DIGESTIVE ENDOSCOPY, Issue 3 2009
Naotaka Ogasawara
Gastric schwannomas are rare benign mesenchymal tumors. We describe a schwannoma of gastric origin with adjacent external progression. Sections showed a spindle cell tumor arranged in interlaced bundles and fascicles that was S-100 and CD34 positive but c-KIT protein negative. Histology and immunohistochemistry revealed the typical appearance of a gastric schwannoma. Genetic evaluation revealed that the tumor harbored a point mutation in exon 6 of the tumor suppressor neurofibromatosis 2 (NF2) gene, which resulted in an amino acid substitution of NF2 protein, and no mutation in exon 4b of the NF1 gene. In conclusion, we identified a rare mutation of the NF2 gene in gastric schwannoma. A diagnosis can only be definitive when based on histological and immunohistochemical findings. Digestive tract schwannomas are rare mesenchymal tumors that are differentiated from gastrointestinal stromal tumors by the absence of KIT protein. Follow up suggested that complete resection is an effective long-term treatment strategy. [source]

ADAPTIVE REPTILE COLOR VARIATION AND THE EVOLUTION OF THE MCIR GENE

EVOLUTION, Issue 8 2004
Erica Bree Rosenblum
Abstract The wealth of information on the genetics of pigmentation and the clear fitness consequences of many pigmentation phenotypes provide an opportunity to study the molecular basis of an ecologically important trait. The melanocortin-1 receptor (Mc1r) is responsible for intraspecific color variation in mammals and birds. Here, we study the molecular evolution of Mc1r and investigate its role in adaptive intraspecific color differences in reptiles. We sequenced the complete Mc1r locus in seven phylogenetically diverse squamate species with melanic or blanched forms associated with different colored substrates or thermal environments. We found that patterns of amino acid substitution across different regions of the receptor are similar to the patterns seen in mammals, suggesting comparable levels of constraint and probably a conserved function for Mc1r in mammals and reptiles. We also found high levels of silent-site heterozygosity in all species, consistent with a high mutation rate or large long-term effective population size. Mc1r polymorphisms were strongly associated with color differences in Holbrookia maculata and Aspidoscelis inornata. In A. inornata, several observations suggest that Mc1r mutations may contribute to differences in color: (1) a strong association is observed between one Mc1r amino acid substitution and dorsal color; (2) no significant population structure was detected among individuals from these populations at the mitochondrial ND4 gene; (3) the distribution of allele frequencies at Mc1r deviates from neutral expectations; and (4) patterns of linkage disequilibrium at Mc1r are consistent with recent selection. This study provides comparative data on a nuclear gene in reptiles and highlights the utility of a candidate-gene approach for understanding the evolution of genes involved in vertebrate adaptation. [source]

SEQUENCE ANALYSIS OF A NOVEL INSECT PHOSPHOGLYCERATE MUTASE GENE FROM THE CHINESE HONEYBEE, APIS CERANA,

INSECT SCIENCE, Issue 4 2003
Jiang-hong Li
Abstract A clone inserted with 1 104 bp fragment containing a 765bp Open Reading Frame(ORF), encoding a putative 2,3-bisphosphoglycerate(2,3BPG) dependent Phosphoglycerate mutase(dPGAM) that catalyzes the transfer of a phosphate group from the C3 carbon atom to the C2 carbon atom of phosphoglycerate, was screened by mass sequencing from the cDNA library of the venom glands of Apis cerana. The deduced amino acid sequence shared high similarities (39% - 88%)with the dPGAM of 7 other organisms, but the similarities with the iPGAM of 4 other organisms were low (10% - 12%). Moreover, the alignment of Ac-PGAM with the dPGAMs from 7 other organisms showed that all the active site amino acid residues were conserved. This result shows that Ac-PGAM is a typical dPGAM. Thus, this is the second PGAM gene reported in Insecta. Furthermore, phylogenetic analysis showed that the evolutionary tree of PGAMs reflects the systematic relationship of species. [source]

CLONING AND EXPRESSION OF SPODOPTERA LITURA UBIQUITIN GENE

INSECT SCIENCE, Issue 1 2003
LI Zhao-fei
Abstract Ubiquitin (UBI) plays a very important role in regulated non-lysosomal ATP dependent protein degradation. In the present work, the coding sequence of Spodoptera litura UBI gene was isolated (GenBank Accession No. AF436066). The length of this ORF is 228bp, encoding a protein with Mr of 8.56 kD and isoelectric point of 6.56. Multiple sequence alignment indicated that S. litura UBI is very similar to the homologous proteins of other eukaryotic species and it has 84% identity with S. litura nucleopolyhedrovirus (SpltMNPV) UBI at amino acid level. RT-PCR analysis showed that S. litura UBI gene is ubiquitously expressed in larva tissues which are susceptible to SpltMNPV infection. By constructing E. coli expression vector, S. litura UBI was highly expressed and the recombinant protein was purified using Ni-NTA resin column, and currently further study on the function of S. litura UBI in SpltMNPV infection is underway. [source]

CHOLESTERYL ESTER TRANSFER PROTEIN GENE AND CORONARY HEART DISEASE MORTALITY: THE ROTTERDAM STUDY

JOURNAL OF AMERICAN GERIATRICS SOCIETY, Issue 9 2007
M. Carolina Pardo Silva MD
No abstract is available for this article. [source]

CLONING AND SEQUENCING OF THE ,-AMYLASE GENE FROM BACILLUS SUBTILIS US116 STRAIN ENCODING AN ENZYME CLOSELY IDENTICAL TO THAT FROM BACILLUS AMYLOLIQUEFACIENS BUT DISTINCT IN THERMAL STABILITY

JOURNAL OF FOOD BIOCHEMISTRY, Issue 2 2010
EZZEDINE BEN MESSAOUD
ABSTRACT The gene encoding for the ,-amylase AMYUS116 was cloned and sequenced. The amino acid sequence of AMYUS116 exhibited an almost perfect homology with the ,-amylase BACAAM, excluding the residues N205 and N217 of AMYUS116 that were changed to H205 and I217 into BACAAM. Three mutant derivatives from AMYUS116 (N205H, N217I and N205H/N217I) were created by site-directed mutagenesis and their physicochemical and kinetic properties were compared with those of the wild-type enzymes. Therefore, the undertaken amylases mainly generated maltohexaose from starch and had radically the same kinetic parameters and optimum pH and temperature. They, however, were significantly distinct in thermal stability; AMYUS116 was more thermosensible as its half-life time at 80C was 13 min, while those of BACAAM and the double mutant were likewise 38 min. The single-mutant amylases exhibited an identically intermediate thermal stability as their half-life times at 80C were roughly 22 min. PRACTICAL APPLICATIONS Of particular interest to the current search is that the different thermal stability between AMYUS116 and BACAAM can lead to novel findings pertaining to protein stability, which can bring about new strategies for protein engineering. Basically, the comparative study of closely related amylases and the protein engineering of already existing ones are certainly important because they offer opportunities to understand the structure,function relationships of these biocatalysts. [source]

ACUTE APOPTOTIC RESPONSE INDUCED BY THE COLON CARCINOGEN AOM IS DEPENDENT ON P53 GENE and NOT THE APC GENE

JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 2001

Background/objective, Apoptosis is disordered in tumourigensis, however, the importance of apoptosis in relation to DNA damage created at the time of initiation by genotoxic carcinogens, i.e. the acute apoptotic response to genotoxic carcinogens (AARGC), has hardly been explored. p53 and APC are tumor suppressor genes known to be altered frequently in colon cancer, however, it remains unclear whether AARGC is dependent on the function of p53 or APC. p53 ,/,, p53 ± and APCMin/+ mice provide an excellent model to test the biological significance of AARGC in colon in terms of its ability to delete genetically damaged cells that might progress to cancer. Thus, we have tested the hypothesis that p53 and APC play a critical role in AARGC, by studying AARGC in p53+/, , p53 ,/, mice and APCMin/+0. Methods, p53 knockout mice were produced by breeding male p53+/, with female C57BL/J mice or interbreeding p53+/, mice. APCMin/+ mice were produced by breeding male APCMin/+ mice with female C57BL/J mice. Mice geno-typing were confirmed by PCR. At 10,12 weeks age, 44 mice were given a single subcutaneous azoxymethane (AOM 10 mg/kg) injection to induce AARGC, and killed 6 h later (the time of the maximal response). There were eight p53,/, mice, 11 p53+/, mice, nine p53+/+mice, 12 APCMin/+ mice, and six APC+/+ mice. Three p53,/, mice, four p53+/, mice, seven p53+/+ mice, two APCMin/+, and six APC+/+ mice without AOM injection were used as controls. Apoptosis in colon was measured by classic morphological H & E criteria. Results, In p53+/+ mice, AOM induced a significant increase in apoptosis (4.70 ± 0.35, SEM, apoptotic cells per crypt column) in the distal colon, located almost exclusively in the proliferative compartment. In comparison to the pattern of apoptosis observed in the p53+/+ mice, the apoptotic response of p53,/, mice was almost nonexistent (0.12 ± 0.06) while in p53+/, mice it was significantly suppressed by approximately 50% (2.26 ± 0.28); P < 0.01. In contrast to the importance of p53 gene on AARGC, absence of the APC gene had no obvious effect on AARGC: APCMin/+ mice (5.07 ± 0.30) and APC+/+ (5.50 ± 0.33); P > 0.05. Conclusion, p53 function appears to be critically important for carcinogen-induced apoptosis in colon, while APC homeostasis appears not to be involved in this type of apoptosis. The loss of just one allele of p53, interferes with its function. Further studies are required to determine whether defective AARGC in p53 knockout mice puts them at increased risk of subsequent events in tumorigensis, and whether AARGC can be regulated by known protective agents. [source]

OLIGONUCLEOTIDE PRIMERS FOR THE DETECTION OF BIOLUMINESCENT DINOFLAGELLATES REVEAL NOVEL LUCIFERASE SEQUENCES AND INFORMATION ON THE MOLECULAR EVOLUTION OF THIS GENE,

JOURNAL OF PHYCOLOGY, Issue 2 2008
Andrea Baker
Bioluminescence is reported in members of 18 dinoflagellate genera. Species of dinoflagellates are known to have different bioluminescent signatures, making it difficult to assess the presence of particular species in the water column using optical tools, particularly when bioluminescent populations are in nonbloom conditions. A "universal" oligonucleotide primer set, along with species and genus-specific primers specific to the luciferase gene were developed for the detection of bioluminescent dinoflagellates. These primers amplified luciferase sequences from bioluminescent dinoflagellate cultures and from environmental samples containing bioluminescent dinoflagellate populations. Novel luciferase sequences were obtained for strains of Alexandrium cf. catenella (Whedon et Kof.) Balech and Alexandrium fundyense Balech, and also from a strain of Gonyaulax spinifera (Clap. et Whitting) Diesing, which produces bioluminescence undetectable to the naked eye. The phylogeny of partial luciferase sequences revealed five significant clades of the dinoflagellate luciferase gene, suggesting divergence among some species and providing clues on their molecular evolution. We propose that the primers developed in this study will allow further detection of low-light-emitting bioluminescent dinoflagellate species and will have applications as robust indicators of dinoflagellate bioluminescence in natural water samples. [source]

,-TUBULIN GENE OF PORPHYRA PURPUREA ( RHODOPHYTA),

JOURNAL OF PHYCOLOGY, Issue 5 2002
Ron M. MacKay
The life cycle of the marine red alga Porphyra purpurea (Roth) C. Agardh includes a shell-boring filamentous sporophyte and a leafy gametophyte. A single intronless gene for the microtubule protein ,-tubulin was discovered by molecular cloning of P. purpurea cDNA and genomic DNA. This gene, named TubB1, encodes a ,-tubulin with a divergent amino acid sequence, showing 74% identity with the conserved ,-tubulin of Chlamydomonas reinhardtii P. A. Dangeard. Southern hybridization analysis of nuclear DNA confirmed that P. purpurea has a single TubB1 gene. Transcripts (1.8 kb) of TubB1 are present in the sporophyte and gametophyte. Codon bias indicates strong expression of TubB1. The divergent nature of the TubB1 genes suggests that the absence of axonemal structures has allowed substantial genetic drift in red algal ,-tubulin genes. [source]

Characterization of a novel Toll/interleukin-1 receptor (TIR)-TIR gene differentially expressed in common bean (Phaseolus vulgaris cv. Othello) undergoing a defence response to the geminivirus Bean dwarf mosaic virus

MOLECULAR PLANT PATHOLOGY, Issue 2 2007
YOUNG-SU SEO
SUMMARY Common bean (Phaseolus vulgaris L.) cultivar (cv.) Othello develops a hypersensitive response-associated vascular resistance to infection by Bean dwarf mosaic virus (BDMV), a single-stranded DNA virus (genus Begomovirus, family Geminiviridae). A PCR-based cDNA subtraction approach was used to identify genes involved in this resistance response. Eighteen clones, potentially involved with BDMV resistance, were identified based upon being up-regulated in BDMV-infected tissues and/or having sequence similarity with known resistance-associated genes. Analysis of these clones revealed potential genes involved in pathogen defence, including pathogenesis-related protein genes and resistance gene analogues (RGAs). Further characterization of one RGA, F1-10, revealed that it encodes a predicted protein with a double Toll/interleukin-1 receptor (TIR) motif. Full-length (F1-10) and spliced (F1-10sp) forms of the RGA were strongly up-regulated in BDMV-infected cv. Othello hypocotyl tissues by 4 days post-inoculation, but not in equivalent mock-inoculated tissues. In agroinfiltration experiments, F1-10, but not F1-10sp, mediated resistance to BDMV in the susceptible common bean cv. Topcrop. By contrast, transgenic Nicotiana benthamiana lines expressing F1-10 or F1-10sp were not resistant to BDMV. Interestingly, when these transgenic lines were inoculated with the potyvirus Bean yellow mosaic virus, some F1-10 lines showed a more severe symptom phenotype compared with non-transgenic control plants. Based on these findings, F1-10 was named: Phaseolus vulgaris VIRUS response TIR-TIR GENE 1 (PvVTT1). [source]

PROMISCUITY AND THE RATE OF MOLECULAR EVOLUTION AT PRIMATE IMMUNITY GENES

EVOLUTION, Issue 8 2010
Gabriela Wlasiuk
Recently, a positive correlation between basal leukocyte counts and mating system across primates suggested that sexual promiscuity could be an important determinant of the evolution of the immune system. Motivated by this idea, we examined the patterns of molecular evolution of 15 immune defense genes in primates in relation to promiscuity and other variables expected to affect disease risk. We obtained maximum likelihood estimates of the rate of protein evolution for terminal branches of the primate phylogeny at these genes. Using phylogenetically independent contrasts, we found that immunity genes evolve faster in more promiscuous species, but only for a subset of genes that interact closely with pathogens. We also observed a significantly greater proportion of branches under positive selection in the more promiscuous species. Analyses of independent contrasts also showed a positive effect of group size. However, this effect was not restricted to genes that interact closely with pathogens, and no differences were observed in the proportion of branches under positive selection in species with small and large groups. Together, these results suggest that mating system has influenced the evolution of some immunity genes in primates, possibly due to increased risk of acquiring sexually transmitted diseases in species with higher levels of promiscuity. [source]

GENES WITH SOCIAL EFFECTS ARE EXPECTED TO HARBOR MORE SEQUENCE VARIATION WITHIN AND BETWEEN SPECIES

EVOLUTION, Issue 7 2009
Timothy A. Linksvayer
The equilibrium sequence diversity of genes within a population and the rate of sequence divergence between populations or species depends on a variety of factors, including expression pattern, mutation rate, nature of selection, random drift, and mating system. Here, we extend population genetic theory developed for maternal-effect genes to predict the equilibrium polymorphism within species and sequence divergence among species for genes with social effects on fitness. We show how the fitness effects of genes, mating system, and genetic system affect predicted gene polymorphism. We find that, because genes with indirect social effects on fitness effectively experience weaker selection, they are expected to harbor higher levels of polymorphism relative to genes with direct fitness effects. The relative increase in polymorphism is proportional to the inverse of the genetic relatedness between individuals expressing the gene and their social partners that experience the fitness effects of the gene. We find a similar pattern of more rapid divergence between populations or species for genes with indirect social effects relative to genes with direct effects. We focus our discussion on the social insects, organisms with diverse indirect genetic effects, mating and genetic systems, and we suggest specific examples for testing our predictions with emerging sociogenomic tools. [source]

ADAPTIVE POPULATION DIFFERENTIATION IN PHENOLOGY ACROSS A LATITUDINAL GRADIENT IN EUROPEAN ASPEN (POPULUS TREMULA, L.): A COMPARISON OF NEUTRAL MARKERS, CANDIDATE GENES AND PHENOTYPIC TRAITS

EVOLUTION, Issue 12 2007
David Hall
A correct timing of growth cessation and dormancy induction represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees (Rehfeldt et al. 1999; Horvath et al. 2003; Howe et al. 2003). We have studied the deciduous tree European Aspen (Populus tremula) across a latitudinal gradient and compared genetic differentiation in phenology traits with molecular markers. Trees from 12 different areas covering 10 latitudinal degrees were cloned and planted in two common gardens. Several phenology traits showed strong genetic differentiation and clinal variation across the latitudinal gradient, with QST values generally exceeding 0.5. This is in stark contrast to genetic differentiation at several classes of genetic markers (18 neutral SSRs, 7 SSRs located close to phenology candidate genes and 50 SNPs from five phenology candidate genes) that all showed FST values around 0.015. We thus find strong evidence for adaptive divergence in phenology traits across the latitudinal gradient. However, the strong population structure seen at the quantitative traits is not reflected in underlying candidate genes. This result fit theoretical expectations that suggest that genetic differentiation at candidate loci is better described by FST at neutral loci rather than by QST at the quantitative traits themselves. [source]

DO FEMALE SPIDERS SELECT HEAVIER MALES FOR THE GENES FOR BEHAVIORAL AGGRESSIVENESS THEY OFFER THEIR OFFSPRING?

EVOLUTION, Issue 6 2003
S. E. RIECHERT
Abstract., We explore the hypothesis that females choose to mate with heavier males for the genes for behavioral aggressiveness they offer their offspring in the desert spider, Agelenopsis aperta. Behavioral aggressiveness is important to competition for limited resources in the field and is thus correlated with the mass spiders achieve. We established four crosses based on the body mass relationships of parents subjected to selection in their natural environment (female mass/male mass: HI/HI, HI/LO, LO/HI, and LO/LO) and reared the F1 offspring in a noncompetitive laboratory environment. Offspring size and mass at maturity were measured, life history parameters recorded, and behavioral aggressiveness scored in a series of tests. Significant familial effects were detected in all of these measures, but pertinent cross effects were observed only in the assays measuring behavioral aggressiveness. The results were summarized in terms of the fitness costs to HI females of mating with LO males (fewer female offspring of the more aggressive phenotypes) and the benefits to LO females of mating with HI males (fewer fearful offspring of both sexes). [source]

ACCUMULATING POSTZYGOTIC ISOLATION GENES IN PARAPATRY: A NEW TWIST ON CHROMOSOMAL SPECIATION

EVOLUTION, Issue 3 2003
Arcadi Navarro
Abstract Chromosomal rearrangements can promote reproductive isolation by reducing recombination along a large section of the genome. We model the effects of the genetic barrier to gene flow caused by a chromosomal rearrangement on the rate of accumulation of postzygotic isolation genes in parapatry. We find that, if reproductive isolation is produced by the accumulation in parapatry of sets of alleles compatible within but incompatible across species, chromosomal rearrangements are far more likely to favor it than classical genetic barriers without chromosomal changes. New evidence of the role of chromosomal rearrangements in parapatric speciation suggests that postzygotic isolation is often due to the accumulation of such incompatibilities. The model makes testable qualitative predictions about the genetic signature of speciation. [source]

STABILITY AND EVOLUTION OF OVERLAPPING GENES

EVOLUTION, Issue 3 2000
David C. Krakauer
Abstract., When the same sequence of nucleotides codes for regions of more than one functional polypeptide, this sequence contains overlapping genes. Overlap is most common in rapidly evolving genomes with high mutation rates such as viruses, bacteria, and mitochondria. Overlap is thought to be important as: (1) a means of compressing a maximum amount of information into short sequences of structural genes; and (2) as a mechanism for regulating gene expression through translational coupling of functionally related polypeptides. The stability of overlapping codes is examined in relation to the information cost of overlap and the mutation rate of the genome. The degree of overlap in a given population will tend to become monomorphic. Evolution toward partial overlap of genes is shown to depend on a convex cost function of overlap. Overlap does not evolve when expression of overlapping genes is mutually exclusive and produced by rare mutations to the wild-type genome. Assuming overlap increases coupling between functionally related genes, the conditions favoring overlap are explored in relation to the kinetics of gene activation and decay. Coupling is most effective for genes in which the gene overlapping at its 5'end (leading gene) decays rapidly, while the gene overlapping at the 3'end (induced gene) decays slowly. If gene expression can feedback on itself (autocatalysis), then high rates of activation favor overlap. [source]

COMPLETE NUCLEOTIDE SEQUENCE OF SPHEROIDIN GENES OF CALLIPTAMUS IT ALICUS ENTOMOPOXVIRUS(CIEPV) AND GOMPHOCERUS SIBIRICUS ENTOMOPOXVIRUS(GSEPV)

INSECT SCIENCE, Issue 3 2004
Yong-dan Li
Abstract, The spheroidin genes of Calliptamus italicus entomopoxvirus (CiEPV) and Gomphocerus sibiricus entomopoxvirus (GsEPV) were obtained by PCR, and the fragments were cloned, se-quenced and analyzed. The CiEPV and GsEPV spheroidin genes respectively harbored ORFs of 2 922 bps and 2 967 bps that were capable of coding polypeptides of 109.2 and 111.1 kDa. Computer analysis indicated that CiEPV and GsEPV spheroidins shared less than 20% amino acid identities with lepidopteran AmEPV and coleopteran AcEPV spheroidins, but more than 80% amino acid identities with orthopteran OaEPV, MsEPV and AaEPV spheroidins. The CiEPV and GsEPV spheroidins respectively contained 19 and 21 cysteine residues that were particularly abundant at the C-termini, as is the case with those of the other orthopteran EPV spheroidins. The numbers and locations of the cysteine residues of the spheroidins were most similar to those of the spheroidins of EPVs that are virulent on the same insect orders. The promoter regions of the two spheroidin genes were highly conserved (99%) among the orthopteran EPVs and also contained the typical very A+T rich and TAAATG signal mediating transcription of poxvirus late genes. We also sequenced an incomplete ORF downstream of the pheroidin gene of CiEPV and GsEPV. The ORF was in the opposite direction to the spheroidin gene and was homologous to MSV072 putative protein of MsEPV. [source]

ESTABLISHMENT OF MINIMAL AND MAXIMAL TRANSCRIPT LEVELS FOR NITRATE TRANSPORTER GENES FOR DETECTING NITROGEN DEFICIENCY IN THE MARINE PHYTOPLANKTON ISOCHRYSIS GALBANA (PRYMNESIOPHYCEAE) AND THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE),

JOURNAL OF PHYCOLOGY, Issue 4 2009
Lee-Kuo Kang
Nitrate transporter genes (Nrt2) encode high-affinity nitrate transporters in marine phytoplankton, and their transcript levels are potential markers of nitrogen deficiency in eukaryotic phytoplankton. For the proper interpretation of measured Nrt2 transcript abundances, a relative expression assay was proposed and tested in Isochrysis galbana Parke (Prymnesiophyceae) and Thalassiosira pseudonana (Hust.) Hasle et Heimdal (Bacillariophyceae). The minimal transcript levels of Nrt2 genes were achieved by the addition of 100 ,M ammonium, which led to a rapid decline in Nrt2 transcripts in 10,30 min. Experiments using a concentration series revealed that the effective dosage of ammonium to create a minimal transcript level of ,1 ,mol · mol,1 18S rRNA was ,25 ,M in both species. On the other hand, the addition of l -methionine sulfoximine (MSX), an inhibitor of glutamine synthetase, enhanced the Nrt2 transcript level in I. galbana but did not affect that in T. pseudonana. Nitrogen deprivation was used as an alternative means to create maximal Nrt2 transcript levels. By transferring cells into N-free medium for 24 h, Nrt2 transcript levels increased to ,90 ,mol · mol,1 18S rRNA in I. galbana, and to ,800 ,mol · mol,1 18S rRNA in T. pseudonana. The degree of nitrogen deficiency thus can be determined by comparing original Nrt2 transcript levels with the minimal and maximal levels. [source]

SEQUENCE ANALYSIS AND TRANSCRIPTIONAL REGULATION OF IRON ACQUISITION GENES IN TWO MARINE DIATOMS,

JOURNAL OF PHYCOLOGY, Issue 4 2007
Adam B. Kustka
The centric diatom Thalassiosira pseudonana Hasle et Heimdal and the pennate diatom Phaeodactylum tricornutum Bohlin possess genes with translated sequences homologous to high-affinity ferric reductases present in model organisms. Thalassiosira pseudonana also possesses putative genes for membrane-bound ferroxidase (TpFET3) and two highly similar iron (Fe) permeases (TpFTR1 and TpFTR2), as well as a divalent metal (M2+) transporter belonging to the NRAMP superfamily (TpNRAMP). In baker's yeast, the ferroxidase,permease complex transports Fe(II) produced by reductases. We investigated transcript abundances of these genes as a function of Fe quota (QFe). Ferric reductase transcripts are abundant in both species (15%,60% of actin) under low QFe and are down-regulated by 5- to 35-fold at high QFe, suggesting Fe(III) reduction is a common, inducible strategy for Fe acquisition in marine diatoms. Permease transcript abundance was regulated by Fe status in T. pseudonana, but we did not detect significant differences in expression of the copper (Cu)-containing ferroxidase. TpNRAMP showed the most dramatic regulation by QFe, suggesting a role in cellular Fe transport in either cell-surface uptake or vacuolar mobilization. We could not identify ferroxidase or permease homologues in the P. tricornutum genome. The up-regulation of genes in T. pseudonana that appear to be missing altogether from P. tricornutum as well as the finding that P. tricornutum seems to have an efficient system to acquire Fe,, suggest that diverse (and uncharacterized) Fe-uptake systems may be at play within diatom assemblages. Different uptake systems among diatoms may provide a mechanistic basis for niche differentiation with respect to Fe availability in the ocean. [source]

EVIDENCE FOR LATERAL TRANSFER OF AN IE INTRON BETWEEN FUNGAL AND RED ALGAL SMALL SUBUNIT RRNA GENES,

JOURNAL OF PHYCOLOGY, Issue 2 2005
Kirsten M. Müller
A previous study of the North American biogeography of the red algal genus Hildenbrandia noted the presence of group I introns in the nuclear small subunit (SSU) rRNA gene of the marine species H. rubra (Sommerf.) Menegh. Group IC1 introns have been previously reported at positions 516 and 1506 in the nuclear SSU RNA genes in the Bangiales and Hildenbrandiales. However, the presence of an unclassified intron at position 989 in a collection of H. rubra from British Columbia was noted. This intron is a member of the IE subclass and is the first report of this intron type in the red algae. Phylogenetic analyses of the intron sequences revealed a close relationship between this IE intron inserted at position 989 and similar fungal IE introns in positions 989 and 1199. The 989 IE introns formed a moderately to well-supported clade, whereas the 1199 IE introns are weakly supported. Unique structural helices in the P13 domain of the 989 and 1199 IE introns also point to a close relationship between these two clades and provide further evidence for the value of secondary structural characteristics in identifying homologous introns in evolutionarily divergent organisms. The absence of the 989 IE intron in all other red algal nuclear SSU rRNA genes suggests that it is unlikely that this intron was vertically inherited from the common ancestor of the red algal and fungal lineages but rather is the result of lateral transfer between fungal and red algal nuclear SSU rRNA genes. [source]

STRUCTURAL FEATURES OF NUCLEAR GENES IN THE CENTRIC DIATOM THALASSIOSIRA WEISSFLOGII (BACILLARIOPHYCEAE)

JOURNAL OF PHYCOLOGY, Issue 5 2000
E. Virginia Armbrust
Thalassiosira weissflogii (Grun.) Fryxell et Hasle is one of the more commonly studied centric diatoms, and yet molecular studies of this organism are still in their infancy. The ability to identify open reading frames and thus distinguish between introns and exons, coding and noncoding sequence is essential to move from nuclear DNA sequences to predicted amino acid sequences. To facilitate the identification of open reading frames in T. weissflogii, two newly identified nuclear genes encoding ,-tubulin and t -complex polypeptide (TCP)-,, along with six previously published nuclear DNA sequences, were examined for general structural features. The coding region of the nuclear open reading frames had a G + C content of about 49% and could readily be distinguished from noncoding sequence due to a significant difference in G + C content. The introns were uniformly small, about 100 base pairs in size. Furthermore, the 5, and 3, splice sites of introns displayed the canonical GT/AG sequence, further facilitating recognition of noncoding regions. Six of the nuclear open reading frames displayed relatively little bias in the use of synonymous codons, as exemplified by the cDNAs encoding ,-tubulin and TCP-,. Two open reading frames displayed strong bias in the use of particular codons (although the codons used were different), as exemplified by the cDNA encoding fucoxanthin chlorophyll a/c binding protein. Knowledge of codon bias should facilitate, for example, design of degenerate PCR primers and potential heterologous reporter gene constructs. [source]

GENES, CALCIUM AND MODIFYING FACTORS IN HYPERTROPHIC CARDIOMYOPATHY

CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 1-2 2006
Tatiana Tsoutsman
SUMMARY 1Familial hypertrophic cardiomyopathy (FHC) is a primary disorder of the myocardium characterized by remarkable diversity in clinical presentations, ranging from no symptoms to severe heart failure and sudden cardiac death. 2Over the past 15 years, at least 11 genes have been identified, defects of which cause FHC. Most of these genes encode proteins that comprise the basic contractile unit of the heart (i.e. the sarcomere). 3Genetic studies are now beginning to have a major impact on the diagnosis in FHC, as well as in guiding treatment and preventative strategies. Although much is known about which genes cause disease, relatively little is known about the molecular steps leading from the gene defect to the clinical phenotype and what factors modify the expression of the mutant genes. 4Concurrent studies in cell culture and animal models of FHC are now beginning to shed light on the signalling pathways involved in FHC and the role of both environmental and genetic modifying factors. Calcium dysregulation appears to be important in the pathogenesis of FHC. 5Understanding these basic molecular mechanisms will ultimately improve our knowledge of the basic biology of heart muscle function and will therefore provide new avenues for diagnosis and treatment not only for FHC, but also for a range of human cardiovascular diseases. [source]

Gene targeted ablation of high molecular weight fibroblast growth factor-2

DEVELOPMENTAL DYNAMICS, Issue 2 2009
Mohamad Azhar
Abstract Fibroblast growth factor-2 (FGF2) is produced as high molecular weight isoforms (HMW) and a low molecular weight isoform (LMW) by means of alternative usage of translation start sites in a single Fgf2 mRNA. Although the physiological function of FGF2 and FGF2 LMW has been investigated in myocardial capillarogenesis during normal cardiac growth, the role of FGF2 HMW has not been determined. Here, we report the generation of FGF2 HMW-deficient mice in which FGF2 HMW isoforms are ablated by the Tag-and-Exchange gene targeting technique. These mice are normal and fertile with normal fecundity, and have a normal life span. Histological, immunohistochemical, and morphometric analyses indicate normal myocardial architecture, blood vessel, and cardiac capillary density in young adult FGF2 HMW-deficient mice. These mice along with the FGF2- and FGF2 LMW-deficient mice that we have generated previously will be very useful for elucidating the differential functions of FGF2 isoforms in pathophysiology of cardiovascular diseases. Developmental Dynamics 238:351,357, 2009. © 2008 Wiley-Liss, Inc. [source]

An SNF2 factor involved in mammalian development and cellular proliferation

DEVELOPMENTAL DYNAMICS, Issue 1 2001
Eric H. Raabe
Abstract Members of the SNF2 (Sucrose Non-Fermenter) family of chromatin-remodeling proteins function in processes ranging from DNA repair to transcription to methylation. Using differential display, we recently identified a novel member of the SNF2 family that is highly expressed at the mRNA level in proliferating cells and is down-regulated during apoptosis. We have named this gene PASG (Proliferation-Associated SNF2-like Gene). Northern blot analysis of adult mouse tissues shows PASG to be highly expressed in proliferating organs such as thymus, bone marrow, and testis and absent from nonproliferative tissues such as brain and heart. In situ hybridization analysis of mouse embryos shows that PASG is differentially expressed during development, with highest expression in developing face, limbs, skeletal muscle, heart, and tail. In vitro, PASG expression correlates with a shift from a quiescent to a proliferative state. Mice null for PASG (also known as LSH or Hells) are reported to die perinatally, although the mechanism for lethality is unclear (Geiman and Muegge, 2000). To test the hypothesis that PASG functions in cell proliferation, we compared 5-bromodeoxyuridine (BrdU) incorporation in C33A cells transiently transfected with PASG versus empty vector and found that PASG transfected cells showed a significant decrease in the amount of BrdU incorporation. These findings suggest that PASG plays a role in cell proliferation and may function in the development of multiple cell lineages during murine embryogenesis. © 2001 Wiley-Liss, Inc. [source]

Gene,gene interactions between HNF4A and KCNJ11 in predicting Type 2 diabetes in women

DIABETIC MEDICINE, Issue 11 2007
L. Qi
Abstract Aims Recent studies indicate transcription factor hepatocyte nuclear factor 4, (HNF-4,, HNF4A) modulates the transcription of the pancreatic B-cell ATP-sensitive K+ (KATP) channel subunit Kir6.2 gene (KCNJ11). Both HNF4A and KCNJ11 have previously been associated with diabetes risk but little is known whether the variations in these genes interact with each other. Methods We conducted a prospective, nested case,control study of 714 incident cases of Type 2 diabetes and 1120 control subjects from the Nurses' Health Study. Results KCNJ11 E23K was significantly associated with an increased diabetes risk (odds ratio 1.26, 95% CI 1.03,1.53) while HNF4A P2 promoter polymorphisms were associated with a moderately increased risk at borderline significance. By using a logistic regression model, we found significant interactions between HNF4A rs2144908, rs4810424 and rs1884613 and KCNJ11 E23K (P for interaction = 0.017, 0.012 and 0.004, respectively). Carrying the minor alleles of the three HNF4A polymorphisms was associated with significantly greater diabetes risk in women carrying the KCNJ11 allele 23K, but not in those who did not carry this allele. Analyses using the multifactor dimensionality reduction (MDR) method confirmed the gene,gene interaction. We identified that the best interaction model included HNF4A rs2144908 and KCNJ11 E23K. Such a two-locus model showed the maximum cross-validation consistency of 10 out of 10 and a significant prediction accuracy of 54.2% (P = 0.01) on the basis of 1000-fold permutation testing. Conclusions Our data indicate that HNF4A P2 promoter polymorphisms may interact with KCNJ11 E23K in predicting Type 2 diabetes in women. [source]

An Electrochemical DNA Biosensor for the Detection of the Apa I Polymorphism in the Vitamin D Receptor Gene Using Meldola's Blue as a Hybridization Indicator

ELECTROANALYSIS, Issue 5 2010
Nilay Aladag
Abstract Electrochemical detection of nucleic acid base mismatches related to Apa I single nucleotide polymorphism (SNP) in the vitamin D receptor gene was performed successfully using 7-dimethyl-amino-1,2-benzophenoxazinium salt (Meldola's blue, MDB) with 10.9,pmol/100,,L of detection limit. MDB reduction signals obtained from probe, mismatch(probe-SNP containing target) and hybrid(probe-target) modified pencil graphite electrode(PGE) increased respectively. The sensor was able to clearly distinguish perfect match from mismatch DNA in a 30,min. detection time. Several factors affecting on the hybridization and indicator response are studied to maximize sensitivity and selectivity. The advantages of the biosensor are discussed in comparison with previous electrochemical assays for DNA hybridization. [source]

Gene,environment interactions and alcohol use and dependence: current status and future challenges

ADDICTION, Issue 6 2009
Carmen S. Van Der Zwaluw
ABSTRACT Aim To discuss the current status of gene,environment interaction research with regard to alcohol use and dependence. Further, we highlight the difficulties concerning gene,environment studies. Methods Overview of the current evidence for gene,environment interactions in alcohol outcomes, and of the associated challenges in gene,environment studies. Results Attention to the causative roles of gene,environment interactions in alcohol use and dependence is increasing. Studies with twin designs are beginning to examine gene-shared environment effects, and animal studies have investigated gene,environment interaction effects on alcohol intake in primates. Thirteen studies incorporated gene,environment interactions in examining alcohol use or dependence in humans. These studies held a variety of candidate genes and environmental risk factors and their heterogeneity made it impossible to draw firm general conclusions. Conclusions Challenges for future gene,environment studies are abundant, and consist of, for example, the development of clear theoretical assumptions about neurobiological mechanisms and the recruitment of large longitudinal samples that already start in childhood. Replication is essential to prevent an overload of false-positive results. Despite the difficulties, it is crucial to include gene,environment interactions in future studies in order to unravel the aetiological factors of human alcohol outcomes. [source]

Cloning and Characterization of the cDNA Encoding the Masquerade-like Serine Proteinase Homologue Gene of the Silkworm, Bombyx mori

ENTOMOLOGICAL RESEARCH, Issue 3 2002
Doo-Sang PARK
ABSTRACT From Bombyx mori larvae, RT-PCR and cDNA library screening isolated masquerade-like serine proteinase homologue cDNA gene, proposed to be related to insect immunity and its characteristics were examined. The isolated gene is composed of 1.3 kb of nucleotide and 420 amino acid residues were encoded. According to the results of database search, the isolated gene showed high sequence homology with Holotrichia and Tenebrio's 45 kDa protein, Drosophila CG5390 gene. Moreover, it is composed of regulatory domain and catalytic domain, which is characteristic of serine proteinase that can be found in the insect immune reaction and embryonic development processes. Enzyme activation site by proteolytic cleavage and the sequence of three amino acids participate in the catalytic triad of enzyme and 14 cystein residues used in disulfide bridges are well conserved with the compared genes. The mRNA expression was increased following E. coli injection and constitutive expression was also observed before injection by Northern blot analysis. [source]

Gene and protein expression in experimental status epilepticus

EPILEPSIA, Issue 2007
Katarzyna Lukasiuk
First page of article [source]

Loss of the Potassium Channel ,-Subunit Gene, KCNAB2, Is Associated with Epilepsy in Patients with 1p36 Deletion Syndrome

EPILEPSIA, Issue 9 2001
Heidi A. Heilstedt
Summary: ,Purpose: Clinical features associated with chromosome 1p36 deletion include characteristic craniofacial abnormalities, mental retardation, and epilepsy. The presence and severity of specific phenotypic features are likely to be correlated with loss of a distinct complement of genes in each patient. We hypothesize that hemizygous deletion of one, or a few, critical gene(s) controlling neuronal excitability is associated with the epilepsy phenotype. Because ion channels are important determinants of seizure susceptibility and the voltage-gated K+ channel ,-subunit gene, KCNAB2, has been localized to 1p36, we propose that deletion of this gene may be associated with the epilepsy phenotype. Methods: Twenty-four patients were evaluated by fluorescence in situ hybridization with a probe containing KCNAB2. Clinical details were obtained by neurologic examination and EEG. Results: Nine patients are deleted for the KCNAB2 locus, and eight (89%) of these have epilepsy or epileptiform activity on EEG. The majority of patients have a severe seizure phenotype, including infantile spasms. In contrast, of those not deleted for KCNAB2, only 27% have chronic seizures, and none had infantile spasms. Conclusions: Lack of the , subunit would be predicted to reduce K+ channel,mediated membrane repolarization and increase neuronal excitability, suggesting a possible relation between loss of this gene and the development of seizures. Because some patients with seizures were not deleted for KCNAB2, there may be additional genes within 1p36 that contribute to epilepsy in this syndrome. Hemizygosity of this gene in a majority of monosomy 1p36 syndrome patients with epilepsy suggests that haploinsufficiency for KCNAB2 is a significant risk factor for epilepsy. [source]