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Sequence Differences (sequence + difference)

Distribution by Scientific Domains

Life Sciences	75%
Medical Sciences	10%
Chemistry	10%

Distribution within Life Sciences

Evolution	13%

Selected Abstracts

Ossification sequence of the avian order anseriformes, with comparison to other precocial birds

JOURNAL OF MORPHOLOGY, Issue 9 2008
Erin E. Maxwell
Abstract Ossification sequences are poorly known for most amniotes, and yet they represent an important source of morphogenetic, phylogenetic, and life history information. Here, the author describes the ossification sequences of three ducks, the Common Eider Somateria mollissima dresseri, the Pekin Duck Anas platyrhynchos, and the Muscovy Duck Cairina moschata. Sequence differences exist both within and among these species, but are generally minor. The Common Eider has the most ossified skeleton prior to hatching, contrary to what is expected in a subarctic migrant species. This may be attributed to a tradeoff between growth rate and locomotory performance. Growth rate is higher in hatchlings with more cartilaginous skeletons, but this may compromise locomotion. No major ossification sequence differences were observed in the craniofacial skeleton when compared with Galliformes, which suggests that the influence of adult morphology on ossification sequence might be relatively minor in many taxa. Galliformes and Anseriformes, while both highly ossified at hatching, differ in the location of their late-stage ossification centers. In Anseriformes, these are most often located in the appendicular skeleton, whereas in Galliformes they are in the thoracic region and form the ventilatory apparatus. J. Morphol., 2008. © 2008 Wiley-Liss, Inc. [source]

Use of sequence-based typing and multiplex PCR to identify clonal lineages of outbreak strains of Acinetobacter baumannii

CLINICAL MICROBIOLOGY AND INFECTION, Issue 8 2007
J. F. Turton
Abstract Representatives (n = 31) of outbreak strains of Acinetobacter baumannii from five countries fell into three clear groups, designated Groups 1,3, based on their ompA (outer-membrane protein A), csuE (part of a pilus assembly system required for biofilm formation) and blaOXA-51-like (the intrinsic carbapenemase gene in A. baumannii) gene sequences. With the exception of the closely related alleles within the Group 1 clonal complex, alleles at each locus were highly distinct from each other, with a minimum of 14 nucleotide differences between any two alleles. Isolates within a group shared the same combination of alleles at the three loci, providing compelling evidence that the outbreak strains investigated belonged to three clonal lineages. These corresponded to the previously identified European clones I,III. Sequence differences among the alleles were used to design multiplex PCRs to rapidly assign isolates belonging to particular genotypes to sequence groups. In the UK, genotypes belonging to the Group 1 clonal complex have been particularly successful, accounting for the vast majority of isolates referred from hospitals experiencing problems with Acinetobacter. [source]

Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification

JOURNAL OF FISH BIOLOGY, Issue 6 2001
H. Takeyama
Restriction analysis detected two types of bigeye tuna (, and ,); the , type was in the majority in the Atlantic but nearly absent in the Indo-Pacific. The , type shared a larger number of restriction sites with other species than the conspecific , type, but bigeye-specific nucleotide substitutions with a novel diagnostic restriction profile were found. Although the nucleotide sequence difference between Atlantic and Pacific sub-species of the northern bluefin tuna was nearly the largest among species, individuals possessing the Atlantic type of mtDNA were found at very low frequency in the Pacific and vice versa. Previous RFLP markers were found to be diagnostic for the other five species (albacore, blackfin, longtail, southern bluefin and yellowfin tunas). Genetic information is provided to discriminate all Thunnus species regardless of their origin and to identify the ocean of capture in the northern bluefin and bigeye tunas. [source]

BIODIVERSITY OF CORALLINE ALGAE IN THE NORTHEASTERN ATLANTIC INCLUDING CORALLINA CAESPITOSA SP.

JOURNAL OF PHYCOLOGY, Issue 1 2009
NOV. (CORALLINOIDEAE, RHODOPHYTA)
The Corallinoideae (Corallinaceae) is represented in the northeastern Atlantic by Corallina officinalis L.; Corallina elongata J. Ellis et Sol.; Haliptilon squamatum (L.) H. W. Johans., L. M. Irvine et A. M. Webster; and Jania rubens (L.) J. V. Lamour. The delimitation of these geniculate coralline red algae is based primarily on morphological characters. Molecular analysis based on cox1 and 18S rRNA gene phylogenies supported the division of the Corallinoideae into the tribes Janieae and Corallineae. Within the Janieae, a sequence difference of 46,48 bp (8.6%,8.9%) between specimens of H. squamatum and J. rubens in the cox1 phylogeny leads us to conclude that they are congeneric. J. rubens var. rubens and J. rubens var. corniculata (L.) Yendo clustered together in both phylogenies, suggesting that for those genes, there was no genetic basis for the morphological variation. Within the Corallineae, it appears that in some regions, the name C. elongata has been misapplied. C. officinalis samples formed two clusters that differed by 45,54 bp (8.4%,10.0%), indicating species-level divergence, and morphological differences were sufficient to define two species. One of these clusters was consistent with the morphology of the type specimen of C. officinalis (LINN 1293.9). The other species cluster is therefore described here as Corallina caespitosa sp. nov. This study has demonstrated that there is a clear need for a revision of the genus Corallina to determine the extent of "pseudocryptic" diversity in this group of red algae. [source]

Genetic variability of Tomato spotted wilt virus in Australia and validation of real time RT-PCR for its detection in single and bulked leaf samples

ANNALS OF APPLIED BIOLOGY, Issue 4 2005
R G DIETZGEN
Summary The potential for large-scale use of a sensitive real time reverse transcription polymerase chain reaction (RT-PCR) assay was evaluated for the detection of Tomato spotted wilt virus (TSWV) in single and bulked leaf samples by comparing its sensitivity with that of DAS-ELISA. Using total RNA extracted with RNeasy® or leaf soak methods, real time RT-PCR detected TSWV in all infected samples collected from 16 horticultural crop species (including flowers, herbs and vegetables), two arable crop species, and four weed species by both assays. In samples in which DAS-ELISA had previously detected TSWV, real time RT-PCR was effective at detecting it in leaf tissues of all 22 plant species tested at a wide range of concentrations. Bulk samples required more robust and extensive extraction methods with real time RT-PCR, but it generally detected one infected sample in 1000 uninfected ones. By contrast, ELISA was less sensitive when used to test bulked samples, once detecting up to 1 infected in 800 samples with pepper but never detecting more than 1 infected in 200 samples in tomato and lettuce. It was also less reliable than real time RT-PCR when used to test samples from parts of the leaf where the virus concentration was low. The genetic variability among Australian isolates of TSWV was small. Direct sequencing of a 587 bp region of the nucleoprotein gene (S RNA) of 29 isolates from diverse crops and geographical locations yielded a maximum of only 4.3% nucleotide sequence difference. Phylogenetic analysis revealed no obvious groupings of isolates according to geographic origin or host species. TSWV isolates, that break TSWV resistance genes in tomato or pepper did not differ significantly in the N gene region studied, indicating that a different region of the virus genome is responsible for this trait. [source]

Genetic Identification of Pelagic Shark Body Parts for Conservation and Trade Monitoring

CONSERVATION BIOLOGY, Issue 4 2002
Mahmood Shivji
Difficulties with the identification of many commonly fished sharks and their body parts has resulted in a global dearth of catch and trade information, making reliable assessment of exploitation effects and conservation needs for individual species nearly impossible. We developed and tested a highly streamlined molecular genetic approach based on species-specific, polymerase-chain-reaction primers in an eight-primer multiplex format to discriminate simultaneously between body parts from six shark species common in worldwide pelagic fisheries. The species-specific primers are based on DNA sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus. The primers and multiplex format accurately and sensitively distinguished samples from each of three lamnid ( Isurus oxyrinchus, Isurus paucus, and Lamna nasus) and three carcharhinid ( Prionace glauca, Carcharhinus obscurus, and Carcharhinus falciformis) species from all but one other shark species encountered in the North Atlantic fishery. Furthermore, the three lamnid primers were robust enough in their discriminatory power to be useful for species diagnosis on a global scale. Preliminary testing of dried fins from Asian and Mediterranean commercial markets suggests that our genetic approach will be useful for determining the species of origin of detached fins, thus allowing the monitoring of trade in shark fins for conservation assessment. Our approach will also facilitate detection of products from protected and other at-risk shark species and may prove useful as a model for development of the high-throughput, genetic, species-diagnosis methods typically required in conservation and management contexts. Resumen: La conservación y manejo de tiburones fundamentado a nivel de especie es una necesidad imperativa debido a la creciente demanda de aletas de tiburón y el reconocimiento de que las especies individuales de tiburones responden de manera distinta a la explotación. Las dificultades para la identificación de muchos tiburones capturados comúnmente, así como de partes de su cuerpo, han resultado en una escasez global de información sobre capturas y comercialización, haciendo casi imposible el poder realizar evaluaciones de los efectos de la explotación y de las necesidades de conservación. Desarrollamos y evaluamos un método altamente estilizado de genética molecular basado en detonadores de la reacción en cadena de la polimerasa, especie-específicos, en un formato múltiple de ocho detonadores para discriminar simultáneamente entre las partes del cuerpo de seis especies de tiburones provenientes de pesquerías pelágicas mundiales comunes. Los detonadores especie-específicos están basados en diferencias en las secuencias de ADN entre especies del locus espaciador 2 nuclear, ribosomal, transcrito. Los detonadores y el formato múltiple distinguen muestras con precisión y sensitividad de cada uno de los tres lámnidos ( Isurus oxyrinchus, Isurus paucus y Lamna nasus) y tres especies de carcarínidos ( Prionace glauca, Carcharhinus obscurus y Carcharhinus falciformis) especies todas encontradas en las pesquerías de Norteamérica, excepto una. Mas aún, los detonadores de los tres lamnidos fueron lo suficientemente robustos en su poder discriminante como para ser usados para el diagnóstico de especies a escala mundial. Las pruebas preliminares de aletas secas de los mercados comerciales de Asia y el Mediterráneo sugieren que nuestro método genético puede ser útil para determinar la especie de origen de las aletas separadas, permitiendo así usar el monitoreo de las aletas de tiburón para evaluaciones de conservación. Nuestro método también podría facilitar la detección de productos provenientes de especies protegidas o en riesgo y podría resultar útil como un modelo para el desarrollo de métodos genéticos de alto rendimiento para el diagnóstico de especies, métodos típicamente requeridos en los contextos de conservación y manejo. [source]

Electrophoretic analysis of sequence variability in three mitochondrial DNA regions for ascaridoid parasites of human and animal health significance

ELECTROPHORESIS, Issue 13 2008
Ming-Wei Li
Abstract Sequence variability in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1), NADH dehydrogenase subunits 1 and 4 (nad1 and nad4), among and within Toxocara canis, T. cati, T. malaysiensis, T. vitulorum and Toxascaris leonina from different geographical origins was examined by a mutation-scanning approach. A portion of the cox1 gene (pcox1), a portion of the nad1 and nad4 genes (pnad1 and pnad4) were amplified separately from individual ascaridoid nematodes by polymerase chain reaction and the amplicons analyzed by single-strand conformation polymorphism (SSCP). Representative samples displaying sequence variation in SSCP profiles were subjected to sequencing in order to define genetic markers for their specific identification and differentiation. While the intra-specific sequence variations within each of the five ascaridoid species were 0.2,3.7% for pcox1, 0,2.8% for pnad1 and 0,2.3% for pnad4, the inter-specific sequence differences were significantly higher, being 7.9,12.9% for pcox1, 10.7,21.1% for pnad1 and 12.9,21.7% for pnad4, respectively. Phylogenetic analyses based on the combined sequences of pcox1, pnad1 and pnad4 revealed that the recently described species T. malaysiensis was more closely related to T. cati than to T. canis. These findings provided mtDNA evidence for the validity of T. malaysiensis and also demonstrated clearly the usefulness and attributes of the mutation-scanning sequencing approach for studying the population genetic structures of these and other nematodes of socio-economic importance. [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]

Crystal structure of the soluble form of the redox-regulated chloride ion channel protein CLIC4

FEBS JOURNAL, Issue 19 2005
Dene R. Littler
The structure of CLIC4, a member of the CLIC family of putative intracellular chloride ion channel proteins, has been determined at 1.8 Å resolution by X-ray crystallography. The protein is monomeric and it is structurally similar to CLIC1, belonging to the GST fold class. Differences between the structures of CLIC1 and CLIC4 are localized to helix 2 in the glutaredoxin-like N-terminal domain, which has previously been shown to undergo a dramatic structural change in CLIC1 upon oxidation. The structural differences in this region correlate with the sequence differences, where the CLIC1 sequence appears to be atypical of the family. Purified, recombinant, wild-type CLIC4 is shown to bind to artificial lipid bilayers, induce a chloride efflux current when associated with artificial liposomes and produce an ion channel in artificial bilayers with a conductance of 30 pS. Membrane binding is enhanced by oxidation of CLIC4 while no channels were observed via tip-dip electrophysiology in the presence of a reducing agent. Thus, recombinant CLIC4 appears to be able to form a redox-regulated ion channel in the absence of any partner proteins. [source]

Sequence analysis of genes encoding structural and nonstructural proteins of a human group B rotavirus detected in Calcutta, India

JOURNAL OF MEDICAL VIROLOGY, Issue 4 2001
Nobumichi Kobayashi
Abstract Nucleotide sequences of RNA segments encoding structural proteins(VP4, VP6, and VP7) and nonstructural proteins(NSP1 and NSP3) of a human group B rotavirus CAL-1, which was detected in Calcutta, India, were determined and their relatedness with cognate genes of other group B rotaviruses was analyzed. The CAL-1 genes showed generally high sequence identities (more than 90%) to those of human group B rotavirus, adult diarrheal rotavirus (ADRV) in China, while identities with bovine, murine, and ovine viruses were considerably lower (58,73%). Among RNA segments analyzed, sequence identity of the VP6 gene was relatively high compared with other gene segments. In the CAL-1 VP7 sequence, many characteristics were shared by ADRV, but not by other animal group B rotaviruses. In contrast, VP4 and NSP3 of CAL-1 were single animo acid and 23 amino acids longer than those of ADRV strain, respectively, due to differences of a few nucleotides. These findings suggested that human group B rotaviruses CAL-1 and ADRV might have originated from a common ancestral virus distinct from animal group B rotaviruses reported so far, while some notable sequence differences indicated the distinct nature of these viruses. J. Med. Virol. 64:583,588, 2001. © 2001 Wiley-Liss, Inc. [source]

Ossification sequence of the avian order anseriformes, with comparison to other precocial birds

Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana

MOLECULAR ECOLOGY, Issue 13 2009
JENNIFER M. REININGA
Abstract Molecular population genetic analysis of three chromosomal regions in Arabidopsis thaliana suggested that balancing selection might operate to maintain variation at three novel candidate adaptive trait genes, including SOLUBLE STARCH SYNTHASE I (SSI), PLASTID TRANSCRIPTIONALLY ACTIVE 7(PTAC7), and BELL-LIKE HOMEODOMAIN 10 (BLH10). If balanced polymorphisms are indeed maintained at these loci, then we would expect to observe functional variation underlying the previously detected signatures of selection. We observe multiple replacement polymorphisms within and in the 32 amino acids just upstream of the protein,protein interacting BELL domain at the BLH10 locus. While no clear protein sequence differences are found between allele types in SSI and PTAC7, these two genes show evidence for allele-specific variation in expression levels. Geographical patterns of allelic differentiation seem consistent with population stratification in this species and a significant longitudinal cline was observed at all three candidate loci. These data support a hypothesis of balancing selection at all three candidate loci and provide a basis for more detailed functional work by identifying possible functional differences that might be selectively maintained. [source]

Sigma factor selectivity in Borrelia burgdorferi: RpoS recognition of the ospE/ospF/elp promoters is dependent on the sequence of the ,10 region

MOLECULAR MICROBIOLOGY, Issue 6 2006
Christian H. Eggers
Summary Members of the ospE/ospF/elp lipoprotein gene families of Borrelia burgdorferi, the Lyme disease agent, are transcriptionally upregulated in response to the influx of blood into the midgut of an infected tick. We recently have demonstrated that despite the high degree of similarity between the promoters of the ospF (PospF) and ospE (PospE) genes of B. burgdorferi strain 297, the differential expression of ospF is RpoS-dependent, while ospE is controlled by ,70. Herein we used wild-type and RpoS-deficient strains of B. burgdorferi and Escherichia coli to analyse transcriptional reporters consisting of a green fluorescent protein (gfp) gene fused to PospF, PospE, or two hybrid promoters in which the ,10 regions of PospF and PospE were switched [PospF (E , 10) and PospE,(F , 10) respectively]. We found that the PospF,10 region is both necessary and sufficient for RpoS-dependent recognition in B. burgdorferi, while ,70 specificity for PospE is dependent on elements outside of the ,10 region. In E. coli, sigma factor selectivity for these promoters was much more permissive, with expression of each being primarily due to ,70. Alignment of the sequences upstream of each of the ospE/ospF/elp genes from B. burgdorferi strains 297 and B31 revealed that two B31 ospF paralogues [erpK (BBM38) and erpL (BBO39)] have ,10 regions virtually identical to that of PospF. Correspondingly, expression of gfp reporters based on the erpK and erpL promoters was RpoS-dependent. Thus, the sequence of the PospF,10 region appears to serve as a motif for RpoS recognition, the first described for any B. burgdorferi promoter. Taken together, our data support the notion that B. burgdorferi utilizes sequence differences at the ,10 region as one mechanism for maintaining the transcriptional integrity of RpoS-dependent and -independent genes activated at the onset of tick feeding. [source]

The basis of asymmetry in IS2 transposition

MOLECULAR MICROBIOLOGY, Issue 4 2001
Leslie A. Lewis
In the first step of IS2 transposition, the formation of an IS2 minicircle, the roles of the two IS ends differ. Terminal cleavage initiates exclusively at the right inverted repeat (IRR) , the donor end , whereas IRL is always the target. At the resulting minicircle junction, the two abutted ends are separated by a spacer of 1 or 2 basepairs. In this study, we have identified the determinants of donor and target function. The inability of IRL to act as a donor results largely from two sequence differences between IRL and IRR , an extra basepair between the conserved transposase binding sequences and the end of the element, and a change of the terminal dinucleotide from CA-3, to TA-3,. These two changes also impose a characteristic size on the minicircle junction spacer. The only sequences required for the efficient target function of IRL appear to be contained within the segment from position 11,42. Although IRR can function as a target, its shorter length and additional contacts with transposase (positions 1,7) result in minicircles with longer, and inappropriate, spacers. We propose a model for the synaptic complex in which the terminus of IRL makes different contacts with the transposase for the initial and final strand transfer steps. The sequence differences between IRR and IRL, and the behavioural characteristics of IRL that result from them, have probably been selected because they optimize expression of transposase from the minicircle junction promoter, Pjunc. [source]

Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops

MOLECULAR PLANT PATHOLOGY, Issue 2 2010
INGE M. HANSSEN
SUMMARY Taxonomy:Pepino mosaic virus (PepMV) belongs to the Potexvirus genus of the Flexiviridae family. Physical properties: PepMV virions are nonenveloped flexuous rods that contain a monopartite, positive-sense, single-stranded RNA genome of 6.4 kb with a 3, poly-A tail. The genome contains five major open reading frames (ORFs) encoding a 164-kDa RNA-dependent RNA polymerase (RdRp), three triple gene block proteins of 26, 14 and 9 kDa, and a 25-kDa coat protein. Genome diversity: Four PepMV genotypes, with an intergenotype RNA sequence identity ranging from 78% to 95%, can be distinguished: the original Peruvian genotype (LP); the European (tomato) genotype (EU); the American genotype US1; and the Chilean genotype CH2. Transmission: PepMV is very efficiently transmitted mechanically, and a low seed transmission rate has been demonstrated. In addition, bumblebees have been associated with viral transmission. Host range: Similar to other Potexviruses, PepMV has a rather narrow host range that is thought to be largely restricted to species of the Solanaceae family. After originally being isolated from pepino (Solanum muricatum), PepMV has been identified in natural infections of the wild tomato species S. chilense, S. chmielewskii, S. parviflorum and S. peruvianum. PepMV is causing significant problems in the cultivation of the glasshouse tomato Solanum lycopersicum, and has been identified in weeds belonging to various plant families in the vicinity of tomato glasshouses. Symptomatology: PepMV symptoms can be very diverse. Fruit marbling is the most typical and economically devastating symptom. In addition, fruit discoloration, open fruit, nettle-heads, leaf blistering or bubbling, leaf chlorosis and yellow angular leaf spots, leaf mosaic and leaf or stem necrosis have been associated with PepMV. The severity of PepMV symptoms is thought to be dependent on environmental conditions, as well as on the properties of the viral isolate. Minor nucleotide sequence differences between isolates from the same genotype have been shown to lead to enhanced aggressiveness and symptomatology. Control: Prevention of infection through strict hygiene measures is currently the major strategy for the control of PepMV in tomato production. Cross-protection can be effective, but only under well-defined and well-controlled conditions, and the effectiveness depends strongly on the PepMV genotype. [source]

Brief communication: Methods of sequence heterochrony for describing modular developmental changes in human evolution

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2009
Gregory E. Blomquist
Abstract Interest in the developmental changes leading to apomorphic features of human anatomy is longstanding. Although most research has focused on quantitative measures of size and shape, additional information may be available in the sequence of events in development, including aspects of phenotypic integration. I apply two recently proposed techniques for analyzing developmental sequences to literature data on human and chimpanzee age of limb element ossification center appearance in radiographs. The event-pair cracking method of Jeffery et al. (Syst Biol 51 [2002] 478,491) offers little additional insight on sequence differences in this data set than a simpler difference of ranks. Both reveal shifts in timing that are likely related to locomotor differences between the two species. Poe's (Evolution 58 [2004] 1852,1855) test for modularity in a sequence identifies the ankle, wrist, and hind limb as developmental modules, which may correspond to localized combinations of developmental genes. Ossification patterns of the rays of the hand and foot show little modularity. Integrating these and other methods of sequence analysis with traditional metrics of size and shape remains an underdeveloped area of inquiry. Am J Phys Anthropol 2009. © 2008 Wiley-Liss, Inc. [source]

Identification of a Second rRNA Gene Unit in the Perkinsus andrewsi Genome

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2004
WOLF T. PECHER
ABSTRACT. Perkinsus species are parasitic protozoa of mollusks, currently classified within the Perkinsozoa, a recently established phylum that is basal to the Apicomplexa and Dinozoa. Ribosomal RNA (rRNA) genes and their intergenic spacers have been used to support the taxonomy of Perkinsus species, the description of new species, and to develop molecular probes for their detection and identification. We previously described ultrastructure, behavior in culture, and partial sequence of the rRNA locus of a Perkinsus species isolated from the baltic clam Macoma balthica. The rRNA genes and intergenic spacers of this Perkinsus isolate differed from those described in the currently accepted species to a degree that led to its designation as a new species, Perkinsus andrewsi. In this study, we identify an additional rRNA gene unit (rRNA-B) in the P. andrewsi holotype, and report the complete sequences of both rRNA gene units. Except for the 5. 8S, all regions of the rRNA-B gene unit exhibited sequence differences from that initially described (rRNA-A). Each rRNA gene unit is arranged in a "head-to-tail" tandem repeat. This is the first report demonstrating two distinct rRNA units in a Perkinsus species. [source]

Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2009
Sean C. Gay
The Tbd_0210 gene of the chemolithotrophic bacterium Thiobacillus denitrificans is annotated to encode a 60.5,kDa bifunctional enzyme with ATP sulfurylase and APS kinase activity. This putative bifunctional enzyme was cloned, expressed and structurally characterized. The 2.95,Å resolution X-ray crystal structure reported here revealed a hexameric assembly with D3 symmetry. Each subunit contains a large N-terminal sulfurylase-like domain and a C-terminal APS kinase domain reminiscent of the two-domain fungal ATP sulfurylases of Penicillium chrysogenum and Saccharomyces cerevisiae, which also exhibit a hexameric assembly. However, the T. denitrificans enzyme exhibits numerous structural and sequence differences in the N-terminal domain that render it inactive with respect to ATP sulfurylase activity. Surprisingly, the C-terminal domain does indeed display APS kinase activity, indicating that this gene product is a true APS kinase. Therefore, these results provide the first structural insights into a unique hexameric APS kinase that contains a nonfunctional ATP sulfurylase-like domain of unknown function. [source]

DNA sequence variation in the ITS-1 rDNA subunit and host relationships in sorghum midge, Stenodiplosis sorghicola (Coquillett) (Diptera: Cecidomyiidae), in Australia

AUSTRALIAN JOURNAL OF ENTOMOLOGY, Issue 2 2002
Bradley C Congdon
Abstract Sequence variation in the internal transcribed spacer (ITS-1) ribosomal DNA subunit was examined for sorghum midge obtained from introduced and native hosts in south-eastern and central Queensland. No variation was observed relative to host plant or geographical distance for midges collected from two introduced hosts, grain sorghum (Sorghum bicolor) and Johnson grass (S. halepense); however, sequence differences were observed between midges from introduced and native hosts and among midges from a single native host, slender bluegrass (Dichanthium affine). No evidence was observed of introduced midges on native hosts, or vice versa. These results agree with previously hypothesised host distributions for native and introduced midges in Australia, and expand the sample of introduced hosts to include Johnson grass. They suggest that Stenodiplosis sorghicola, the principal midge infesting grain sorghum, is also the most common species on Johnson grass. This confirms that Johnson grass plays a role in the population dynamics of S. sorghicola and suggests that midges originating from Johnson grass may influence levels of infestation in grain sorghum. [source]

Insecticide resistance in the aphid Myzus persicae (Sulzer): chromosome location and epigenetic effects on esterase gene expression in clonal lineages

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2003
LINDA M. FIELD
Insecticide treatment of the aphid Myzus persicae (Sulzer) has led to the evolution of several insecticide resistance mechanisms, including the detoxification of insecticides by elevated esterases. This results from amplification of one of two closely related esterase genes (E4 or FE4) with up to 80 copies in the most resistant aphids. The amplified E4 genes are at a single site linked to a chromosomal translocation and resistance can be unstable. Individuals within a clone lose their elevated esterase and resistant phenotype, a good example of ,clonal variation'. This loss of esterase is accompanied by a loss of the corresponding mRNA but the amplified genes are retained with no detectable sequence differences. However, the expressed E4 genes contain 5-methylcytosine, which is lost at the same time as the genes are turned off. This is in direct contrast with vertebrate genes where DNA methylation causes gene silencing, but it does suggest that the resistant phenotype in M. persicae is under epigenetic control. One hypothesis is that 5-methylcytosine in E4 genes facilitates expression by preventing the production of incorrectly initiated transcripts. It is interesting that we have never detected silencing of amplified FE4 genes, possibly because they are at multiple loci and therefore less likely to be subject to synchronous control. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 79, 107,113. [source]