Abridged 5S rDNA units in sea beet (Beta vulgaris subsp. maritima)

Genome ◽  
2005 ◽  
Vol 48 (2) ◽  
pp. 352-354 ◽  
Author(s):  
Daniel J Turner ◽  
Terence A Brown
Keyword(s):  
Network Analysis ◽  
Beta Vulgaris ◽  
5S Rdna ◽  
Full Length ◽  
Rdna Repeat ◽  
Chain Reaction ◽  
Repeat Units ◽  
Unit Classes ◽  
Polymerase Chain ◽  
5S Gene

Amplification by polymerase chain reaction of the 5S rDNA repeat units of Beta vulgaris subsp. maritima resulted in a 350-bp product corresponding to the full-length 5S unit, but also revealed 4 abridged unit classes, each with a deletion that removed most of the spacer and 12–76 bp of the coding sequence. Each abridged type lacks at least 1 of the conserved elements involved in transcription of the 5S gene, and so appear to be nonfunctional. Network analysis revealed that the abridged units are evolving in the same manner as the full-length versions.Key words: 5S rDNA, Beta vulgaris subsp. maritima, network analysis, sea beet.

The 5S rRNA gene diversity in Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen, and Baum (Poaceae: Triticeae): Possible contribution of the H genome to the origin of Kengyilia

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 79-85 ◽  
Author(s):  
Bernard R Baum ◽  
L Grant Bailey
Keyword(s):  
Gene Diversity ◽  
5S Rdna ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
5S Dna ◽  
5S Rrna Gene ◽  
Polymerase Chain

Fifty-three units of 5S rDNA sequences from five accessions of Kengyilia rigidula, a member of the tribe Triticeae that also includes wheat, barley, rye, and their wild relatives, have been amplified by the polymerase chain reaction (PCR), cloned, and sequenced. The genome of K. rigidula consists of three haplomes, St, P, and Y. An evaluation of the aligned sequences of the diverse 53 different 5S DNA units yielded three 5S-unit classes. One unit class, Long S1, was assignable to the St haplome, one unit class, the Long P1, was assignable to the P haplome, and a third unit class, Long H1, was assignable to the H haplome. The last was expected to be assignable to the Y haplome, based on previous knowledge. Evolutionary scenarios are put forward to explain this finding. Among those possibilities is that the number of copies of units assignable to the Y haplome is very small and difficult to detect. Short units, reported earlier in K. alatavica, were not found in K. rigidula. Key words: 5S RNA gene, genomes, Triticeae, 5S DNA unit classes.

scholarly journals A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Dna Markers ◽  
5S Rdna ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Species Specific ◽  
Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

The 5S rRNA gene in sea barley (Hordeum marinum Hudson sensu lato): sequence variation among repeat units and relationship to the X haplome in barley (Hordeum)

Genome ◽  
1998 ◽  
Vol 41 (5) ◽  
pp. 652-661 ◽  
Author(s):  
Bernard R Baum ◽  
Douglas A Johnson
Keyword(s):  
Sequence Variation ◽  
Current Knowledge ◽  
Cladistic Analysis ◽  
5S Rdna ◽  
The Other ◽  
Rrna Gene ◽  
Repeat Units ◽  
Unit Classes ◽  
Unit Class ◽  
5S Rrna Gene

We have investigated the molecular diversity of the 5S rDNA units in sea barley, comprising Hordeum marinum and Hordeum geniculatum. Although we were unable to detect "short" units after screening of 639 clones, we found two unit classes, one 602-607 bp long and the other 507-512 bp long. We classify the shortest unit class of the two as belonging to the "long H1" unit class, identified in previous papers. The longest unit class is not similar to any unit class so far identified, and is therefore unique. It was coined by us as the "long X1," to reflect the X haplome. We present a summary of all the unit classes so far described in Hordeum. We carried out a cladistic analysis, based on the "long H1" (orthologous) sequences, that included H. vulgare, H. spontaneum, H. bulbosum, H. marinum, H. geniculatum, and H. bogdanii. As a result, the first three grouped in one clade, and the other three in the other clade, with the latter clade being more isolated. These results reflect current knowledge of relationships based on morphology, cytology, and genome analysis. Furthermore, the sequences from the 5S unit classes may be potentially useful as DNA probes for genomic identification and genetic transfer in the Triticeae.Key words: 5S rDNA, genomes, X haplome, sea barley, Triticeae.

Construction of a Full-Length Murine Proα2(I) Collagen cDNA by the Polymerase Chain Reaction

1991 ◽  
Vol 97 (6) ◽  
pp. 980-984 ◽  
Author(s):  
Charlotte L Phillips ◽  
Laura W Lever ◽  
Sheldon R Pinnell ◽  
Leigh D Quarles ◽  
Richard J Wenstrup
Keyword(s):  
Polymerase Chain Reaction ◽  
Full Length ◽  
Chain Reaction ◽  
Polymerase Chain

The 5S rRNA gene in wall barley (Hordeum murinum L. sensu lato): Sequence variation among repeat units and relationship to the Y haplome in the genus Hordeum (Poaceae: Triticeae)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 854-866 ◽  
Author(s):  
Bernard R Baum ◽  
Douglas A Johnson
Keyword(s):  
Current Model ◽  
5S Rdna ◽  
Rrna Gene ◽  
Sequence Information ◽  
Rdna Unit ◽  
Repeat Units ◽  
Unit Classes ◽  
Unit Class ◽  
Hordeum Murinum ◽  
Cladistic Analyses

The molecular diversity of the 5S rDNA units in 13 accessions of wall barley, which include Hordeum murinum, H. leporinum, and H. glaucum, is reported. Our analyses, based on 54 sequenced clones, indicate the presence of two sequence classes not previously seen in other barley species; namely, the long Y1 unit class and the short Y1 unit class. In addition, the accumulation of new sequence information has allowed us to refine previous groups. Using these new results, along with previously published work, we present a summary of all the unit classes described to date and potential correspondences between 5S rDNA unit classes and haplomes identified previously. In H. murinum, we found the long H1 and long X2 unit classes, and in one of six accessions referable to H. glaucum we found the unique short Y1 unit class. Our cladistic analyses, using orthologous sequences, provide support for the current model for the relationships among several species within the Triticeae.Key words: 5S rDNA, Y haplome, genomes, wall barley, Triticeae.

scholarly journals Identification of β-Glucosidase Aggregating Factor (BGAF) and Mapping of BGAF Binding Regions on Maize β-Glucosidase

2000 ◽  
Vol 276 (15) ◽  
pp. 11895-11901 ◽  
Author(s):  
David J. Blanchard ◽  
Muzaffer Cicek ◽  
Jialun Chen ◽  
Asim Esen
Keyword(s):  
Null Allele ◽  
Terminal Region ◽  
Binding Assays ◽  
Terminal Sequence ◽  
Chain Reaction ◽  
Chimeric Enzymes ◽  
Repeat Units ◽  
Maize Genotypes ◽  
Polymerase Chain ◽  
A Site

In certain maize genotypes (nulls), β-glucosidase does not enter the gel and therefore cannot be detected on zymograms. Such genotypes were initially thought to be homozygous for a null allele at theglu1gene. We have shown that a β-glucosidase aggregating factor (BGAF) is responsible for the null phenotype, and it specifically interacts with maize β-glucosidases and forms large insoluble aggregates. To understand the mechanism of the β-glucosidase-BGAF interaction, we constructed chimeric enzymes by domain swapping between the maize β-glucosidase isozymes Glu1 and Gu2, to which BGAF binds, and the sorghum β-glucosidase (dhurrinase) isozyme Dhr1, to which BGAF does not bind. The results of binding assays with 12 different chimeric enzymes showed that an N-terminal region (Glu50-Val145) and an extreme C-terminal region (Phe466-Ala512) together form the BGAF binding site on the enzyme surface. In addition, we purified BGAF, determined its N-terminal sequence, amplified the BGAF cDNA by reverse transcriptase-polymerase chain reaction, expressed it inEscherichia coli, and showed that it encodes a protein whose binding and immunological properties are identical to the native BGAF isolated from maize tissues. A data base search revealed that BGAF is a member of the jasmonite-induced protein family. Interestingly, the deduced BGAF sequence contained an octapeptide sequence (G(P/R)WGGSGG) repeated twice. Each of these repeat units is postulated to be involved in forming a site for binding to maize β-glucosidases and thus provides a plausible explanation for the divalent function of BGAF predicted from binding assays.

Toward Understanding the Function of Amelogenin Using Transgenic Mice

1996 ◽  
Vol 10 (2) ◽  
pp. 208-214 ◽  
Author(s):  
K. Ibaraki-O'Connor ◽  
K. Nakata ◽  
M.F. Young
Keyword(s):  
Southern Blotting ◽  
Signal Sequence ◽  
Transgenic Animals ◽  
Full Length ◽  
Pcr Analysis ◽  
Coding Region ◽  
Chain Reaction ◽  
Mammalian Expression ◽  
Ectopic Production ◽  
Polymerase Chain

The purpose of this study was to establish transgenic mouse lines as a tool to investigate the function of amelogenin during mineralization by causing ectopic production of amelogenin and studying its effect. The mouse amelogenin (mAme) was cloned from a 16-day-old whole mouse embryo cDNA library and was determined to be "full-length" mouse amelogenin (with a complete coding region) by comparison with the mouse amelogenin reported previously by Snead et al. (1985) and Lau et al. (1992). The overexpression construct contained: (1) the rat osteocalcin (OC) promoter (1.8 kb); (2) the adenovirus splicing casettes, including introgenic (Int) sequence (0.3 kb); (3) the full-length mAme cDNA (0.8 kb); and (4) the polyadenylation signal sequence from the pSG5 mammalian expression vector. Both Southern blotting and polymerase chain-reaction (PCR) analyses were performed, by means of a specific probe and a pair of oligodeoxynucleotides to OclntmAme(A)+, respectively. The animals which showed transgene-positive in both analyses were further used to establish F1 animals. Heterozygocity was confirmed with F1 animals by PCR analysis of DNA from the F0 x FVB/N pups. Three independent transgenic F1 heterozygous lines (640t, 706t, and 708t) have now been established. The generation of F2 homozygous lines is under way. The heterozygous transgenic animals are currently being analyzed for alterations in the morphology and structure of various bone tissues.

scholarly journals Full-Length Sequence of Mouse Acupuncture-Induced 1-L (Aig1l) Gene Including Its Transcriptional Start Site

2011 ◽  
Vol 2011 ◽  
pp. 1-7
Author(s):  
Mika Ohta ◽  
Aki Sugano ◽  
Shuji Goto ◽  
Surini Yusoff ◽  
Yushi Hirota ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Polymerase Chain Reaction ◽  
Tissue Distribution ◽  
Cdna Sequence ◽  
Transcriptional Start Site ◽  
Full Length ◽  
Start Site ◽  
Chain Reaction ◽  
Polymerase Chain

We have been investigating the molecular efficacy of electroacupuncture (EA), which is one type of acupuncture therapy. In our previous molecular biological study of acupuncture, we found an EA-induced gene, named acupuncture-induced 1-L (Aig1l), in mouse skeletal muscle. The aims of this study consisted of identification of the full-length cDNA sequence ofAig1lincluding the transcriptional start site, determination of the tissue distribution ofAig1land analysis of the effect of EA onAig1lgene expression. We determined the complete cDNA sequence including the transcriptional start site via cDNA cloning with the cap site hunting method. We then analyzed the tissue distribution ofAig1lby means of northern blot analysis and real-time quantitative polymerase chain reaction. We used the semiquantitative reverse transcriptase-polymerase chain reaction to examine the effect of EA onAig1lgene expression. Our results showed that the complete cDNA sequence ofAig1lwas 6073 bp long, and the putative protein consisted of 962 amino acids. All seven tissues that we analyzed expressed theAig1lgene. In skeletal muscle, EA induced expression of theAig1lgene, with high expression observed after 3 hours of EA. Our findings thus suggest that theAig1lgene may play a key role in the molecular mechanisms of EA efficacy.

scholarly journals miR-206 Promotes Cancer Progression by Targeting Full-Length Neurokinin-1 Receptor in Breast Cancer

2019 ◽  
Vol 18 ◽  
pp. 153303381987516 ◽  
Author(s):  
Yu Zhou ◽  
Meng Wang ◽  
Yingna Tong ◽  
Xiaobin Liu ◽  
Lufang Zhang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Full Length ◽  
Luciferase Reporter ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Neurokinin 1

Substance P plays a pivotal role in human cancer development and progression by binding to its receptor, neurokinin-1. Neurokinin-1 has 2 isoforms: full-length neurokinin-1 and truncated neurokinin-1, the latter lacking the cytoplasmic terminal 96-amino acid residues of the full-length protein. We have identified 3 candidate miR-206 target sites within the 3′-untranslated region of the full-length neurokinin-1 gene from bioinformatics database searches. In the present study, real-time quantitative polymerase chain reaction was performed to quantify the expression of miR-206, and the expression of neurokinin-1 and full-length neurokinin-1 was detected by immunohistochemistry in 82 clinical cases of breast cancer and paired adjacent normal tissues. The miR-206 target gene was demonstrated by using a dual-luciferase reporter assay, quantitative real-time polymerase chain reaction, and Western blotting. Transwell migration and invasion, colony formation, and proliferation assays were performed to evaluate the effects of miR-206 expression on various aspects of breast cancer cell behavior in vitro. We showed that miR-206 expression is upregulated in breast cancer cell lines and breast cancer tissues when compared to that in adjacent normal tissues, and full-length neurokinin-1 expression inversely correlates with Tumor Lymph Node Metastasis (TNM) stage and lymph node metastasis. Western blotting, quantitative real-time polymerase chain reaction, and dual-luciferase reporter assays demonstrated that miR-206 binds the 3′-untranslated region of full-length neurokinin-1 messenger RNA, regulating protein expression. We showed that the overexpression of miR-206 promotes breast cancer cell invasion, migration, proliferation, and colony formation in vitro. The present study furthers the current understanding of the mechanisms underlying breast cancer pathogenesis and may be useful for the development of novel targeted therapies.

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