CANCER SCIENCE, Issue 10 2000
Takashi Hirano
The N-terminal amino acid sequence of TA02 (molecular weight 35.0 kDa, isoelectric point 5.29), which is associated with primary lung adenocarcinoma, was determined and a fragment peptide was used to generate mouse monoclonal antibodies (mAbs) against TA02. The amino acid sequence suggested that TA02 might be homologous with napsin A, a new type of aspartic proteinase. In this context, we confirmed the expression of napsin A in primary lung adenocarcinoma using reversetranscription polymerare chain reaction (RT-PCR) and showed that the TA02 mAbs reacted with glutathione-S-transferase (GST)-napsin A fusion protein. We concluded that TA02 is the same molecule as napsin A, and showed immunohistochemically that it is distributed mainly in type II pneumocytes, alveolar macrophages, renal tubules and exocrine glands and ducts in the pancreas. In particular, type II pneumocytes and alveolar macrophages showed high expression of TA02 among human normal tissues. In primary lung adenocarcinoma, 47 out of 58 (81.0%) primary lesions were positive. All well-differentiated adenocarcinomas except those of goblet cell type showed high expression of TA02. In addition, two out of seven (28.6%) large cell carcinomas showed low expression of TA02. The other histopathological types of primary lung cancer did not express TA02 at all. A few cases of renal cell cancer, pancreatic cancer, breast cancer, thyroid cancer, colon cancer and ovarian cancer showed low expression, but the staining patterns were completely different from that of primary lung adenocarcinoma, which showed a granular staining pattern. Our novel mAbs should be valuable for immunochemical detection of TA02/napsin A. [source]

RNA interference by expressing short hairpin RNA in the Ciona intestinalis embryo

DEVELOPMENT GROWTH & DIFFERENTIATION, Issue 6 2008
Aya Nishiyama
We carried out RNA interference by expressing short hairpin RNA (shRNA) in the Ciona intestinalis embryo. For this purpose, we identified a gene encoding U6 small nuclear RNA (snRNA) in the C. intestinalis genome. The 1-kb sequence upstream of the U6 snRNA gene was sufficient for directing transcription of short RNA as revealed by Northern blot hybridization. An shRNA-expressing plasmid vector was constructed, in which shRNA-encoding oligonucleotides are inserted downstream of the U6 promoter. An shRNA that contained a sequence homologous to the C. intestinalis tyrosinase gene (Ci-tyrosinase) suppressed melanization of pigment cells in the brain of morphologically normal tailbud embryos. An shRNA that perfectly matched the translated sequence of enhanced green fluorescent protein (EGFP) (a mutant type of Aequorea victoria green fluorescent protein) suppressed the expression of the coelectroporated EGFP transgene. These results suggest that the expression of shRNA interferes with functions of both endogenous and exogenous genes. The shRNA-expressing plasmid constructed in the present study provides an easy and inexpensive alternative for the functional analysis of genes in ascidian embryos. [source]

Two neuron clusters in the stem of postembryonic zebrafish brain specifically express relaxin -3 gene: First evidence of nucleus incertus in fish

DEVELOPMENTAL DYNAMICS, Issue 12 2008
Aldo Donizetti
Abstract We examined the spatial expression of the relaxin -3 gene in the developing zebrafish brain, one of the vertebrate model systems in which this gene has been identified. Until the pharyngula stage, the gene is expressed diffusely in the brain, where, starting at about 40 hpf, the transcripts appear restricted in a midbrain cell cluster of the periaqueductal gray. Later, at 72 hpf, the transcripts are still evident in that cluster and distributed in a larger cell number; at this stage, the gene is also expressed posteriorly, in a smaller cell group that, as we report for the first time, could be homologous to mammalian nucleus incertus. The gene expression persists in both cell clusters at 96 hpf. This pattern indicates both conserved and divergent expression features of the relaxin -3 gene among developing zebrafish and rat brains, where only scattered cells express the gene in the periaqueductal gray. Developmental Dynamics 237:3864,3869, 2008. © 2008 Wiley-Liss, Inc. [source]

The zebrafish bHLH PAS transcriptional regulator, single-minded 1 (sim1), is required for isotocin cell development

DEVELOPMENTAL DYNAMICS, Issue 8 2006
Jennifer L. Eaton
Abstract A wide range of physiological and behavioral processes, such as social, sexual, and maternal behaviors, learning and memory, and osmotic homeostasis are influenced by the neurohypophysial peptides oxytocin and vasopressin. Disruptions of these hormone systems have been linked to several neurobehavioral disorders, including autism, Prader-Willi syndrome, affective disorders, and obsessive-compulsive disorder. Studies in zebrafish promise to reveal the complex network of regulatory genes and signaling pathways that direct the development of oxytocin- and vasopressin-like neurons, and provide insight into factors involved in brain disorders associated with disruption of these systems. Isotocin, which is homologous to oxytocin, is expressed early, in a simple pattern in the developing zebrafish brain. Single-minded 1 (sim1), a member of the bHLH-PAS family of transcriptional regulatory genes, is required for terminal differentiation of mammalian oxytocin cells and is a master regulator of neurogenesis in Drosophila. Here we show that sim1 is expressed in the zebrafish forebrain and is required for isotocin cell development. The expression pattern of sim1 mRNA in the embryonic forebrain is dynamic and complex, and overlaps with isotocin expression in the preoptic area. We provide evidence that the role of sim1 in zebrafish neuroendocrine cell development is evolutionarily conserved with that of mammals. Developmental Dynamics 235:2071,2082, 2006. © 2006 Wiley-Liss, Inc. [source]

An automated in situ hybridization screen in the medaka to identify unknown neural genes

DEVELOPMENTAL DYNAMICS, Issue 3 2005
Carole Deyts
Abstract Despite the fact that a large body of factors that play important roles in development are known, there are still large gaps in understanding the genetic pathways that govern these processes. To find previously unknown genes that are expressed during embryonic development, we optimized and performed an automated whole-mount in situ hybridization screen on medaka embryos at the end of somitogenesis. Partial cDNA sequences were compared against public databases and identified according to similarities found to other genes and gene products. Among 321 isolated genes showing specific expression in the central nervous system in at least one of five stages of development, 55.14% represented genes whose functions are already documented (in fish or other model organisms). Additionally, 16.51% were identified as conserved unknown genes or genes with unknown function. We provide new data on eight of these genes that presented a restricted expression pattern that allowed for formulating testable hypotheses on their developmental roles, and that were homologous to mammalian molecules of unknown function. Thus, gene expression screening in medaka is an efficient tool for isolating new regulators of embryonic development, and can complement genome-sequencing projects that are producing a high number of genes without ascribed functions. Developmental Dynamics 234:698,708, 2005. © 2005 Wiley-Liss, Inc. [source]

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

DEVELOPMENTAL DYNAMICS, Issue 3 2005
Jin Hiruta
Abstract 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/FoxE4 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. Developmental Dynamics 233:1031,1037, 2005. © 2005 Wiley-Liss, Inc. [source]

Specification of the enveloping layer and lack of autoneuralization in zebrafish embryonic explants

DEVELOPMENTAL DYNAMICS, Issue 1 2005
Charles G. Sagerström
Abstract We have analyzed the roles of cell contact during determination of the outermost enveloping layer (EVL) and deeper neurectoderm in zebrafish embryos. Outer cells, but not deeper cells, are specified to express the EVL-specific marker, cyt1 by late blastula. EVL specification requires cell contact or close cell proximity, because cyt1 is not expressed after explant dissociation. The EVL may be homologous to the Xenopus epithelial layer, including the ventral larval epidermis. While Xenopus epidermal cytokeratin gene expression is activated by bone morphogenetic protein (BMP) signaling, zebrafish cyt1 is not responsive to BMPs. Zebrafish early gastrula ectodermal explants are specified to express the neural markers opl (zic1) and otx2, and this expression is prevented by BMP4. Dissociation of zebrafish explants prevents otx2 and opl expression, suggesting that neural specification in zebrafish requires cell contact or close cell proximity. This finding is in contrast to the case in Xenopus, where ectodermal dissociation leads to activation of neural gene expression, or autoneuralization. Our data suggest that distinct mechanisms direct development of homologous lineages in different vertebrates. Developmental Dynamics 232:85,97, 2005. © 2004 Wiley-Liss, Inc. [source]

Morphogenetic domains in the yolk syncytial layer of axiating zebrafish embryos

DEVELOPMENTAL DYNAMICS, Issue 4 2001
Leonard A. D'Amico
Abstract The yolk syncytial layer (YSL) of the teleostean yolk cell is known to play important roles in the induction of cellular mesendoderm, as well as the patterning of dorsal tissues. To determine how this extraembryonic endodermal compartment is subdivided and morphologically transformed during early development, we have examined collective movements of vitally stained YSL nuclei in axiating zebrafish embryos by using four-dimensional confocal microscopy. During blastulation, gastrulation, and early segmentation, zebrafish YSL nuclei display several highly patterned movements, which are organized into spatially distinct morphogenetic domains along the anterior-posterior and dorsal-ventral axes. During the late blastula period, with the onset of epiboly, nuclei throughout the YSL initiate longitudinal movements that are directed along the animal-vegetal axis. As epiboly progresses, nuclei progressively recede from the advancing margin of the epibolic YSL. However, a small group of nuclei is retained at the YSL margin to form a constricting blastoporal ring. During mid-gastrulation, YSL nuclei undergo convergent-extension behavior toward the dorsal midline, with a subset of nuclei forming an axial domain that underlies the notochord. These highly patterned movements of YSL nuclei share remarkable similarities to the morphogenetic movements of deep cells in the overlying zebrafish blastoderm. The macroscopic shape changes of the zebrafish yolk cell, as well as the morphogenetic movements of its YSL nuclei, are homologous to several morphogenetic behaviors that are regionally expressed within the vegetal endodermal cell mass of gastrulating Xenopus embryos. In contrast to the cellular endoderm of Xenopus, the dynamics of zebrafish YSL show that a syncytial endodermal germ layer can express a temporal sequence of morphogenetic domains without undergoing progressive steps of cell fate restriction. © 2001 Wiley-Liss, Inc. [source]

GABAergic modulation of primary gustatory afferent synaptic efficacy

DEVELOPMENTAL NEUROBIOLOGY, Issue 2 2002
Andrew A. Sharp
Abstract Modulation of synaptic transmission at the primary sensory afferent synapse is well documented for the somatosensory and olfactory systems. The present study was undertaken to test whether GABA impacts on transmission of gustatory information at the primary afferent synapse. In goldfish, the vagal gustatory input terminates in a laminated structure, the vagal lobes, whose sensory layers are homologous to the mammalian nucleus of the solitary tract. We relied on immunoreactivity for the GABA-transporter, GAT-1, to determine the distribution of GABAergic synapses in the vagal lobe. Immunocytochemistry showed dense, punctate GAT-1 immunoreactivity coincident with the layers of termination of primary afferent fibers. The laminar nature and polarized dendritic structure of the vagal lobe make it amenable to an in vitro slice preparation to study early synaptic events in the transmission of gustatory input. Electrical stimulation of the gustatory nerves in vitro produces synaptic field potentials (fEPSPs) predominantly mediated by ionotropic glutamate receptors. Bath application of either the GABAA receptor agonist muscimol or the GABAB receptor agonist baclofen caused a nearly complete suppression of the primary fEPSP. Coapplication of the appropriate GABAA or GABAB receptor antagonist bicuculline or CGP-55845 significantly reversed the effects of the agonists. These data indicate that GABAergic terminals situated in proximity to primary gustatory afferent terminals can modulate primary afferent input via both GABAA and GABAB receptors. The mechanism of action of GABAB receptors suggests a presynaptic locus of action for that receptor. © 2002 Wiley Periodicals, Inc. J Neurobiol 52: 133,143, 2002 [source]

New arthrodires (Family Williamsaspididae) from Wee Jasper, New South Wales (Early Devonian), with comments on placoderm morphology and palaeoecology

ACTA ZOOLOGICA, Issue 2009
Gavin C. Young
Abstract Two new arthrodire species represented by articulated trunk armours from the Early Devonian (Emsian) limestones of the Burrinjuck area are placed in a new genus Elvaspis (E. tuberculata, E. whitei), assigned to the Family Williamsaspididae. On new evidence of the dermal neck-joint and shape of the median dorsal plate this family is reassigned from the Phlyctaeniina to the Brachythoraci. The strongly ornamented post-branchial lamina of the trunk armour relates to a recent hypothesis that special post-branchial denticles in placoderms are homologous to pharyngeal denticles of crown-gnathostomes rather than modified external tubercles. Variable development of the post-branchial lamina and its ornament in different placoderm subgroups, with specific resemblance to the external ornament characteristic of that subgroup, indicates that modification of normal external dermal ornament is the most parsimonious interpretation. A comparison of fish diversity in modern and ancient tropical reef environments is consistent with an equilibrium model for species diversification through time. [source]

Morpho-anatomy of the lobopod Magadictyon cf. haikouensis from the Early Cambrian Chengjiang Lagerstätte, South China

ACTA ZOOLOGICA, Issue 4 2007
Jianni Liu
Abstract Magadictyon haikouensis (Luo and Hu, 1999) from the Early Cambrian Chengjiang Lagerstätte, an incomplete specimen of a large lobopod with strong appendages, has been regarded as related to the lobopods Microdictyon and Onychodictyon. Newly discovered complete specimens of Magadictyon cf. haikouensis (found by the Early Life Institute field team) show that the taxon, in addition to its strong appendages with appendicules, also had a head bearing similar caecum-like structures to those of the arthropod Naraoia and Chelicerate, ,Peytoia'-like mouthparts and frontal appendages. Because of their similarity, the caecum-like structures of Magadictyon cf. haikouensis are considered to be homologous with those of stem-group arthropods. The ,Peytoia'-like mouthparts and the frontal appendages are similar to those of the AOPK (Anomalocaris,Opabinia,Pambdelurion,Kerygmachela) group. In addition, the appendages with appendicules show that Magadictyon cf. haikouensis is closely related to Onychodictyon. Therefore, Magadictyon cf. haikouensis is regarded here as a rare transitional form between lobopods and arthropods. Besides, together with other lobopods, the morphology of Magadictyon cf. haikouensis demonstrates that the Cambrian lobopods appear to have been diverse and not particularly closely related to one another, and do not seem to represent a monophyletic clade. [source]

Minireview: On the homology of the protocoel in Cephalochordata and ,lower' Deuterostomia

ACTA ZOOLOGICA, Issue 1 2002
Thomas Stach
Abstract Hypotheses regarding the homology of the protocoel in planktonic deuterostome larvae and mesodermal structures in ontogenetic stages of cephalochordates are evaluated. The prevalent ,classical' hypothesis describes the protocoel as being homologous with the diverticula of Hatschek, which, on the left side, develop into the preoral pit, subsequently into Hatschek's pit and groove (in part). This hypothesis is based mainly on the position of Hatschek's diverticula anterior to the rest of the mesoderm during their enterocoelic origin. It is shown here that during development the mesodermal segment that develops into Hatschek's nephridium is the most anterior one prior to formation of Hatschek's diverticula, and this segment assumes an anteriormost position after differentiation of Hatschek's diverticula. Additional similarities between this segment and protocoels are: (i) presence of endomesodermal cells with podocytic extensions, (ii) excretory function, (iii) relatively early ontogenetic origin, (iv) probable lack of association with nervous structures, (v) probable ectodermal origin of a portion of the canal, and (vi) position relative to the mouth opening. Therefore, homology between the protocoel and the segment that becomes Hatschek's nephridium is proposed. It is concluded that a glandular structure homologous to the diverticula of Hatschek and anterior to the protocoel/Hatschek's nephridium is a synapomorphy of notochordates or chordates. [source]

The male postabdomen of Stolotermes inopinus: a termite with unusually well-developed external genitalia (Dictyoptera: Isoptera: Stolotermitinae)

ACTA ZOOLOGICA, Issue 2 2000
Klaus-Dieter Klass
Abstract Klass, K.-D., Thorne, B. L. and Lenz, M. 2000. The male postabdomen of Stolotermes inopinus: a termite with unusually well-developed external genitalia (Dictyoptera: Isoptera: Stolotermitinae). ,Acta Zoologica (Stockholm) 81: 121,130 Stolotermes inopinus has large external male genitalia (phallic lobe), which contrast with the small genital papillae or lack of external genitalia of other Isoptera. As in the genital papilla of Mastotermesdarwiniensis, a ventral sclerite pair is present, the gonopore is located ventroterminally on the phallic lobe, and the genital area is entirely symmetrical , suggesting that this may be the groundplan condition of Isoptera. The relations of the phallic lobe to surrounding components like the subgenital plate, paraprocts, and certain muscles and nerves indicate that the lobe of S. inopinus is homologous with the phallomeres of other Dictyoptera. The bilateral symmetry and simple structure, however, are in strong contrast to the asymmetry and high complexity found in male genitalia of Blattaria and Mantodea. The postabdominal nervous system of S. inopinus resembles that of the cockroach Periplaneta americana. Indications are given that the Stolotermitinae are related to the Kalotermitidae, Rhinotermitidae, and Termitidae rather than to the Termopsinae. [source]

Cell surface glycoconjugates in the olfactory system of lungfish Protopterus annectens Owen

ACTA ZOOLOGICA, Issue 2 2000
Valeria Franceschini
Abstract Franceschini, V. Lazzari, M. and Ciani, F. 2000. Cell surface glycoconjugates in the olfactory system of lungfish Protopterus annectens Owen. ,Acta Zoologica (Stockholm) 81: 131,137 Lectin binding was performed on the olfactory system of lungfish Protopterus annectens to identify specific glycoconjugates on the cell surface of olfactory receptor cells. The lectin histochemical patterns and the Western blot analysis indicate that the receptor cells of the olfactory mucosa are characterized by high density of ,-N-acetyl- d -galactosamine residues on the saccharidic chains of the surface glycoproteins. Other lectins display a regional pattern between the regions of the olfactory bulbs. This different histochemical lectin pattern might be due to a different regional segregation of the olfactory projections. On the other hand it could allow the identification of an area corresponding to the accessory olfactory bulb of terrestrial vertebrates in the ventrolateral region of Protopterus olfactory bulb. The presence in the dipnoan olfactory system of a vomeronasal organ homologous to the organ in amphibians is discussed. Moreover, the selective lectin binding on the surface of primary olfactory neurones suggests that specific cell surface glycoproteins may have a role in the axonal growth due to the continuous cycle of proliferation and the death of olfactory receptor cells. [source]

Quantification of SMN1 and SMN2 genes by capillary electrophoresis for diagnosis of spinal muscular atrophy

ELECTROPHORESIS, Issue 13 2008
Chun-Chi Wang
Abstract We present the first CE method for the separation and quantification of SMN1 and SMN2 genes. Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder deleted or mutated in SMN1 gene and retained at least one copy of SMN2 gene. However, these two genes are highly homologous, differentiation and quantification of SMN1 and SMN2 are therefore required in diagnosis to identify SMA patients and carriers. We developed a fluorescence-labeled conformation-sensitive CE method to quantitatively analyze PCR products covering the variable position in the SMN1/SMN2 genes using a copolymer solution composed of hydroxyethylcellulose and hydroxypropylcellulose. The DNA samples included 24 SMA patients, 52 parents of SMA patients (obligatory carriers), and 255 controls. Those 331 samples were blind analyzed to evaluate the method, and the results compared with those obtained using denaturing HPLC (DHPLC). Validation of accuracy was performed by comparing the results with those of DHPLC. Nine of total samples showed different results. Diagnosis of one fetus DNA among them was related to abortion or not, which was further confirmed by gel electrophoresis and DNA sequencing. Our method showed good coincidence with them, and proved the misdiagnosis of DHPLC. This simple and reliable CE method is a powerful tool for clinical genotyping of large populations to detect carriers and SMA patients. [source]

Tissue-specific variation of heat shock protein gene expression in relation to diapause in the bumblebee Bombus terrestris

ENTOMOLOGICAL RESEARCH, Issue 1 2008
Back-Guen KIM
Abstract Diapause-associated expression patterns of heat shock protein genes (hsp) were determined in the queen of the bumblebee Bombus terrestris, a pollination insect. Partial cDNA sequences of three hsp genes ,shsp, hsc70 and hsp90, were obtained, and the deduced amino acid sequences were found to be highly homologous with corresponding hsp of hymenopteran insects. Using northern hybridization, the transcript level of each gene was compared in six stages relating to diapause: pre-mating, post-mating, chilling for 1, 2 and 3 months, and post-chilling. The transcript level was also compared in four tissues of adult queens: brain, thoracic muscle, gut and ovary. The transcript levels of the three hsp genes changed at various rates in relation to diapause, and each pattern was highly tissue-specific. Overall patterns of hsc70 and hsp90 expression were similar in each tissue. The shsp level in the brain was downregulated after 1 month chilling, but its level in the ovary was upregulated during a long chilling period; levels in muscle and gut did not change in relation to diapause. The levels of both hsc70 and hsp90 in muscle were gradually upregulated in late diapause and postdiapause stages, but levels in the ovary were downregulated during the chilling period, while levels in the brain and gut did not change in relation to diapause. Our results show that the three hsp genes were differentially regulated in stage- and tissue-specific manners throughout diapause, and suggest unique physiological roles for these genes in relation to diapause in each tissue of queen bumblebees. [source]

Three structurally homologous isothiocyanates exert "Janus" characteristics in human HepG2 cells

ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 3 2009
Evelyn Lamy
Abstract In this study, we used the single cell gel electrophoresis (SCGE) assay and the micronucleus (MN) test to investigate the DNA damaging effects and the antigenotoxic potencies of three structurally related ITCs in human HepG2 cells. The results show that all three ITCs possess the characteristic of a "Janus" compound, i.e., they exert both significant genotoxicity and antigenotoxicity, depending on the concentrations used in the test systems applied. Regression line analysis of the results derived by SCGE analysis showed genotoxic potency of the ITCs in the following order: 3-methylthiopropyl ITC (MTPITC) > 4-methylthiobutyl ITC (MTBITC) > 5-methylthiopentyl ITC (MTPeITC); however, this order in genotoxic potency was not confirmed by MN analysis. Additionally, the MN test showed significant mutagenicity of the test substances at higher concentrations when compared with the SCGE assay. Twenty-four hour-treatment of the cells with the ITCs, followed by a 1-hr recovery period, showed significant DNA repair in the SCGE assay at a concentration ,10 ,M MTPITC, ,3 ,M MTBITC, and ,0.1 ,M MTPeITC, respectively. In antigenotoxicity studies, the most effective concentration of MTPITC and MTPeITC toward B(a)P-induced DNA damage was 0.1 ,M in both test systems. MTBITC suppressed MN formation in B(a)P-treated cells to the background level at a concentration of 1 ,M. The ambivalent character of the ITCs under studymust be further clarified, especially in the possiblecontext of high dose therapeutic applications. Environ. Mol. Mutagen. 2009. © 2009 Wiley-Liss, Inc. [source]

A model for targeted substitution mutagenesis during SOS replication of double-stranded DNA containing cis-syn cyclobutane thymine dimers

ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 9 2006
Helen A. Grebneva
Abstract A model for ultraviolet mutagenesis is described that is based on the formation of rare tautomeric bases in pyrimidine dimers. It is shown that during SOS synthesis the modified DNA-polymerase inserts canonical bases opposite the dimers; the inserted bases are capable of forming hydrogen bonds with bases in the template DNA. SOS-replication of double-stranded DNA having thymine dimers, with one or both bases in a rare tautomeric conformation, results in targeted transitions, transversions, or one-nucleotide gaps. Structural analysis indicates that one type of dimer containing a single tautomeric base (TT1*, with the "*" indicating a rare tautomeric base and the subscript referring to the particular conformation) can cause A:T , G:C transition or homologous A:T , T:A transversion, while another dimer (TT2*) can cause a one-nucleotide gap. The dimers containing T4* result in A:T , C:G transversion, while TT5* dimers can cause A:T , C:G transversion or homologous A:T , T:A transversion. If both bases in the dimer are in a rare tautomeric form, then tandem mutations or double-nucleotide gaps can be formed. The dimers containing the rare tautomeric forms T1 *,, T2*,, T3*,, T4*,, and T5*, may not result in mutations. The question of whether dimers containing T4*, and T5*, result in mutations requires further investigation. Environ. Mol. Mutagen., 2006. © 2006 Wiley-Liss, Inc. [source]

A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases

ENVIRONMENTAL MICROBIOLOGY, Issue 3 2008
Kashif Riaz
Summary A metagenomic library of 10 121 clones, generated from bacteria inhabiting a pasture soil from France, was screened for the presence of fosmids conferring either N -acylhomoserine lactone (NAHL) synthesis or NAHL degradation ability upon their Escherichia coli host. No clone producing NAHLs was identified whereas one, containing a 31 972 bp insert in fosmid p2H8, allowed NAHL degradation. This led to the cloning and identification of a gene, qlcA, encoding an NAHL-lactonase activity, as judged by lactone-ring closure and HPLC/MS analyses of NAHL degradation products. The qlcA gene efficiently quenched quorum-sensing regulated pathogenic functions when expressed in Pectobacterium carotovorum. The QlcA peptide belongs to the family of zinc-dependent metallohydrolases and appears to be distantly related to other NAHL-lactonases discovered in Agrobacterium, Bacillus, Photorhabdus and Rhizobium. In-silico analysis of the metagenomic insert revealed the occurrence of 20 orf, with a constant GC% and codon usage, suggesting a unique bacterial origin. Nine out of these 20 orf were homologous to genes encoding biosynthesis of arginine; they were clustered with an unusual succession argFJADBCRGH. The fosmid p2H8 is able to complement the argA, argB and argC mutants in E. coli. Phylogenetic analysis showed that 9 orf out of 20 were related to sequences from members of the Acidobacteria, supporting the hypothesis that the analysed insert might be originated from an organism related to this phylum. [source]

Lung CD11c+ cells from mice deficient in Epstein-Barr virus-induced gene,3 (EBI-3) prevent airway hyper-responsiveness in experimental asthma

EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 6 2007
Michael Hausding
Abstract Epstein-Barr virus-induced gene (EBI)-3 codes for a soluble type,1 cytokine receptor homologous to the p40 subunit of IL-12 that is expressed by antigen-presenting cells following activation. Here, we analyzed the functional role of EBI-3 in a murine model of asthma associated with airway hyper-responsiveness (AHR) in ovalbumin-sensitized mice. Upon allergen challenge, EBI-3,/, mice showed less severe AHR, decreased numbers and degranulation of eosinophils and a significantly reduced number of VCAM-1+ cells in the lungs as compared to wild-type littermates. We thus analyzed lung CD11c+ cells before and after allergen challenge in these mice and found that before allergen challenge, lung CD11c+ cells isolated from EBI-3,/, mice express markers of a more plasmacytoid phenotype without releasing IFN-, as compared to those from wild-type littermates. Moreover, allergen challenge induced the development of myeloid CD11c+ cells in the lungs of EBI-3,/, mice, which released increased amounts of IL-10 and IL-12 while not expressing IFN-,. Finally, inhibition of EBI-3 expression in lung DC could prevent AHR in adoptive transfer studies by suppressing mediator release of effector cells into the airways. These results indicate a novel role for EBI-3 in controlling local immune responses in the lungs in experimental asthma. [source]

Structural and functional differences between the promoters of independently expressed killer cell Ig-like receptors

EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 7 2005
Bergen, Jeroen van
Abstract Killer Ig-like receptors (KIR) are important for the recognition and elimination of diseased cells by human NK cells. Myeloid leukemia patients given a hematopoietic stem cell transplantation, for example, benefit from KIR-mediated NK alloreactivity directed against the leukemia cells. To establish an effective NK cell repertoire, most KIR genes are expressed stochastically, independently of the others. However, the sequences upstream of the coding regions of these KIR genes are highly homologous to the recently identified KIR3DL1 promoter (91.1,99.6% sequence identity), suggesting that they are regulated by similar if not identical mechanisms of transcriptional activation. We investigated the effects of small sequence differences between the KIR3DL1 promoter and other KIR promoters on transcription factor binding and promoter activity. Surprisingly, electrophoretic mobility shift assays and promoter-reporter assays revealed significant structural and functional differences in the cis-acting elements of these highly homologous KIR promoters, suggesting a key role for transcription factors in independent control of expression of specific KIR loci. Thus, the KIR repertoire may be shaped by a combination of both gene-specific and stochastic mechanisms. [source]

Toll-like receptor 9 binds single-stranded CpG-DNA in a sequence- and pH-dependent manner

EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 9 2004
Mark Rutz
Abstract Toll-like receptors (TLR) recognize bacterial and viral components, but direct interaction of receptor and ligand is unclear. Here, we demonstrate that TLR9 binds directly and sequence-specifically to single-stranded unmethylated CpG-DNA containing a phosphodiester backbone. TLR9-CpG-DNA interaction occurs at the acidic pH (6.5,5.0) found in endosomes and lysosomes. By sequence comparison we identified a potential CpG-DNA binding domain homologous to that described for methyl-CpG-DNA binding proteins. Amino acid substitutions in this region abrogated CpG-DNA binding and led to loss of NF-,B activation. Furthermore, chloroquine and quinacrine, therapeutic agents for autoimmune diseases like rheumatoid arthritis and systemic lupus erythematosus, directly blocked TLR9-CpG-DNA interaction but not TLR2-Pam3Cys binding. Our results demonstrate direct binding of TLR9 to CpG-DNA and suggest that the therapeutic activity of chloroquine and quinacrine in autoimmune diseases may be due to its activity as a TLR9 antagonist and inhibitor of endosomal acidification. [source]

Calcium,calmodulin-dependent protein kinase II phosphorylation modulates PSD-95 binding to NMDA receptors

EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 10 2006
Fabrizio Gardoni
Abstract At the postsynaptic membrane of excitatory synapses, NMDA-type receptors are bound to scaffolding and signalling proteins that regulate the strength of synaptic transmission. The cytosolic tails of the NR2A and NR2B subunits of NMDA receptor bind to calcium,calmodulin-dependent protein kinase II (CaMKII) and to members of the MAGUK family such as PSD-95. In particular, although NR2A and NR2B subunits are highly homologous, the sites of their interaction with CaMKII as well as the regulation of this binding differ. We identified PSD-95 phosphorylation as a molecular mechanism responsible for the dynamic regulation of the interaction of both PSD-95 and CaMKII with the NR2A subunit. CaMKII-dependent phosphorylation of PSD-95 occurs both in vitro, in GST-PSD-95 fusion proteins phosphorylated by purified active CaMKII, and in vivo, in transfected COS-7 as well as in cultured hippocampal neurons. We identified Ser73 as major phosphorylation site within the PDZ1 domain of PSD-95, as confirmed by point mutagenesis experiments and by using a phospho-specific antibody. PSD-95 Ser73 phosphorylation causes NR2A dissociation from PSD-95, while it does not interfere with NR2B binding to PSD-95. These results identify CaMKII-dependent phosphorylation of the PDZ1 domain of PSD-95 as a mechanism regulating the signalling transduction pathway downstream NMDA receptor. [source]

Conservation of arthropod midline netrin accumulation revealed with a cross-reactive antibody provides evidence for midline cell homology

EVOLUTION AND DEVELOPMENT, Issue 3 2009
Wendy Simanton
SUMMARY Although many similarities in arthropod CNS development exist, differences in axonogenesis and the formation of midline cells, which regulate axon growth, have been observed. For example, axon growth patterns in the ventral nerve cord of Artemia franciscana differ from that of Drosophila melanogaster. Despite such differences, conserved molecular marker expression at the midline of several arthropod species indicates that midline cells may be homologous in distantly related arthropods. However, data from additional species are needed to test this hypothesis. In this investigation, nerve cord formation and the putative homology of midline cells were examined in distantly related arthropods, including: long- and short-germ insects (D. melanogaster, Aedes aeygypti, and Tribolium castaneum), branchiopod crustaceans (A. franciscana and Triops longicauditus), and malacostracan crustaceans (Porcellio laevis and Parhyale hawaiensis). These comparative analyses were aided by a cross-reactive antibody generated against the Netrin (Net) protein, a midline cell marker and regulator of axonogenesis. The mechanism of nerve cord formation observed in Artemia is found in Triops, another branchiopod, but is not found in the other arthropods examined. Despite divergent mechanisms of midline cell formation and nerve cord development, Net accumulation is detected in a well-conserved subset of midline cells in branchiopod crustaceans, malacostracan crustaceans, and insects. Notably, the Net accumulation pattern is also conserved at the midline of the amphipod P. hawaiensis, which undergoes split germ-band development. Conserved Net accumulation patterns indicate that arthropod midline cells are homologous, and that Nets function to regulate commissure formation during CNS development of Tetraconata. [source]

The dynamics of developmental system drift in the gene network underlying wing polyphenism in ants: a mathematical model

EVOLUTION AND DEVELOPMENT, Issue 3 2008
Marcos Nahmad
SUMMARY Understanding the complex interaction between genotype and phenotype is a major challenge of Evolutionary Developmental Biology. One important facet of this complex interaction has been called "Developmental System Drift" (DSD). DSD occurs when a similar phenotype, which is homologous across a group of related species, is produced by different genes or gene expression patterns in each of these related species. We constructed a mathematical model to explore the developmental and evolutionary dynamics of DSD in the gene network underlying wing polyphenism in ants. Wing polyphenism in ants is the ability of an embryo to develop into a winged queen or a wingless worker in response to an environmental cue. Although wing polyphenism is homologous across all ants, the gene network that underlies wing polyphenism has evolved. In winged ant castes, our simulations reproduced the conserved gene expression patterns observed in the network that controls wing development in holometabolous insects. In wingless ant castes, we simulated the suppression of wings by interrupting (up- or downregulating) the expression of genes in the network. Our simulations uncovered the existence of four groups of genes that have similar effects on target gene expression and growth. Although each group is comprised of genes occupying different positions in the network, their interruption produces vestigial discs that are similar in size and shape. The implications of our results for understanding the origin, evolution, and dissociation of the gene network underlying wing polyphenism in ants are discussed. [source]

Molecular paleoecology: using gene regulatory analysis to address the origins of complex life cycles in the late Precambrian

EVOLUTION AND DEVELOPMENT, Issue 1 2007
Ewan F. Dunn
SUMMARY Molecular paleoecology is the application of molecular data to test hypotheses made by paleoecological scenarios. Here, we use gene regulatory analysis to test between two competing paleoecological scenarios put forth to explain the evolution of complex life cycles. The first posits that early bilaterians were holobenthic, and the evolution of macrophagous grazing drove the exploitation of the pelagos by metazoan eggs and embryos, and eventually larvae. The alternative hypothesis predicts that early bilaterians were holopelagic, and new adult stages were added on when these holopelagic forms began to feed on the benthos. The former hypothesis predicts that the larvae of protostomes and deuterostomes are not homologous, with the implication that larval-specific structures, including the apical organ, are the products of convergent evolution, whereas the latter hypothesis predicts homology of larvae, specifically homology of the apical organ. We show that in the sea urchin, Strongylocentrotus purpuratus, the transcription factors NK2.1 and HNF6 are necessary for the correct spatial expression profiles of five different cilia genes. All of these genes are expressed exclusively in the apical plate after the mesenchyme-blastula stage in cells that also express NK2.1 and HNF6. In addition, abrogation of SpNK2.1 results in embryos that lack the apical tuft. However, in the red abalone, Haliotis rufescens, NK2.1 and HNF6 are not expressed in any cells that also express these same five cilia genes. Nonetheless, like the sea urchin, the gastropod expresses both NK2.1 and FoxA around the stomodeum and foregut, and FoxA around the proctodeum. As we detected no similarity in the development of the apical tuft between the sea urchin and the abalone, these molecular data are consistent with the hypothesis that the evolution of mobile, macrophagous metazoans drove the evolution of complex life cycles multiple times independently in the late Precambrian. [source]

Evolution of astacin-like metalloproteases in animals and their function in development

EVOLUTION AND DEVELOPMENT, Issue 2 2006
Frank Möhrlen
SUMMARY Astacin-like metalloproteases are ubiquitous in the animal kingdom but their phylogenetic relationships and ancient functions within the Metazoa are unclear. We have cloned and characterized four astacin-like cDNAs from the marine hydroid Hydractinia echinata and performed a database search for related genes in the draft genome sequence of the sea anemone Nematostella vectensis. These sequences and those of higher animals' astacins were subjected to phylogenetic analysis revealing five clusters within the Eumetazoa. The bone morphogenetic protein-1/tolloid-like astacins were represented in all eumetazoan phyla studied. The meprins were only found in vertebrates and cnidarians. Two clusters were taxon-specific, and one cluster represented astacins, which probably evolved after the split of the Cnidaria. Interestingly, grouping of astacins according to the protease catalytic domain alone resulted in clusters of proteins with similar overall domain architecture. The Hydractinia astacins were expressed in distinct cells during metamorphosis and some also during wound healing. Previously characterized cnidarian astacins also act during development. Based on our phylogeny, however, we propose that the developmental function of most of them is not homologous to the developmental function assigned to higher animals' astacins. [source]

Larval and adult brains,

EVOLUTION AND DEVELOPMENT, Issue 5 2005
Claus Nielsen
Summary Apical organs are a well-known structure in almost all ciliated eumetazoan larvae, although their function is poorly known. A review of the literature indicates that this small ganglion is the "brain" of the early larva, and it seems probable that it represents the brain of the ancestral, holopelagic ancestor of all eumetazoans, the gastraea. This early brain is lost before or at metamorphosis in all groups. Protostomes (excluding phoronids and brachiopods) appear to have brains of dual origin. Their larvae develop a pair of cephalic ganglia at the episphere lateral to the apical organ, and these two ganglia become an important part of the adult brain. The episphere and the cerebral ganglia show Otx expression, whereas Hox gene expression has not been seen in this part of the brain. A ventral nervous system develops around the blastopore, which becomes divided into mouth and anus by fusion of the lateral blastopore lips. The circumblastoporal nerve ring becomes differentiated into a nerve ring around the mouth, becoming part of the adult brain, a pair of ventral nerve cords, in some cases differentiated into a chain of ganglia, and a ring around the anus. This part of the nervous system appears to be homologous with the oral nerve ring of cnidarians. This interpretation is supported by the expression of Hox genes around the cnidarian mouth and in the ventral nervous system of the protostomes. The development of phoronids, brachiopods, echinoderms, and enteropneusts does not lead to the formation of an episphere or to differentiation of cerebral ganglia. In general, a well-defined brain is lacking, and Hox genes are generally not expressed in the larval organs, although this has not been well studied. [source]

Expression of Hoxa-11 and Hoxa-13 in the pectoral fin of a basal ray-finned fish, Polyodon spathula: implications for the origin of tetrapod limbs

EVOLUTION AND DEVELOPMENT, Issue 3 2005
Brian D. Metscher
Summary Paleontological and anatomical evidence suggests that the autopodium (hand or foot) is a novel feature that distinguishes limbs from fins, while the upper and lower limb (stylopod and zeugopod) are homologous to parts of the sarcopterygian paired fins. In tetrapod limb development Hoxa-11 plays a key role in differentiating the lower limb and Hoxa-13 plays a key role in differentiating the autopodium. It is thus important to determine the ancestral functions of these genes in order to understand the developmental genetic changes that led to the origin of the tetrapod autopodium. In particular it is important to understand which features of gene expression are derived in tetrapods and which are ancestral in bony fishes. To address these questions we cloned and sequenced the Hoxa-11 and Hoxa-13 genes from the North American paddlefish, Polyodon spathula, a basal ray-finned fish that has a pectoral fin morphology resembling that of primitive bony fishes ancestral to the tetrapod lineage. Sequence analysis of these genes shows that they are not orthologous to the duplicated zebrafish and fugu genes. This implies that the paddlefish has not duplicated its HoxA cluster, unlike zebrafish and fugu. The expression of Hoxa-11 and Hoxa-13 in the pectoral fins shows two main phases: an early phase in which Hoxa-11 is expressed proximally and Hoxa-13 is expressed distally, and a later phase in which Hoxa-11 and Hoxa-13 broadly overlap in the distal mesenchyme of the fin bud but are absent in the proximal fin bud. Hence the distal polarity of Hoxa-13 expression seen in tetrapods is likely to be an ancestral feature of paired appendage development. The main difference in HoxA gene expression between fin and limb development is that in tetrapods (with the exception of newts) Hoxa-11 expression is suppressed by Hoxa-13 in the distal limb bud mesenchyme. There is, however, a short period of limb bud development where Hoxa-11 and Hoxa-13 overlap similarly to the late expression seen in zebrafish and paddlefish. We conclude that the early expression pattern in tetrapods is similar to that seen in late fin development and that the local exclusion by Hoxa-13 of Hoxa-11 from the distal limb bud is a derived feature of limb developmental regulation. [source]

Expression of Pax258 in the gastropod statocyst: insights into the antiquity of metazoan geosensory organs

EVOLUTION AND DEVELOPMENT, Issue 6 2003
Elizabeth K. O'brien
Summary Most animals have sensory systems that allow them to balance and orient relative to the pull of gravity. Structures responsible for these functions range from very simple statocysts found in many aquatic invertebrates to the complex inner ear of mammals. Previous studies suggest that the specialized mechanosensory structures responsible for balance in vertebrates and insects may be homologous based on the requirement and expression of group II Pax genes (i.e., Pax-2/5/8 genes). Here we report the expression of a Pax-258 gene in the statocysts and other chemosensory and mechanosensory cells during the development of the gastropod mollusk Haliotis asinina, a member of the Lophotrochozoa. Based on the phylogenetic distribution of geo-sensory systems and the consistent expression of Pax-258 in the cells that form these systems, we propose that Pax-258, along with POU-III and -IV genes, has an ancient and conserved role in the formation of structures responsible for balance and geotaxis in eumetazoans. [source]