X-ray diffraction data suggests that the protein is likely to possess a hexameric oligomerization with 32 symmetry which has not been observed in the other six known classes of this enzyme.

Expression pattern of Cubitus interruptus from the mulberry silkworm Bombyx mori in late developmental stages

A partial genomic clone of Bombyx mori homologue of the segment polarity gene Cubitus interruptus (BmCi), encoding the conserved zinc finger domain and harbouring two introns, has been characterized. BmCi was expressed in the silkglands of B. mori from embryonic to the late larval stages(3rd, 4th and 5th intermoults). The expression was confined to the anterior region of the middle silkglands, overlapping with the domain of sericin-2 expression and excluding the domains of Bm invected expression, namely the middle and posterior regions of the middle silkglands. In the wing discs, the expression was restricted to the anterior compartment, which increased from 4th to 5th larval intermoults and declined later in the pupal wing buds. In gonadal tissues (both ovaries and testes) BmCi was expressed from the larval to pupal stages. The transcripts were localized to the sperm tubes containing spermatogonia in the testis of Bombyx larvae. BmCi expression, however, was not detected in any of these tissues during the moulting stages. Expression of Ci in the wing discs and gonads is evolutionarily conserved, while the silkgland represents a novel domain. Our results imply that BmCi is involved in the specification and maintenance of micro-compartment identity within the middle silkglands.

Transient analysis in Al-doped barium strontium titanate thin films grown by pulsed laser deposition

Thin films of (Ba0.5Sr0.5)TiO3 (BST) with different concentrations of Al doping were grown using a pulsed laser deposition technique. dc leakage properties were studied as a function of Al doping level and compared to that of undoped BST films. With an initial Al doping level of 0.1 at. % which substitutes Ti in the lattice site, the films showed a decrease in the leakage current, however, for 1 at. % Al doping level the leakage current was found to be relatively higher. Current time measurements at elevated temperatures on 1 at. % Al doped BST films revealed space-charge transient type characteristics. A complete analysis of the transient characteristics was carried out to identify the charge transport process through variation of applied electric field and ambient temperature. The result revealed a very low mobility process comparable to ionic motion, and was found responsible for the observed feature. Calculation from ionic diffusivity and charge transport revealed a conduction process associated with an activation energy of around 1 eV. The low mobility charge carriers were identified as oxygen vacancies in motion under the application of electric field. Thus a comprehensive understanding of the charge transport process in highly acceptor doped BST was developed and it was conclusive that the excess of oxygen vacancies created by intentional Al doping give rise to space-charge transient type characteristics. © 2001 American Institute of Physics.

Dynamically Reconfigurable Regular Expression Matching Architecture

Regular Expressions are generic representations for a string or a collection of strings. This paper focuses on implementation of a regular expression matching architecture on reconfigurable fabric like FPGA. We present a Nondeterministic Finite Automata based implementation with extended regular expression syntax set compared to previous approaches. We also describe a dynamically reconfigurable generic block that implements the supported regular expression syntax. This enables formation of the regular expression hardware by a simple cascade of generic blocks as well as a possibility for reconfiguring the generic blocks to change the regular expression being matched. Further,we have developed an HDL code generator to obtain the VHDL description of the hardware for any regular expression set. Our optimized regular expression engine achieves a throughput of 2.45 Gbps. Our dynamically reconfigurable regular expression engine achieves a throughput of 0.8 Gbps using 12 FPGA slices per generic block on Xilinx Virtex2Pro FPGA.

NETGEM: Network Embedded Temporal GEnerative Model for gene expression data

Background: Temporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation. Results: We present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks. Conclusions: NETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems. The source code for NETGEM is available from https://github.com/vjethava/NETGEM

Linear stability, transient growth and the role of viscosity stratification in compressible Couette flow

Linear stability and the nonmodal transient energy growth in compressible plane Couette flow are investigated for two prototype mean flows: (a) the uniform shear flow with constant viscosity, and (b) the nonuniform shear flow with stratified viscosity. Both mean flows are linearly unstable for a range of supersonic Mach numbers (M). For a given M, the critical Reynolds number (Re) is significantly smaller for the uniform shear flow than its nonuniform shear counterpart; for a given Re, the dominant instability (over all streamwise wave numbers, α) of each mean flow belongs to different modes for a range of supersonic M. An analysis of perturbation energy reveals that the instability is primarily caused by an excess transfer of energy from mean flow to perturbations. It is shown that the energy transfer from mean flow occurs close to the moving top wall for “mode I” instability, whereas it occurs in the bulk of the flow domain for “mode II.” For the nonmodal transient growth analysis, it is shown that the maximum temporal amplification of perturbation energy, Gmax, and the corresponding time scale are significantly larger for the uniform shear case compared to those for its nonuniform counterpart. For α=0, the linear stability operator can be partitioned into L∼L̅ +Re2 Lp, and the Re-dependent operator Lp is shown to have a negligibly small contribution to perturbation energy which is responsible for the validity of the well-known quadratic-scaling law in uniform shear flow: G(t∕Re)∼Re2. In contrast, the dominance of Lp is responsible for the invalidity of this scaling law in nonuniform shear flow. An inviscid reduced model, based on Ellingsen-Palm-type solution, has been shown to capture all salient features of transient energy growth of full viscous problem. For both modal and nonmodal instability, it is shown that the viscosity stratification of the underlying mean flow would lead to a delayed transition in compressible Couette flow.