Comparative expression analysis of transcription factor genes in the endostyle of invertebrate chordates

The endostyle of invertebrate chordates is a pharyngeal organ that is thought to be homologous with the follicular thyroid of vertebrates. Although thyroid-like features such as iodine-concentrating and peroxidase activities are located in the dorsolateral part of both ascidian and amphioxus endostyles, the structural organization and numbers of functional units are different. To estimate phylogenetic relationships of each functional zone with special reference to the evolution of the thyroid, we have investigated, in ascidian and amphioxus, the expression patterns of thyroid-related transcription factors such as TTF-2/MoxE4 and Pax2/5/8, as well as the forkhead transcription factors FoxQ1 and FoxA. Comparative gene expression analyses depicted an overall similarity between ascidians and amphioxus endostyles, while differences in expression patterns of these genes might be specifically related to the addition or elimination of a pair of glandular zones. Expressions of Ci-FoxE and BbFoxE4 suggest that the ancestral FoxE class might have been recruited for the formation of thyroid-like region in a possible common ancestor of chordates. Furthermore, coexpression of FoxE4, Pax2/5/8, and TPO in the dorsolateral part of both ascidian and amphioxus endostyles suggests that genetic basis of the thyroid function was already in place before the vertebrate lineage. (c) 2005 Wiley-Liss, Inc.

Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

Genomic organization and expression analysis of Toll-like receptor 3 in grass carp (Ctenopharyngodon idella)

Toll-like receptor 3 (TLR3) participates in the innate immune response by recognizing viral pathogens. To investigate grass carp immune system responding to GCRV (grass carp reovirus) infection, the full-length cDNA sequence and genomic organization of grass carp TLR3 (CiTLR3) was identified and characterized. The full-length genome sequence of CiTLR3 is composed of 5668 nucleotides, including five exons and four introns. The full-length of CiTLR3 cDNA is 3681 bp in length and encodes a polypeptide of 904 amino acids with an estimated molecular mass of 102,765 Da and a predicted isoelectric point of 8.35. Analysis of the deduced amino acid sequence indicated that CiTLR3 has four main structural domains, including a signal peptide sequence, 14 LRR (leucine-rich repeat) motifs, a transmembrane region and a TIR (Toll/interleukin-1 receptor) domain. It is most similar to the crucian carp (Carassius auratus) TLR3 amino acid sequence with an identity of 99%. Quantitative RT-PCR analysis showed that CiTLR3 transcripts were significantly up-regulated starting at day 1 and continued through day 7 following GCRV infection (P < 0.05). These data implied that CiTLR3 is involved in antiviral defense, provide molecular and functional information for grass carp TLR3, and implicate their role in mediating immune protection against grass carp viral diseases. (C) 2009 Elsevier Ltd. All rights reserved.

Structural, optical and intraband absorption properties of vertically aligned In0.32Ga0.68As/GaAs quantum dots superlattices

The self-organization growth of In0.32Ga0.68As/GaAs quantum dots (QDs) superlattices is investigated by molecular beam epitaxy. It is found that high growth temperature and low growth rate are favorable for the formation of perfect vertically aligned QDs superlattices. The aspect ratio (height versus diameter) of QD increases from 0.16 to 0.23 with increase number of bi-layer. We propose that this shape change play a significant role to improve the uniformity of QDs superlattices. Features in the variable temperature photoluminescence characteristics indicate the high uniformity of the QDs. Strong infrared absorption in the 8-12 mum was observed. Our results suggest the promising applications of QDs in normal sensitive infrared photodetectors. (C) 2001 Elsevier Science B.V. All rights reserved.

Structural and infrared absorption properties of self-organized InGaAs GaAs quantum dots multilayers

Self-organized InGaAs/GaAs quantum dots (QDs) stacked multilayers have been prepared by solid source molecular beam epitaxy. Cross-sectional transmission electron microscopy shows that the InGaAs QDs are nearly perfectly vertically aligned in the growth direction [100]. The filtering effect on the QDs distribution is found to be the dominant mechanism leading to vertical alignment and a highly uniform size distribution. Moreover, we observe a distinct infrared absorption from the sample in the range of 8.6-10.7 mu m. This indicates the potential of QDs multilayer structure for use as infrared photodetector.

Structural and optical characterization of InAs nanostructures grown on high-index InP substrates

The structural and optical properties of InAs layers grown on high-index InP surfaces by molecular beam epitaxy are investigated in order to understand the self-organization of quantum dots and quantum wires on novel index surfaces. Four different InP substrate orientations have been examined, namely, (1 1 1)B, (3 1 1)A, and (3 1 1)B and (1 0 0). A rich variety of InAs nanostructures is formed on the surfaces. Quantum wire-like morphology is observed on the (1 0 0) surface, and evident island formation is found on (1 1 1)A and (3 1 1)B by atomic force microscopy. The photoluminescence spectra of InP (1 1 1)A and (3 1 1)B samples show typical QD features with PL peaks in the wavelength range 1.3-1.55 mu m with comparable efficiency. These results suggest that the high-index substrates are promising candidates for production of high-quality self-organized QD materials for device applications. (C) 1999 Elsevier Science B.V. All rights reserved.

Structural and infrared absorption properties of self-organized InGaAs GaAs quantum dots multilayers

Self-organized InGaAs/GaAs quantum dots (QDs) stacked multilayers have been prepared by solid source molecular beam epitaxy. Cross-sectional transmission electron microscopy shows that the InGaAs QDs are nearly perfectly vertically aligned in the growth direction [100]. The filtering effect on the QDs distribution is found to be the dominant mechanism leading to vertical alignment and a highly uniform size distribution. Moreover, we observe a distinct infrared absorption from the sample in the range of 8.6-10.7 mu m. This indicates the potential of QDs multilayer structure for use as infrared photodetector.