EVOLUTION, Issue 8 2009
Nolan C. Kane
While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct. [source]

Cloning, chromosomal localization and characterization of the murine mucin gene orthologous to human MUC4

FEBS JOURNAL, Issue 13 2002
Jean-Luc Desseyn
We report here the full coding sequence of a novel mouse putative membrane-associated mucin containing three extracellular EGF-like motifs and a mucin-like domain consisting of at least 20 tandem repeats of 124,126 amino acids. Screening a cosmid and a BAC libraries allowed to isolate several genomic clones. Genomic and cDNA sequence comparisons showed that the gene consists of 25 exons and 24 introns covering a genomic region of ,,52 kb. The first intron is ,,16 kb in length and is followed by an unusually large exon (, 9.5 kb) encoding Ser/Thr-rich tandemly repeated sequences. Radiation hybrid mapping localized this new gene to a mouse region of chromosome 16, which is the orthologous region of human chromosome 3q29 encompassing the large membrane-anchored mucin MUC4. Contigs analysis of the Human Genome Project did not reveal any other mucin on chromosome 3q29 and, interestingly, our analysis allowed the determination of the genomic organization of the human MUC4 and showed that its exon/intron structure is identical to that of the mouse gene we cloned. Furthermore, the human MUC4 shares considerable homologies with the mouse gene. Based on these data, we concluded that we isolated the mouse ortholog of MUC4 we propose as Muc4. Expression studies showed that Muc4 is ubiquitous like SMC and MUC4, with highest levels of expression in trachea and intestinal tract. [source]

Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in China

FEMS MICROBIOLOGY ECOLOGY, Issue 2 2008
Yong-Qing Ni
Abstract The genetic variability among 32 Chinese Acidithiobacillus spp. environmental isolates and four reference strains representing three recognized species of the genus Acidithiobacillus was characterized by using a combination of molecular methods, namely restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes and 16S,23S rRNA gene intergenic spacers, repetitive element PCR, arbitrarily primed PCR and 16S rRNA gene sequence analyses. 16S rRNA gene sequences revealed that all Acidithiobacillus spp. strains could be assigned to seven groups, three of which encompassed the Acidithiobacillus ferrooxidans strains from various parts of the world. A comparative analysis of the phylogenetic Group 1 and 2 was undertaken. Restriction fragment length polymorphism results allowed us to separate the 35 Acidithiobacillus strains into 15 different genotypes. An integrated phenotypic and genotypic analysis indicated that the distribution of A. ferrooxidans strains among the physiological groups were in agreement with their distribution among the genomic groups, and that no clear correlation was found between the genetic polymorphism of the Acidithiobacillus spp. strains and either the geographic location or type of habitats from which the strains were isolated. In addition, five unidentified sulfur-oxidizing isolates may represent one or two novel species of the genus Acidithiobacillus. The results showed that the Chinese Acidithiobacillus spp. isolates exhibited a high degree of genomic and phenotypic heterogeneity. [source]

Genomic and clinical analyses of 2p24 and 12q13-q14 amplification in alveolar rhabdomyosarcoma: A report from the Children's Oncology Group

GENES, CHROMOSOMES AND CANCER, Issue 8 2009
Frederic G. Barr
Alveolar rhabdomyosarcoma (ARMS) is an aggressive pediatric cancer that is related to the skeletal muscle lineage and characterized by recurrent chromosomal translocations. Within the ARMS category, there is clinical and genetic heterogeneity, consistent with the premise that "primary" genetic events collaborate with "secondary" events to give rise to subsets with varying clinical features. Previous studies demonstrated that genomic amplification occurs frequently in ARMS. In the current study, we used oligonucleotide arrays to localize two common amplicons to the 2p24 and 12q13-q14 chromosomal regions. Based on the copy number array data, we sublocalized the minimum common regions of 2p24 and 12q13-q14 amplification to a 0.83 Mb region containing the DDX1 and MYCN genes, and a 0.55 Mb region containing 27 genes, respectively. Using fluorescent in situ hybridization assays to measure copy number of the 2p24 and 12q13-q14 regions in over 100 cases, we detected these amplicons in 13% and 12% of cases, respectively. Comparison with fusion status revealed that 2p24 amplification occurred preferentially in cases positive for PAX3-FOXO1 or PAX7-FOXO1 while 12q13-q14 amplification occurred preferentially in PAX3-FOXO1 -positive cases. Expression studies demonstrated that MYCN was usually overexpressed in cases with 2p24 amplification while multiple genes were overexpressed in cases with 12q13-q14 amplification. Finally, although 2p24 amplification did not have a significant association with clinical outcome, 12q13-q14 amplification was associated with significantly worse failure-free and overall survival that was independent of gene fusion status. © 2009 Wiley-Liss, Inc. [source]

Genomic and immunophenotypical differences between hepatocellular carcinoma with and without cirrhosis

HISTOPATHOLOGY, Issue 6 2010
Maria S Tretiakova
Tretiakova M S, Shabani-Rad M T, Guggisberg K, Hart J, Anders R A & Gao Z-h (2010) Histopathology,56, 683,693 Genomic and immunophenotypical differences between hepatocellular carcinoma with and without cirrhosis Aims:, To compare the expression of genes involved in p53, Wnt/,-catenin, and retinoblastoma (Rb) 1 pathways between cirrhosis-associated hepatocellular carcinoma (HCC-C) and hepatocellular carcinoma arising in non-cirrhotic liver (HCC-NC). Methods and results:, The gene expression profile was analysed using oligo-DNA arrays, and then validated at protein level in a tissue microarray using immunohistochemistry. Compared with their background non-neoplastic liver tissue, HCC-C showed a significantly higher rate of p53, ,-catenin (protein only) and cyclin D1 expression, whereas HCC-NC showed a significantly higher rate of p21Waf1/cip1 and p27Kip1 expression. HCC-C had a significantly higher rate of p53 expression and a significantly lower rate of p21waf1/cip1 expression than HCC-NC. There was no statistically significant association between the expression of genetic markers and tumour histological grade, underlying aetiology, or lymphovascular invasion. Aberrant ,-catenin expression was more commonly seen in single tumours in comparison with multiple tumours. Increased p16INK4 and p21waf1/cip1 expression was more commonly observed in large-sized tumours (>50 mm) than small-sized tumours. Conclusions:, Alteration of the p53 pathway plays a more important role in the pathogenesis of HCC-C, whereas alterations in cell cycle regulators p21waf1/cip1 and p27Kip1 play a more important role in the pathogenesis of HCC-NC. [source]

Genetics and genomics of ankylosing spondylitis

IMMUNOLOGICAL REVIEWS, Issue 1 2010
Gethin P. Thomas
Summary:, Ankylosing spondylitis (AS) is a common, highly heritable arthropathy, the pathogenesis of which is poorly understood. The mechanism by which the main gene for the disease, HLA-B27, leads to AS is unknown. Genetic and genomic studies have demonstrated involvement of the interleukin-23 (IL-23) signaling pathway in AS, a finding which has stimulated much new research into the disease and has led to therapeutic trials. Several other genes and genetic regions, including further major histocompatibility complex (MHC) and non-MHC loci, have been shown to be involved in the disease, but it is not clear yet how they actually induce the condition. These findings have shown that there is a strong genetic overlap between AS and Crohn's disease in particular, although there are also major differences in the genes involved in the two conditions, presumably explaining their different presentations. Genomic and proteomic studies are in an early phase but have potential both as diagnostic/prognostic tools and as a further hypothesis-free tool to investigate AS pathogenesis. Given the slow progress in studying the mechanism of association of HLA-B27 with AS, these may prove to be more fruitful approaches to investigating the pathogenesis of the disease. [source]

Physiological functions of imprinted genes

JOURNAL OF CELLULAR PHYSIOLOGY, Issue 3 2002
Benjamin Tycko
Genomic imprinting in gametogenesis marks a subset of mammalian genes for parent-of-origin-dependent monoallelic expression in the offspring. Embryological and classical genetic experiments in mice that uncovered the existence of genomic imprinting nearly two decades ago produced abnormalities of growth or behavior, without severe developmental malformations. Since then, the identification and manipulation of individual imprinted genes has continued to suggest that the diverse products of these genes are largely devoted to controlling pre- and post-natal growth, as well as brain function and behavior. Here, we review this evidence, and link our discussion to a website (http://www.otago.ac.nz/IGC) containing a comprehensive database of imprinted genes. Ultimately, these data will answer the long-debated question of whether there is a coherent biological rationale for imprinting. © 2002 Wiley-Liss, Inc. [source]

Genomic and cDNA microsatellites from apricot (Prunus armeniaca L.)

MOLECULAR ECOLOGY RESOURCES, Issue 4 2004
L. S. HAGEN
Abstract We developed primers for the amplification of 24 polymorphic nuclear microsatellites in apricot (Prunus armeniaca L.). Thirteen loci originated from three genomic libraries enriched for TC, TG and AAG motifs. Eight loci were developed from three fruit EST (Expressed-Sequence-Tag) libraries and three from a leaf cDNA microsatellite-enriched library. There were up to nine alleles per polymorphic locus in 12 different cultivars. No difference in allele numbers were shown between cDNA and genomic-source loci. Mean expected heterozygosity was 0.65 (range: 0.15,0.87). Mendelian segregation was confirmed for all loci. These markers should be helpful for diversity studies, genome mapping and cultivar identification in apricot and related species. [source]

Suillus bovinus glutamine synthetase gene organization, transcription and enzyme activities in the Scots pine mycorrhizosphere developed on forest humus

NEW PHYTOLOGIST, Issue 2 2004
Jarmo T. Juuti
Summary ,,Glutamine synthetase (GS) expression and activity is of central importance for cellular ammonium assimilation and recycling. Thus, a full characterization of this enzyme at the molecular level is of critical importance for a better understanding of nitrogen (N) assimilation in the mycorrhizal symbiosis. ,,Genomic and cDNA libraries of Suillus bovinus were constructed to isolate the GS gene, glnA, and corresponding cDNAs. The transcription initiation site was identified and transcription and enzyme activities were characterized in pure culture mycelium and mycorrhiza, and extramatrical mycelium samples harvested from Scots pine,Suillus bovinus microcosms grown on forest humus. ,,Pure culture mycelium, mycorrhiza and extramatrical mycelium all exhibited equivalent levels of GS transcription, translation and enzyme activities. However, levels of transcription and enzyme activity did not correlate as a large majority of detectable transcripts showed specific 5,-end truncation. ,,Our data suggest that GS is constitutively expressed and not directly affected by environmental conditions of the symbiotic N uptake. Any changes in the intracellular ammonium level are most likely handled by regulatory flexibility of GS at enzyme level. [source]

Identification of wheat,Thinopyrum intermedium 2Ai-2 ditelosomic addition and substitution lines with resistance to barley yellow dwarf virus

PLANT BREEDING, Issue 2 2006
Z. S. Lin
Abstract Among the regenerated plants derived from immature hybrid embryos of wheat,Thinopyrum intermedium disomic addition line Z6 × common wheat variety ,Zhong8601', a plant with a telocentric chromosome and barley yellow dwarf virus (BYDV) resistance was obtained. The telocentric chromosome paired with an entire Thinopyrum chromosome to form a heteromorphic bivalent at meiotic metaphase I. Genomic in situ hybridization showed that the telosome originated from Th. intermedium. Two ditelosomic additions and one disomic substitution were identified among the offspring of the plant. Two random amplified polymorphic DNA molecular markers were identified among 150 random primers used to detect the different arms of the alien chromosome. These might be useful for developing translocation lines with BYDV resistance. [source]

Molecular cytogenetic analysis of a durum wheat ×Thinopyrum distichum hybrid used as a new source of resistance to Fusarium head blight in the greenhouse

PLANT BREEDING, Issue 5 2001
Q. Chen
Abstract Fusarium head blight (FHB, scab), caused by Fusarium graminearum Schwabe, is a serious and damaging disease of wheat. Although some hexaploid wheat lines express a good level of resistance to FHB, the resistance available in hexaploid wheat has not yet been transferred to durum wheat. A germplasm collection of Triticum durum× alien hybrid lines was tested as a potential source of resistance to FHB under controlled conditions. Their FHB reaction was evaluated in three tests against conidial suspensions of three strains of F. graminearum at the flowering stage. Two T. durum×Thinopyrum distichum hybrid lines, ,AFR4' and ,AFR5,, expressed a significantly higher level of resistance to the spread of FHB than other durum-alien hybrid lines and a resistant common wheat line ,Nyu-Bay'. Genomic in situ hybridization using total genomic DNA from alien grass species demonstrated that ,AFR5' had 13 or 14 alien genome chromosomes plus 27 or 28 wheat chromosomes, while ,AFR4' had 22 alien genome and 28 wheat chromosomes. All of the alien chromosomes present in these two lines belonged to the J genome. ,AFR5' is likely to be more useful as a source of FHB resistance than ,AFR4' because of its relatively normal meiotic behaviour, high fertility and fewer number of alien chromosomes. ,AFR5' shows good potential as a source for transferring FHB resistance gene into wheat. The development of T. durum addition lines carrying resistance genes from ,AFR5' is underway. [source]

Book Review: Applying Genomic and Proteomic Microarray Technology in Drug Discovery.

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 14 2005
By Robert S. Matson
No abstracts. [source]

Genomic and Proteomic Evidence for a Second Family of Dense Core Granule Cargo Proteins in Tetrahymena thermophila

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2005
GRANT R. BOWMAN
Abstract. In addition to a family of structurally related proteins encoded by the Granule lattice (GRL) genes, the dense core granules in Tetrahymena thermophila contain a second, more heterogeneous family of proteins that can be defined by the presence of a domain homologous to ,/,-crystallins. The founding members of the family, Induced during Granule Regeneration 1 (IGR1) and Granule Tip 1 (GRT1), were identified in previous screens for granule components. Analysis of the recently sequenced T. thermophila macronuclear genome has now uncovered 11 additional related genes. All family members have a single ,/,-crystallin domain, but the overall predicted organization of family members is highly variable, and includes three other motifs that are conserved between subsets of family members. To demonstrate that these proteins are present within granules, polypeptides from a subcellular fraction enriched in granules were analyzed by mass spectrometry. This positively identified four of the predicted novel ,/,-crystallin domain proteins. Both the functional evidence for IGR1 and GRT1 and the variability in the overall structure of this new protein family suggest that its members play roles that are distinct from those of the GRL family. [source]

Folate synthesis in plants: the last step of the p -aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyase

THE PLANT JOURNAL, Issue 4 2004
Gilles J.C. Basset
Summary In plants, the last step in the synthesis of p -aminobenzoate (PABA) moiety of folate remains to be elucidated. In Escherichia coli, this step is catalyzed by the PabC protein, a , -lyase that converts 4-amino-4-deoxychorismate (ADC) , the reaction product of the PabA and PabB enzymes , to PABA and pyruvate. So far, the only known plant enzyme involved in PABA synthesis is ADC synthase, which has fused domains homologous to E. coli PabA and PabB and is located in plastids. ADC synthase has no lyase activity, implying that plants have a separate ADC lyase. No such lyase is known in any eukaryote. Genomic and phylogenetic approaches identified Arabidopsis and tomato cDNAs encoding PabC homologs with putative chloroplast-targeting peptides. These cDNAs were shown to encode functional enzymes by complementation of an E. coli pabC mutant, and by demonstrating that the partially purified recombinant proteins convert ADC to PABA. Plant ADC lyase is active as dimer and is not feedback inhibited by physiologic concentrations of PABA, its glucose ester, or folates. The full-length Arabidopsis ADC lyase polypeptide was translocated into isolated pea chloroplasts and, when fused to green fluorescent protein, directed the passenger protein to Arabidopsis chloroplasts in transient expression experiments. These data indicate that ADC lyase, like ADC synthase, is present in plastids. As shown previously for the ADC synthase transcript, the level of ADC lyase mRNA in the pericarp of tomato fruit falls sharply as ripening advances, suggesting that the expression of these two enzymes is coregulated. [source]

Genomic imprinting in the development and evolution of psychotic spectrum conditions

BIOLOGICAL REVIEWS, Issue 4 2008
Bernard Crespi
Abstract I review and evaluate genetic and genomic evidence salient to the hypothesis that the development and evolution of psychotic spectrum conditions have been mediated in part by alterations of imprinted genes expressed in the brain. Evidence from the genetics and genomics of schizophrenia, bipolar disorder, major depression, Prader-Willi syndrome, Klinefelter syndrome, and other neurogenetic conditions support the hypothesis that the etiologies of psychotic spectrum conditions commonly involve genetic and epigenetic imbalances in the effects of imprinted genes, with a bias towards increased relative effects from imprinted genes with maternal expression or other genes favouring maternal interests. By contrast, autistic spectrum conditions, including Kanner autism, Asperger syndrome, Rett syndrome, Turner syndrome, Angelman syndrome, and Beckwith-Wiedemann syndrome, commonly engender increased relative effects from paternally expressed imprinted genes, or reduced effects from genes favouring maternal interests. Imprinted-gene effects on the etiologies of autistic and psychotic spectrum conditions parallel the diametric effects of imprinted genes in placental and foetal development, in that psychotic spectrum conditions tend to be associated with undergrowth and relatively-slow brain development, whereas some autistic spectrum conditions involve brain and body overgrowth, especially in foetal development and early childhood. An important role for imprinted genes in the etiologies of psychotic and autistic spectrum conditions is consistent with neurodevelopmental models of these disorders, and with predictions from the conflict theory of genomic imprinting. [source]

Robustness Analysis of the Escherichiacoli Metabolic Network

BIOTECHNOLOGY PROGRESS, Issue 6 2000
Jeremy S. Edwards
Genomic, biochemical, and strain-specific data can be assembled to define an in silico representation of the metabolic network for a select group of single cellular organisms. Flux-balance analysis and phenotypic phase planes derived therefrom have been developed and applied to analyze the metabolic capabilities and characteristics of Escherichia coli K-12. These analyses have shown the existence of seven essential reactions in the central metabolic pathways (glycolysis, pentose phosphate pathway, tricarboxylic acid cycle) for the growth in glucose minimal media. The corresponding seven gene products can be grouped into three categories: (1) pentose phosphate pathway genes, (2) three-carbon glycolytic genes, and (3) tricarboxylic acid cycle genes. Here we develop a procedure that calculates the sensitivity of optimal cellular growth to altered flux levels of these essential gene products. The results indicate that the E. coli metabolic network is robust with respect to the flux levels of these enzymes. The metabolic flux in the transketolase and the tricarboxylic acid cycle reactions can be reduced to 15% and 19%, respectively, of the optimal value without significantly influencing the optimal growth flux. The metabolic network also exhibited robustness with respect to the ribose-5-phosphate isomerase, and the ribose-5-phosephate isomerase flux was reduced to 28% of the optimal value without significantly effecting the optimal growth flux. The metabolic network exhibited limited robustness to the three-carbon glycolytic fluxes both increased and decreased. The development presented another dimension to the use of FBA to study the capabilities of metabolic networks. [source]

Chlamydia pneumoniae and atherosclerosis

CELLULAR MICROBIOLOGY, Issue 2 2004
Robert J. Belland
Summary Exposure to Chlamydia pneumoniae is extremely common, and respiratory infections occur repeatedly among most people. Strong associations exist between C. pneumoniae infection and atherosclerosis as demonstrated by: (i) sero-epidemiological studies showing that patients with cardiovascular disease have higher titres of anti- C. pneumoniae antibodies compared with control patients; (ii) detection of the organism within atherosclerotic lesions, but not in adjacent normal tissue by immunohistochemistry, polymerase chain reaction and electron microscopy and by culturing the organism from lesions; and (iii) showing that C. pneumoniae can either initiate lesion development or cause exacerbation of lesions in rabbit and mouse animal models respectively. The association of this organism with atherosclerosis has also provided sufficient impetus to conduct a variety of human secondary prevention antibiotic treatment trials. The results of these studies have been mixed and, thus far, no clear long-lasting benefit has emerged from these types of investigations. Studies of C. pneumoniae pathogenesis have shown that the organism can infect many cell types associated with both respiratory and cardiovascular sites, including lung epithelium and resident alveolar macrophages, circulating monocytes, arterial smooth muscle cells and vascular endothelium. Infected cells have been shown to exhibit characteristics associated with the development of cardiovascular disease (e.g. secretion of proinflammatory cytokines and procoagulants by infected endothelial cells and foam cell formation by infected macrophages). More detailed analysis of C. pneumoniae pathogenesis has been aided by the availability of genomic sequence information. Genomic and proteomic analyses of C. pneumoniae infections in relevant cell types will help to define the pathogenic potential of the organism in both respiratory and cardiovascular disease. [source]

Amplifying Nuclear and Mitochondrial DNA from African Elephant Ivory: a Tool for Monitoring the Ivory Trade

CONSERVATION BIOLOGY, Issue 6 2003
KENINE E. COMSTOCK
cacería furtiva; elefante africano; Loxodonta africana; marfil; microsatélites Abstract: The ability to extract DNA from ivory provides the basis for genetically tracking the origin of poached ivory and thus has important implications for elephant conservation and management. We describe a method to isolate and amplify both genomic and mitochondrial DNA from African elephant ivory that requires very small amounts of ivory taken from any location on the tusk. We pulverized ivory and isolated DNA with a modified QIAamp kit. Ivory as old as 10 to 20 years, stored at ambient conditions, was amenable to DNA isolation with this method. The isolated DNA was robustly amplified at 16 elephant microsatellite loci and two mitochondrial DNA loci. This method has important applications for the forensic analysis of poached African elephant ivory. It enables determination of where stronger antipoaching efforts are needed and provides the basis for monitoring the extent of the trade as well as the consequences of future international trade decisions. Resumen: La habilidad para extraer ADN del marfil proporciona la base para rastrear genéticamente el origen de marfil furtivo y por tanto tiene implicaciones importantes para la conservación y el manejo de elefantes. Describimos un método para aislar y amplificar ADN genómico y mitocondrial de marfil de elefante africano que requiere de cantidades muy pequeñas de marfil tomadas de cualquier parte del colmillo. Pulverizamos el marfil y aislamos el ADN con un equipo QIAamp modificado. Con este método, fue posible aislar el ADN de marfil de 10 a 20 años, conservado en condiciones ambientales. El ADN aislado fue amplificado robustamente en 16 loci microsatélite y dos loci de ADN mitocondrial. Este método tiene aplicaciones importantes para el análisis forense de marfil de elefantes africanos cazados furtivamente. Permite la identificación de sitios donde se requieren mayores esfuerzos para combatir la cacería furtiva y proporciona la base para monitorear la extensión del comercio así como las consecuencias de decisiones futuras de comercio internacional. [source]

Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution

DEVELOPMENTAL DYNAMICS, Issue 3 2006
Yuich Okuda
Abstract Group B1 Sox genes encode HMG domain transcription factors that play major roles in neural development. We have identified six zebrafish B1 sox genes, which include pan-vertebrate sox1a/b, sox2, and sox3, and also fish-specific sox19a/b. SOX19A/B proteins show a transcriptional activation potential that is similar to other B1 SOX proteins. The expression of sox19a and sox3 begins at approximately the 1,000-cell stage during embryogenesis and becomes confined to the future ectoderm by the shield stage. This is reminiscent of the epiblastic expression of Sox2 and/or Sox3 in amniotes. As development progresses, these six B1 sox genes display unique expression patterns that overlap distinctly from one region to another. sox19a expression is widespread in the early neuroectoderm, resembling pan-neural Sox2 expression in amniotes, whereas zebrafish sox2 shows anterior-restricted expression. Comparative genomics suggests that sox19a/b and mammalian Sox15 (group G) have an orthologous relationship and that the B1/G Sox genes arose from a common ancestral gene through two rounds of genome duplication. It seems likely, therefore, that each B1/G Sox gene has gained a distinct expression profile and function during vertebrate evolution. Developmental Dynamics 235:811,825, 2006. © 2006 Wiley-Liss, Inc. [source]

Xenopus, the next generation: X. Tropicalis genetics and genomics

DEVELOPMENTAL DYNAMICS, Issue 4 2002
Nicolas Hirsch
Abstract A small, fast-breeding, diploid relative of the frog Xenopus laevis, Xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics. X. tropicalis shares advantages of X. laevis as a classic embryologic system, but its simpler genome and shorter generation time make it more convenient for multigenerational genetic, genomic, and transgenic approaches. Its embryos closely resemble those of X. laevis, except for their smaller size, and assays and molecular probes developed in X. laevis can be readily adapted for use in X. tropicalis. Genomic manipulation techniques such as gynogenesis facilitate genetic screens, because they permit the identification of recessive phenotypes after only one generation. Stable transgenic lines can be used both as in vivo reporters to streamline a variety of embryologic and molecular assays, or to experimentally manipulate gene expression through the use of binary constructs such as the GAL4/UAS system. Several mutations have been identified in wild-caught animals and during the course of generating inbred lines. A variety of strategies are discussed for conducting and managing genetic screens, obtaining mutations in specific sequences, achieving homologous recombination, and in developing and taking advantage of the genomic resources for Xenopus tropicalis. © 2002 Wiley-Liss, Inc. [source]

Drosophila RSK negatively regulates bouton number at the neuromuscular junction

DEVELOPMENTAL NEUROBIOLOGY, Issue 4 2009
Matthias Fischer
Abstract Ribosomal S6 kinases (RSKs) are growth factor-regulated serine-threonine kinases participating in the RAS-ERK signaling pathway. RSKs have been implicated in memory formation in mammals and flies. To characterize the function of RSK at the synapse level, we investigated the effect of mutations in the rsk gene on the neuromuscular junction (NMJ) in Drosophila larvae. Immunostaining revealed transgenic expressed RSK in presynaptic regions. In mutants with a full deletion or an N-terminal partial deletion of rsk, an increased bouton number was found. Restoring the wild-type rsk function in the null mutant with a genomic rescue construct reverted the synaptic phenotype, and overexpression of the rsk -cDNA in motoneurons reduced bouton numbers. Based on previous observations that RSK interacts with the Drosophila ERK homologue Rolled, genetic epistasis experiments were performed with loss- and gain-of-function mutations in Rolled. These experiments provided evidence that RSK mediates its negative effect on bouton formation at the Drosophila NMJ by inhibition of ERK signaling. © 2009 Wiley Periodicals, Inc. Develop Neurobiol 2009 [source]

Genome-wide P -element screen for Drosophila synaptogenesis mutants

DEVELOPMENTAL NEUROBIOLOGY, Issue 4 2006
Faith L.W. Liebl
Abstract A molecular understanding of synaptogenesis is a critical step toward the goal of understanding how brains "wire themselves up," and then "rewire" during development and experience. Recent genomic and molecular advances have made it possible to study synaptogenesis on a genomic scale. Here, we describe the results of a screen for genes involved in formation and development of the glutamatergic Drosophila neuromuscular junction (NMJ). We screened 2185 P -element transposon mutants representing insertions in ,16% of the entire Drosophila genome. We first identified recessive lethal mutants, based on the hypothesis that mutations causing severe disruptions in synaptogenesis are likely to be lethal. Two hundred twenty (10%) of all insertions were homozygous lethal. Two hundred five (93%) of these lethal mutants developed at least through late embryogenesis and formed neuromusculature. We examined embryonic/larval NMJs in 202 of these homozygous mutants using immunocytochemistry and confocal microscopy. We identified and classified 88 mutants with altered NMJ morphology. Insertion loci in these mutants encode several different types of proteins, including ATP- and GTPases, cytoskeletal regulators, cell adhesion molecules, kinases, phosphatases, RNA regulators, regulators of protein formation, transcription factors, and transporters. Thirteen percent of insertions are in genes that encode proteins of novel or unknown function. Complementation tests and RT-PCR assays suggest that approximately 51% of the insertion lines carry background mutations. Our results reveal that synaptogenesis requires the coordinated action of many different types of proteins,perhaps as much as 44% of the entire genome,and that transposon mutageneses carry important caveats that must be respected when interpreting results generated using this method. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006 [source]

A new dimension in combining data?

ACTA ZOOLOGICA, Issue 1 2010
The use of morphology, phylogenomic data in metazoan systematics
Abstract Giribet, G. 2010. A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics. ,Acta Zoologica (Stockholm) 91: 11,19 Animal phylogenies have been traditionally inferred by using the character state information derived from the observation of a diverse array of morphological and anatomical features, but the incorporation of molecular data into the toolkit of phylogenetic characters has shifted drastically the way researchers infer phylogenies. A main reason for this is the ease at which molecular data can be obtained, compared to, e.g., traditional histological and microscopical techniques. Researchers now routinely use genomic data for reconstructing relationships among animal phyla (using whole genomes or Expressed Sequence Tags) but the amount of morphological data available to study the same phylogenetic patterns has not grown accordingly. Given the disparity between the amounts of molecular and morphological data, some authors have questioned entire morphological programs. In this review I discuss issues related to the combinability of genomic and morphological data, the informativeness of each set of characters, and conclude with a discussion of how morphology could be made scalable by utilizing new techniques that allow for non-intrusive examination of large amounts of preserved museum specimens. Morphology should therefore remains a strong field in evolutionary and comparative biology, as it continues to provide information for inferring phylogenetic patterns, is an important complement for the patterns derived from the molecular data, and it is the common nexus that allows studying fossil taxa with large data sets of molecular data. [source]

Cover Picture: Electrophoresis 7'09

ELECTROPHORESIS, Issue 7 2009
Article first published online: 16 APR 200
Issue no. 7 is a special issue on "Biomarker Discovery and Related Topics". It has 18 articles distributed among four parts including genomic, proteomic, glycoproteomic and metabolomic markers. "New separation technologies, improvements of existing methods and intuitive, elegant applications are providing a representative snapshot on the "state-of-the-art" of the bioanalytical aspects of biomarker discovery today". In addition, as recognition of his significant contribution to the field, this special issue is dedicated to the 70th birthday of Professor Barry L. Karger. [source]

Capillary electrophoresis-laser induced fluorescence analysis of endogenous damage in mitochondrial and genomic DNA

ELECTROPHORESIS, Issue 13 2005
Michaela Wirtz
Abstract Reactive oxygen molecules are formed in vivo as by-products of normal aerobic metabolism. All organisms dependent on oxygen are inevitably exposed to these species so that DNA damage can occur in both genomic and mitochondrial DNA (mtDNA). In order to determine endogenous DNA damage we have developed an analytical method that involves the isolation and hydrolysis of genomic DNA or mtDNA, the labeling of modified and unmodified nucleotides and micellar electrokinetic chromatography with laser-induced fluorescence detection. With this method we have found etheno-adenine, thymine glycol, uracil, hypoxanthine, and 5-methylcytosine. These were identified by the addition of internal standards to the genomic or mtDNA. There are a large number of other signals in the electropherograms of mtDNA that we have never found in genomic DNA analysis because they are at lower concentration in the genome. In the DNA of untreated patients with chronic lymphocytic leukemia (CLL), uracil and high levels of etheno-adenine were found, which can be explained by antioxidant enzyme alterations and oxidative stress in the CLL lymphocytes. [source]

Delayed genomic and acute nongenomic action of glucocorticosteroids in seasonal allergic rhinitis

EUROPEAN JOURNAL OF CLINICAL INVESTIGATION, Issue 1 2004
H.-C. Tillmann
Abstract Background, Glucocorticosteroids are effective in the treatment of allergic rhinitis, a disease characterized by a variety of symptoms, e.g. rhinorrhea and itching. The time course of symptomatic relief for allergic rhinitis by steroids has not been examined in detail to date, although the onset of steroid action is one of the main discriminations between genomic and nongenomic actions of steroids. We therefore investigated the time course of subjective and objective measures of nasal affection after steroid administration in patients with allergic rhinitis following specific allergen challenge. Methods, Six female and 18 male volunteers (median age 26 years) with a history of allergic rhinitis but currently free of symptoms were included in this randomized, placebo-controlled, double-blind, three-period crossover study. A single dose of either betamethasone (60 mg), methylprednisolone (400 mg) or placebo was given intravenously, 5 min after intranasal allergen provocation. After 10, 20, 60, 150 and 240 min, nasal itching and nasal obstruction were assessed using a standardized visual analogue scale. In addition, nasal airflow was measured by anterior rhinomanometry. Results, Nasal itching was markedly reduced following either of the two steroids within 10 min after administration of study drug. Itching was depressed by 38% following betamethasone (P < 0·05) and by 18% following methylprednisolone (P = 0·07) compared with placebo. Nasal airflow and nasal obstruction were not significantly altered by steroids during the first 2 h of the study. However, after 150 min, nasal airflow was 21% rsp. 19% higher after methylprednisolone and betamethasone (P < 0·05) compared with placebo. After 240 min, nasal airflow was increased by 20% following betamethasone (P < 0·05) and by 19% following methylprednisolone. Nasal obstruction was also beneficially affected by both steroids 150 and 240 min after administration compared with placebo (P < 0·05 for both time points following betamethasone). Conclusion, This study for the first time shows rapid in vivo effects of external glucocorticosteroids in humans. Itching, a pathophysiologically complex sensation, is favourably influenced by steroids within 10 min, therefore presumably via nongenomic mechanisms. Though no detailed mechanisms can be derived from this study, steroid interaction with receptors in the central nervous system may play an important role in mediating this effect. [source]

GENETIC STUDY: Interaction of SLC6A4 and DRD2 polymorphisms is associated with a history of delirium tremens

ADDICTION BIOLOGY, Issue 1 2010
Victor M. Karpyak
ABSTRACT Several genetic polymorphisms have been reported to be associated with alcohol withdrawal seizures (AWS) and delirium tremens (DT). To replicate and further explore these findings, we investigated the effects of 12 previously reported candidate genetic variations in two groups of alcohol-dependent European Americans with a history of withdrawal, which differed according to the presence (n = 112) or absence (n = 92) of AWS and/or DT. Associations of AWS and/or DT with the genomic and clinical characteristics and gene,gene interaction effects were investigated using logistic regression models. None of the polymorphisms were significantly associated with AWS/DT after correction for multiple testing. However, we found a significant interaction effect of the SLC6A4 promoter polymorphism (5-HTTLPR) and DRD2 exon 8 single nucleotide polymorphism rs6276 on AWS and/or DT history (P = 0.009), which became more significant after adjustment for lifetime maximum number of drinks consumed per 24 hours (P < 0.001). Subsequent analysis revealed an even stronger association of the SLC6A4,DRD2 interaction with DT (P < 0.0001), which remained significant after Bonferroni correction. Results reveal decreased likelihood of DT in alcoholics that carry the DRD2 rs6276 G allele and SLC6A4 LL genotype. This study provides the first evidence to implicate the interaction between serotonin and dopamine neurotransmission in the etiology of DT. Replication is necessary to verify this potentially important finding. [source]

Co-induction of activity-dependent genes in songbirds

EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 7 2005
Tarciso A. F. Velho
Abstract Song behavior in songbirds induces the expression of activity-dependent genes in brain areas involved in perceptual processing, production and learning of song. This genomic response is thought to represent a link between neuronal activation and long-term changes in song-processing circuits of the songbird brain. Here we demonstrate that Arc, an activity-regulated gene whose product has dendritic localization and is associated with synaptic plasticity, is rapidly induced by song in the brain of zebra finches. We show that, in the context of song auditory stimulation, Arc expression is induced in several telencephalic auditory areas, most prominently the caudomedial nidopallium and mesopallium, whereas in the context of singing, Arc is also induced in song control areas, namely nucleus HVC, used as a proper name, the robust nucleus of the arcopallium and the interface nucleus of the nidopallium. We also show that song-induced Arc expression co-localizes at the cellular level with those of the transcriptional regulators zenk and c-fos, and that the song induction of these three genes is dependent on activation of the mitogen-activated protein kinase signaling pathway. These findings provide evidence for an involvement of Arc in the brain's response to birdsong. They also demonstrate that genes representing distinct genomic and cellular regulatory programs, namely early effectors and transcription factors, are co-activated in the same neuronal cells by a naturally learned stimulus. [source]

RELATIVE CONTRIBUTION OF ADDITIVE, DOMINANCE, AND IMPRINTING EFFECTS TO PHENOTYPIC VARIATION IN BODY SIZE AND GROWTH BETWEEN DIVERGENT SELECTION LINES OF MICE

EVOLUTION, Issue 5 2009
Reinmar Hager
Epigenetic effects attributed to genomic imprinting are increasingly recognized as an important source of variation in quantitative traits. However, little is known about their relative contribution to phenotypic variation compared to those of additive and dominance effects, and almost nothing about their role in phenotypic evolution. Here we address these questions by investigating the relative contribution of additive, dominance, and imprinting effects of quantitative trait loci (QTL) to variation in "early" and "late" body weight in an intercross of mice selected for divergent adult body weight. We identified 18 loci on 13 chromosomes; additive effects accounted for most of the phenotypic variation throughout development, and imprinting effects were always small. Genetic effects on early weight showed more dominance, less additive, and, surprisingly, less imprinting variation than that of late weight. The predominance of additivity of QTL effects on body weight follows the expectation that additive effects account for the evolutionary divergence between selection lines. We hypothesize that the appearance of more imprinting effects on late body weight may be a consequence of divergent selection on adult body weight, which may have indirectly selected for alleles showing partial imprinting effects due to their associated additive effects, highlighting a potential role of genomic imprinting in the response to selection. [source]

CYTONUCLEAR INTERACTIONS CAN FAVOR THE EVOLUTION OF GENOMIC IMPRINTING

EVOLUTION, Issue 5 2009
Jason B. Wolf
Interactions between cytoplasmic (generally organelle) and nuclear genomes may be relatively common and could potentially have major fitness consequences. As in the case of within-genome epistasis, this cytonuclear epistasis can favor the evolutionary coadaptation of high-fitness combinations of nuclear and cytoplasmic alleles. Because cytoplasmic factors are generally uniparentally inherited, the cytoplasmic genome is inherited along with only one of the nuclear haplotypes, and therefore, coadaptation is expected to evolve through the interaction of these coinherited (usually maternally inherited) genomes. Here I show that, as a result of this coinheritance of the two genomes, cytonuclear epistasis can favor the evolution of genomic imprinting such that, when the cytoplasmic factor is maternally inherited, selection favors maternal expression of the nuclear locus and when the factor is paternally inherited selection favors paternal expression. Genomic imprinting evolves in this model because it leads to a pattern of gene expression in the nuclear haplotype that is coadapted with (i.e., adaptively coordinated with) gene expression in the coinherited cytoplasmic genome. [source]