Type-1 ribosome-inactivating protein from iris (Iris hollandica var. Professor Blaauw) binds specific genomic DNA fragments

2001 ◽  
Vol 357 (3) ◽  
pp. 875-880 ◽  
Author(s):  
Qiang HAO ◽  
Willy J. PEUMANS ◽  
Els J. M. van DAMME
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Average Length ◽  
Dna Fragments ◽  
The Novel ◽  
Ribosome Inactivating Protein ◽  
Glycosidase Activity ◽  
Reticulocyte Lysate ◽  
Novel Concept

The capacity of IRIP, a type-1 ribosome-inactivating protein (RIP) isolated from the bulbs of Iris hollandica, to bind specific DNA sequences from a mixture of approx. 200bp (average length) fragments of total genomic DNA from Iris genome was studied. Fragments that were preferentially bound by IRIP were enriched by several cycles of affinity binding and PCR, and were cloned and sequenced. The selected DNA fragments do not share conserved sequences, indicating that IRIP does not bind DNA fragments in a strictly sequence-specific manner. According to sequence analysis, most IRIP-bound fragments contain one or more possible free energy-stable hairpin structure(s) in their secondary structure, which may be the basis for recognition between IRIP and these DNA fragments. Some, but not all, DNA fragments moderately lower the RNA N-glycosidase activity of IRIP towards rabbit reticulocyte lysate ribosomes. IRIP does not remove adenines from the binding fragments, which implies that it does not act as a polynucleotide:adenosine glycosidase towards these DNA fragments. The selective binding of IRIP to conspecific DNA fragments is also discussed in view of the novel concept that RIPs may act as DNA-binding proteins with a regulatory activity on gene expression.

scholarly journals Differential metabolism -associated gene expression of duck pancreatic cells in response to two subtype s of duck hepatitis A virus type 1

2020 ◽  
Author(s):  
Shaohua SHI ◽  
Zhen CHEN ◽  
Yu HUANG ◽  
Cuiqin HUANG ◽  
Rongchang LIU ◽  
...  
Keyword(s):  
Virus Type ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Average Length ◽  
Infected Group ◽  
Antigenic Relationship ◽  
The Novel ◽  
Expression Levels ◽  
Duck Hepatitis

Abstract Background: Duck hepatitis A virus type 1 (DHAV-1) causes a highly contagious disease in domestic ducklings, which is traditionally characterized by lesions in the liver and rarely in the pancreas. However, several outbreaks of DHAV-1, which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. Genomic sequencing indicated variation rates of 3.4-6.5% in the genome of the novel DHAV-1 compared with those of DHAV-1. The antigenic relationship between the novel DHAV-1 and DHAV-1 indicated large variation. Therefore, the novel DHAV-1 was named as DHAV-1 subtype (DHAV-1s). However, the mechanism involved in infection of DHAV-1s is still unclear. Results: In the present study, transcriptome analysis of duck pancreas infected with DHAV-1 and DHAV-1s was carried out. Following deep sequencing with Illumina-Solexa, a total of 53.9 Gb clean data were obtained from the cDNA library of the pancreas and a total of 29,597 unigenes with an average length of 993.43 bp were generated following de novo sequence assembly. The expression levels of D-3-phosphoglyceratedehydrogenase, phosphoserine aminotransferase, phosphoserine phosphatase, which are involved in glycine, serine and threonine metabolism pathway, were significantly downregulated in the DHAV-1s-infected group compared with those of the DHAV-1-infected group.Conclusion: These findings provide information regarding differential expression levels of metabolism-associated genes between the novel DHAV-1s and DHAV-1, indicating that intensive metabolism disorders may contribute to different phenotypes of DHAV-1-infection.

scholarly journals Identification of Campylobacter jejuni ATCC 43431-Specific Genes by Whole Microbial Genome Comparisons

2004 ◽  
Vol 186 (14) ◽  
pp. 4781-4795 ◽  
Author(s):  
Frédéric Poly ◽  
Deborah Threadgill ◽  
Alain Stintzi
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Genomic Library ◽  
Open Reading Frames ◽  
Dna Fragments ◽  
Helicobacter Hepaticus ◽  
Type Iv ◽  
Novel Approach ◽  
The Mean ◽  
Reading Frames

ABSTRACT This study describes a novel approach to identify unique genomic DNA sequences from the unsequenced strain C. jejuni ATCC 43431 by comparison with the sequenced strain C. jejuni NCTC 11168. A shotgun DNA microarray was constructed by arraying 9,600 individual DNA fragments from a C. jejuni ATCC 43431 genomic library onto a glass slide. DNA fragments unique to C. jejuni ATCC 43431 were identified by competitive hybridization to the array with genomic DNA of C. jejuni NCTC 11168. The plasmids containing unique DNA fragments were sequenced, allowing the identification of up to 130 complete and incomplete genes. Potential biological roles were assigned to 66% of the unique open reading frames. The mean G+C content of these unique genes (26%) differs significantly from the G+C content of the entire C. jejuni genome (30.6%). This suggests that they may have been acquired through horizontal gene transfer from an organism with a G+C content lower than that of C. jejuni. Because the two C. jejuni strains differ by Penner serotype, a large proportion of the unique ATCC 43431 genes encode proteins involved in lipooligosaccharide and capsular biosynthesis, as expected. Several unique open reading frames encode enzymes which may contribute to genetic variability, i.e., restriction-modification systems and integrases. Interestingly, many of the unique C. jejuni ATCC 43431 genes show identity with a possible pathogenicity island from Helicobacter hepaticus and components of a potential type IV secretion system. In conclusion, this study provides a valuable resource to further investigate Campylobacter diversity and pathogenesis.

scholarly journals Cryptosporidium parvum Genes Containing Thrombospondin Type 1 Domains

2002 ◽  
Vol 70 (12) ◽  
pp. 6987-6995 ◽  
Author(s):  
Mingqi Deng ◽  
Thomas J. Templeton ◽  
Nicole R. London ◽  
Carrey Bauer ◽  
Alison A. Schroeder ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Large Scale ◽  
Early Stage ◽  
Pcr Analysis ◽  
Adhesive Proteins ◽  
Late Stages

ABSTRACT Cryptosporidium parvum is recognized as an enteropathogen of great worldwide medical and veterinary importance, yet understanding of its pathogenesis has been hampered in part by limited knowledge of the invasion machinery of this parasite. Recently, genes containing thrombospondin type 1 (TSP1) domains have been identified in several genera of apicomplexans, including thrombospondin-related adhesive proteins (TRAPs) that have been implicated as key molecules for parasite motility and adhesion onto host cell surfaces. Previously, a large-scale random survey of the C. parvum genome conducted in our laboratory revealed the presence of multiple genomic DNA sequences with a high degree of similarity to known apicomplexan TRAP genes. In the present study, TBLASTN screening of available C. parvum genomic sequences by using TSP1 domains as queries identified a total of 12 genes possessing TSP1-like domains. All genes have putative signal peptide sequences, one or more TSP1-like domains, plus additional extracellular protein modules such as Kringle, epidermal growth factor, and Apple domains. Two genes, putative paralogs CpTSP8 and CpTSP9, contain predicted introns near their amino termini, which were verified by comparing PCR products from cDNA versus genomic DNA templates. Reverse transcription-PCR analysis of transcript levels reveals that C. parvum TSP genes were developmentally regulated with distinct patterns of expression during in vitro infection. TRAPC1, CpTSP3, and CpTSP11 were expressed at high levels during both early and late stages of infection, whereas CpTSP2, CpTSP5, CpTSP6, CpTSP8, and CpTSP9 were maximally expressed during the late stages of infection. Only CpTSP4 was highly expressed solely at an early stage of infection.

scholarly journals Diabetes segregates as a single locus in crosses between inbred BB rats prone or resistant to diabetes.

1991 ◽  
Vol 174 (1) ◽  
pp. 297-300 ◽  
Author(s):  
H Markholst ◽  
S Eastman ◽  
D Wilson ◽  
B E Andreasen ◽  
A Lernmark
Keyword(s):  
Diabetes Mellitus ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Autosomal Recessive ◽  
Bb Rat ◽  
Recessive Trait ◽  
Autosomal Recessive Trait ◽  
Bb Rats ◽  
Insulin Dependent

Diabetes-prone (DP) BB rats spontaneously develop insulin-dependent diabetes resembling type 1 diabetes mellitus in man. They also exhibit lifelong T cell deficiency. The segregation of both diabetes and lymphopenia was studied in crosses between this inbred line of rats and the related but nondiabetic and nonlymphopenic inbred diabetes-resistant (DR) BB rat line. Diabetes segregated as a single, autosomal recessive trait and was always accompanied by lymphopenia. Among the limited number of differences in the genomic DNA sequences of the two lines, DP and DR BB, one may account for the development of diabetes and lymphopenia in the DP BB rats. It may be possible to screen the genomic DNA for such differences to detect a marker for the phenotypes.

Genomic interspersions determine the size and complexity of transgene loci in transgenic plants produced by microprojectile bombardment

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 691-697 ◽  
Author(s):  
Sergei K Svitashev ◽  
David A Somers
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Microprojectile Bombardment ◽  
Culture Conditions ◽  
Plant Genome ◽  
Dna Fragments ◽  
Chromosomal Breakage ◽  
Multiple Copies ◽  
Transgene Locus

The structure of transgene loci in six transgenic allohexaploid oat (Avena sativa L.) lines produced using microprojectile bombardment was characterized using fluorescence in situ hybridization (FISH) on extended DNA fibers (fiber-FISH). The transgene loci in five lines were composed of multiple copies of delivered DNA interspersed with genomic DNA fragments ranging in size from ca. 3 kb to at least several hundred kilobases, and in greater numbers than detected using Southern blot analysis. Although Southern analysis predicted that the transgene locus in one line consisted of long tandem repeats of the delivered DNA, fiber-FISH revealed that the locus actually contained multiple genomic interspersions. These observations indicated that transgene locus size and structure were determined by the number of transgene copies and, possibly to a greater extent, the number and the length of interspersing genomic DNA sequences within the locus. Large genomic interspersions detected in several lines were most likely the products of chromosomal breakage induced either by tissue culture conditions or, more likely, by DNA delivery into the nucleus using microprojectile bombardment. We propose that copies of transgene along with other extrachromosomal DNA fragments are used as patches to repair double-strand breaks (DSBs) in the plant genome resulting in the formation of transgene loci.Key words: genetic transformation, microprojectile bombardment, transgenic oat, FISH, transgene locus structure.

scholarly journals Differential metabolism-associated gene expression of duck pancreatic cells in response to two subtypes of duck hepatitis A virus type 1

2020 ◽  
Author(s):  
Shaohua SHI ◽  
Zhen CHEN ◽  
Yu HUANG ◽  
Cuiqin HUANG ◽  
Rongchang LIU ◽  
...  
Keyword(s):  
Virus Type ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Average Length ◽  
Infected Group ◽  
Antigenic Relationship ◽  
The Novel ◽  
Expression Levels ◽  
Duck Hepatitis

Abstract Background: Duck hepatitis A virus type 1 (DHAV-1) causes a highly contagious disease in domestic ducklings, which is traditionally characterized by lesions in the liver and rarely in the pancreas. However, several outbreaks of DHAV-1, which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. Genomic sequencing indicated the presence in the variation rates of 3.4-6.5% in the genome of the novel DHAV-1 compared with DHAV-1. The antigenic relationship between the novel DHAV-1 and DHAV-1 indicated large variation. So the novel DHAV-1 was named as DHAV-1 subtype (DHAV-1a). But the mechanism involved in infection of DHAV-1a is still unclear. Results: In the present study, transcriptome analysis of duck pancreas infected with DHAV-1 and DHAV-1a was carried out. Following deep sequencing with Illumina-Solexa, a total of 53.9 Gb clean data were obtained from the cDNA library of the pancreas and a total of 29,597 unigenes with an average length of 993.43 bp were generated following de novo sequence assembly. The expression levels of D-3-phosphoglyceratedehydrogenase, phosphoserine aminotransferase, phosphoserine phosphatase, which are involved in the glycine, serine and threonine metabolism pathway, were significantly down-regulated in the DHAV-1a-infected group compared with those of DHAV-1-infected group. Conclusion: These findings offered different expression levels of metabolism-associated genes between the novel DHAV-1a and DHAV-1, indicating that intensive metabolism disorder may contribute to different phenotypes of DHAV-1-infection.

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