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Nucleotide Identity (nucleotide + identity)
Selected AbstractsHost range, vector relationships and sequence comparison of a begomovirus infecting hibiscus in IndiaANNALS OF APPLIED BIOLOGY, Issue 1 2005R. Rajeshwari Abstract Hibiscus leaf curl disease (HLCuD) occurs widely in India. Infected hibiscus plants show vein thickening, upward curling of leaves and enations on the abaxial leaf surface, reduction in leaf size and stunting. The commonly-occurring weeds (Ageratum conyzoides, Croton bonplandianum and Euphorbia geniculata), Nicotiana benthamiana, Nicotiana glutinosa and Nicotiana tabacum (var. Samsun, Xanthi), cotton and tomato were shown to be susceptible to HLCuD. One of the four species of hibiscus (Hibiscus rosa-sinensis) and 75 of the 101 commercial hybrids/varieties grown in the Bangalore area of southern India were also susceptible. Two virus isolates associated with HLCuD from Bangalore, South India (Ban), and Bhubaneswar, North India (Bhu), were detected serologically and by PCR-mediated amplification of virus genomes. The isolates were characterised by sequencing a fragment of DNA-A component (1288 nucleotides) and an associated satellite DNA molecule of 682 nucleotides. Phylogenetic analyses of these DNA-A sequences clustered them with Old World cotton-infecting begomoviruses and closest to Cotton leaf curl Multan virus (CLCuMV) at 95,97% DNA-A nucleotide identities. The 682-nucleotide satellite DNA molecules associated with the HLCuD samples Ban and Bhu shared 96.9% sequence identity with each other and maximum identity (93.1,93.9% over positions 158,682) with ,1350-nucleotide DNA-, satellite molecules associated with cotton leaf curl disease in Pakistan and India (accession nos AJ298903, AJ316038). HLCuD in India, therefore, appears to be associated with strains of CLCuMV, a cotton-infecting begomovirus from Pakistan, which is transmitted in a persistent manner by Bemisia tabaci. [source] New alk genes detected in Antarctic marine sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 3 2009Emanuele Kuhn Summary Alkane monooxygenases (Alk) are the key enzymes for alkane degradation. In order to understand the dispersion and diversity of alk genes in Antarctic marine environments, this study analysed by clone libraries the presence and diversity of alk genes (alkB and alkM) in sediments from Admiralty Bay, King George Island, Peninsula Antarctica. The results show a differential distribution of alk genes between the sites, and the predominant presence of new alk genes, mainly in the pristine site. Sequences presented 53.10,69.60% nucleotide identity and 50.90,73.40% amino acid identity to alkB genes described in Silicibacter pomeroyi, Gordonia sp., Prauserella rugosa, Nocardioides sp., Rhodococcus sp., Nocardia farcinica, Pseudomonas putida, Acidisphaera sp., Alcanivorax borkumensis, and alkM described in Acinetobacter sp. This is the first time that the gene alkM was detected and described in Antarctic marine environments. The presence of a range of previously undescribed alk genes indicates the need for further studies in this environment. [source] Buffalo (Bubalus bubalis) interleukin-2: sequence analysis reveals high nucleotide and amino acid identity with interleukin-2 of cattle and other ruminantsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4 2002E. Sreekumar Summary A 4400-bp genomic sequence and a 332-bp truncated cDNA sequence of the interleukin-2 (IL-2) gene of Indian water buffalo (Bubalus bubalis) were amplified by polymerase chain reaction and cloned. The coding sequence of the buffalo IL-2 gene was assembled from the 5, end of the genomic clone and the truncated cDNA clone. This sequence had 98.5% nucleotide identity and 98% amino acid identity with cattle IL-2. Three amino acid substitutions were observed at positions 63, 124 and 135. Comparison of the predicted protein structure of buffalo IL-2 with that of human and cattle IL-2 did not reveal significant differences. The putative amino acids responsible for IL-2 receptor binding were conserved in buffalo, cattle and human IL-2. The amino acid sequence of buffalo IL-2 also showed very high identity with that of other ruminants, indicating functional cross-reactivity. [source] cDNA cloning of the polymeric immunoglobulin receptor of the marsupial Macropus eugenii (tammar wallaby)INTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2002C. L. Taylor Summary cDNA encoding a marsupial polymeric immunoglobulin receptor (pIgR) was isolated from Macropus eugenii (tammar wallaby) mammary lymph node primarily by reverse transcriptase coupled polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. This resulted in a 5, truncated clone and, in order to obtain the full-length sequence, genomic walking PCR was utilized. The complete sequence consists of 2696 bp of cDNA and encodes a predicted polypeptide of 732 amino acids. The wallaby sequence is highly conserved in relation to the only other reported marsupial pIgR sequence, that of Trichosurus vulpecula (brushtail possum), having a nucleotide identity of 86.7% and a deduced amino acid identity of 79.9%. The wallaby nucleotide sequence also has a moderate degree of similarity with the pIgR sequences of eutherian mammals, being most similar to that of the rat, with an identity of 63.1%. At the amino acid level, in comparison to eutherian sequences, the wallaby pIgR is most similar to that of humans with an identity of 52.6%. pIgR phylogenetic trees were constructed for tammar wallaby, brushtail possum and several eutherian mammal cDNA and deduced amino acid sequences. In both DNA and protein analyses, the eutherian sequences formed a sister clade to the exclusion of the marsupial sequences, in agreement with the current view of mammalian evolution. [source] Identification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assayJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2010J.L. Weidhaas Abstract Aim:, To identify a DNA sequence specific to a bacterium found in poultry litter that was indicative of faecal contamination by poultry sources. Methods and Results:, Faecally contaminated poultry litter and soils were used as source material for the development of a quantitative polymerase chain reaction (qPCR) method targeting the 16S rRNA gene of a Brevibacterium sp. The identified sequence had 98% nucleotide identity to the 16S rRNA gene of Brevibacterium avium. The qPCR method was tested on 17 soiled litter samples; 40 chicken faecal samples; and 116 nontarget faecal samples from cattle, swine, ducks, geese, and human sewage collected across the United States. The 571-bp product was detected in 76% of poultry-associated samples, but not in 93% of faecal samples from other sources. Marker concentrations were 107,109 gene copies per gram in soiled litter, up to 105 gene copies per gram in spread-site soils, and 107 gene copies per litre in field run-off water. Results were corroborated by a blinded study conducted by a second laboratory. Conclusion:, The poultry-specific PCR product is a useful marker gene for assessing the impact of faecal contamination as a result of land-applied poultry litter. Significance and Impact of the Study:, This study describes the first quantitative, sensitive and specific microbial source tracking method for the detection of poultry litter contamination. [source] Co-circulation of genotype IA and new variant IB hepatitis A virus in outbreaks of acute hepatitis in Hungary,2003/2004JOURNAL OF MEDICAL VIROLOGY, Issue 11 2006Gábor Reuter Abstract Hepatitis A virus (HAV) is one of the most important causes of acute infectious hepatitis worldwide. In Hungary, the reported number of HAV infections has been decreasing in the last four decades, nevertheless, still, each year 500,800 new cases and multiple outbreaks occur, particularly in the northeast region of Hungary. In Hungary, serology is used routinely to establish the diagnosis of HAV infection without genetic analysis of HAV strains for molecular epidemiology. In this study, serum samples collected from symptomatic patients were tested by enzyme-immunoassay (anti-HAV-IgM ELISA) to establish the cause of three acute hepatitis A outbreaks (outbreak 1,from low prevalence region in Southwest Hungary in 2003 and outbreaks 2 and 3 from the endemic region in Northeast Hungary in 2004). Outbreak strains were characterized by reverse transcription-polymerase chain reaction (RT-PCR) amplification of a 360 bp viral VP1/2A region, amplicon sequencing and phylogenetic analysis. Four, seven, and three sera from outbreaks 1, 2, and 3, respectively, were investigated by RT-PCR for HAV genome and HAV RNA was detected in 4 (100%), 4 (57%), and 2 (67%) samples. All strains belonged to genotype I HAV. Outbreak 1 was caused by the new variant subtype IB and outbreaks 2 and 3 caused by genetically identical subtype IA strains. The Hungarian IA and IB hepatitis A viruses had the highest nucleotide identity, 98.4% and 99.0%, to IT-SCH-00 and IT-MAR-02 strains, respectively, detected in year 2000 and 2002 in Italy. Endemic subtype IA and probably imported new variant subtype IB HAV viruses was detected in outbreaks of hepatitis in Hungary that are closely related genetically to HAV strains in Italy. J. Med. Virol. 78:1392,1397, 2006. © 2006 Wiley-Liss, Inc. [source] PCR-based Detection and Differentiation of Anthracnose Pathogens, Colletotrichum gloeosporioides and C. truncatum, from Vegetable Soybean in TaiwanJOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2006L. S. Chen Abstract Anthracnose of vegetable soybean sometimes occurs in summer and causes severe symptoms and yield loss in southern Taiwan. Despite previous reports that Glomerella glycines and Colletotrichum truncatum were causal agents of soybean anthracnose, C. truncatum and C. gloeosporioides (teleomorph G. cingulata), but not G. glycines, were identified as the major pathogens causing anthracnose on the pods and stems of vegetable soybeans from 2003 to 2005. Most strains of C. truncatum and C. gloeosporioides were derived from diseased pods. Morphological formation of fruiting bodies separates the Colletotrichum isolates into two groups. Colletotrichum truncatum forms acervuli only while C. gloeosporioides produces acervuli and/or perithecia. Based on the sequence variation in the ITS1 and ITS2 regions, C. truncatum isolates were highly similar (99,100% nucleotide identity) while C. gloeosporioides isolates diverged into two separate groups that were not associated with morphotype. For early detection of C. truncatum and C. gloeosporioides infection on vegetable soybean plants, two species-specific primer pairs Colg 1/Colg 2 (expected size of 443 bp) and Colg 1/CT 2 (375 bp) were designed that allowed differentiation of C. gloeosporioides and C. truncatum in multiplex polymerase chain reaction. [source] Loss of heterozygosity and transcriptome analyses of a 1.2 Mb candidate ovarian cancer tumor suppressor locus region at 17q25.1-q25.2MOLECULAR CARCINOGENESIS, Issue 3 2005Nadège Presneau Abstract Loss of heterozygosity (LOH) analysis was performed in epithelial ovarian cancers (EOC) to further characterize a previously identified candidate tumor suppressor gene (TSG) region encompassing D17S801 at chromosomal region 17q25.1. LOH of at least one informative marker was observed for 100 (71%) of 140 malignant EOC samples in an analysis of 6 polymorphic markers (cen - D17S1839 - D17S785 - D17S1817 - D17S801 - D17S751 - D17S722 - tel). The combined LOH analysis revealed a 453 kilobase (Kb) minimal region of deletion (MRD) bounded by D17S1817 and D17S751. Human and mouse genome assemblies were used to resolve marker inconsistencies in the D17S1839 - D17S722 interval and identify candidates. The region contains 32 known and strongly predicted genes, 9 of which overlap the MRD. The reference genomic sequences share nearly identical gene structures and the organization of the region is highly collinear. Although, the region does not show any large internal duplications, a 1.5 Kb inverted duplicated sequence of 87% nucleotide identity was observed in a 13 Kb region surrounding D17S801. Transcriptome analysis by Affymetrix GeneChip® and reverse transcription (RT)-polymerase chain reaction (PCR) methods of 3 well characterized EOC cell lines and primary cultures of normal ovarian surface epithelial (NOSE) cells was performed with 32 candidates spanning D17S1839 - D17S722 interval. RT-PCR analysis of 8 known or strongly predicted genes residing in the MRD in 10 EOC samples, that exhibited LOH of the MRD, identified FLJ22341 as a strong candidate TSG. The proximal repeat sequence of D17S801 occurs 8 Kb upstream of the putative promoter region of FLJ22341. RT-PCR analysis of the EOC samples and cell lines identified DKFZP434P0316 that maps proximal to the MRD, as a candidate. While Affymetrix technology was useful for initially eliminating less promising candidates, subsequent RT-PCR analysis of well-characterized EOC samples was essential to prioritize TSG candidates for further study. © 2005 Wiley-Liss, Inc. [source] Serological and molecular detection of Tomato chlorosis virus and Tomato infectious chlorosis virus in tomatoPLANT PATHOLOGY, Issue 2 2009M. Jacquemond Tomato chlorosis virus (ToCV) and Tomato infectious chlorosis virus (TICV) are two criniviruses inducing similar yellowing symptoms in tomato. An approximately 4 kb central region of the genomic RNA2 of French ToCV and TICV isolates was sequenced. TICV, for which no other sequences were available, appeared as a distant species in the genus, being close only to LIYV (Lettuce infectious yellows virus) for some, but not all, proteins. ToCV has more than 98% nucleotide identity with isolates from the US and Spain, and sequencing the CP gene of several isolates collected in different regions in southern France during 2 years suggested a unique origin. Polyclonal antisera were produced using capsid proteins of both viruses expressed in Escherichia coli. DAS-ELISA assays were developed for routine diagnosis and conditions for preparing samples for an optimized detection were determined. No cross-reactions were observed. However, some false-negative results, corresponding to samples giving ELISA readings close to the detection limit were regularly detected, particularly for ToCV (approximately 5% of the samples). A triplex RT-PCR assay was thus developed, which allowed detection of both viruses in a one-step protocol. An internal PCR control was included, which in addition showed that it could be used as a control for the entire RT-PCR procedure. Finally, combining DAS-ELISA in a first round, and triplex RT-PCR for doubtful samples, appeared the best way to achieve a reliable diagnosis of these viruses. [source] Molecular characterization of the CP gene and 3,UTR of Chilli veinal mottle virus from South and Southeast AsiaPLANT PATHOLOGY, Issue 3 2008W. S. Tsai Twenty-four isolates of Chilli veinal mottle virus (ChiVMV) from China, India, Indonesia, Taiwan and Thailand were analysed to determine their genetic relatedness. Pathogenicity of virus isolates was confirmed by induction of systemic mosaic and/or necrotic ringspot symptoms on Capsicum annuum after mechanical inoculation. The 3, terminal sequences of the viral genomic RNA were determined. The coat protein (CP) coding regions ranged from 858 to 864 nucleotides and the 3, untranslated regions (3,UTR) from 275 to 289 nucleotides in length. All isolates had the inverted repeat sequence GUGGNNNCCAC in the 3,UTR. The DAG motif, conserved in aphid-transmitted potyviruses, was observed in all isolates. All 24 isolates were considered as belonging to ChiVMV because of their high CP amino acid and nucleotide identity (more than 94·8 and 89·5%, respectively) with the reported ChiVMV isolates including the pepper vein banding virus (PVBV), the chilli vein-banding mottle virus (CVbMV) and the CVbMV Chiengmai isolate (CVbMV-CM1). Based on phylogenetic analysis, ChiVMV isolates including all 24 isolates tested, PVBV, CVbMV and CVbMV-CM1 can be classified into three groups. In addition, a conserved region of 204 amino acids with more than 90·2% identity was identified in the C terminal of the CP gene of ChiVMV and Pepper veinal mottle virus (PVMV), and may explain the serological cross reaction between these two viruses. The conserved region may also provide useful information for developing transgenic resistance to both ChiVMV and PVMV. [source] Transcriptional regulation of gene expression by the coding sequence: An attempt to enhance expression of human AChEBIOTECHNOLOGY & BIOENGINEERING, Issue 5 2002Claire O. Weill Abstract In a previous report, Morel and Massoulié showed that Bungarus AChE (bBAChE) is produced more efficiently than rat AChE in various expression systems, mainly because the Bungarus coding sequence exerts a stimulatory effect on transcription (Morel and Massoulié, 2000). They reported that a 5, Bungarus fragment could partially transfer this property to a CAT expression vector. This appeared to offer the possibility of increasing the production of recombinant proteins. In the present paper, we show that insertion of this fragment in the transcribed region, before the polyadenylation site, may have either stimulatory or inhibitory effects, depending on the vector and on the reporter gene. Since the stimulatory effect of Bungarus coding region could not be attached to a small number of discrete motifs, we reasoned that it might result from a general feature of the sequence. Therefore it might be possible to partially transfer this property to the very homologous human AChE (hHAChE) coding sequence by modifications based on synonymous codons, which increased nucleotide identity between the 5, fragment (721 nucleotides) of bBAChE and hHAChE from 71% to 85%. The production of human AChE in transfected COS cells was increased nearly 2-fold with this modified construct, but still remained about 4-fold smaller than that of Bungarus AChE. There was no change in expression level in transformed Pichia pastoris. We thus confirm that coding sequences can strongly influence gene expression, but in a manner that depends on the context and cannot yet be predicted. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 490,497, 2002. [source] | |||||||||||||