scholarly journals THE USE OF RESTRICTION FRAGMENT LENGTH POLYMORPHISMS AND DNA DUPLICATIONS TO STUDY THE ORGANIZATION OF THE ACTIN MULTIGENE FAMILY IN DICTYOSTELIUM DISCOIDEUM

Genetics ◽  
1986 ◽  
Vol 112 (1) ◽  
pp. 27-42
Author(s):  
Dennis L Welker ◽  
K Peter Hirth ◽  
Patricia Romans ◽  
Angelika Noegel ◽  
Richard A Firtel ◽  
...  
Keyword(s):  
Linkage Group ◽  
Dictyostelium Discoideum ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Gene Copy ◽  
Actin Genes ◽  
Group I ◽  
Group Ii ◽  
Cloned Gene ◽  
Restriction Fragment Length

ABSTRACT The techniques of restriction fragment length polymorphism analysis and examination of gene copy number in duplication-bearing Dictyostelium discoideum strains have been used to map four actin genes of the wild-type strain NC4 to specific linkage groups. In part, this was accomplished by identification of restriction fragments corresponding to particular cloned actin genes using genespecific probes from unique sequence 5' and 3' untranslated regions. Cloned gene Actin 8 (designation act-8) maps to linkage group I; Actins 12 (act-12) and M6 (actM6) to linkage group II. An uncloned gene (act-100) also maps to linkage group II in the same region as actM6, as defined by a chromosomal duplication. From analysis of other wild isolates of D. discoideum, it was determined that in these isolates at least two actin genes map to linkage group I and at least four map to linkage group II. These results demonstrate the utility of molecular techniques in genetic analysis of Dictyostelium, particularly for developmentally regulated genes that have been cloned but that have no identified mutant phenotypes.

scholarly journals The discoidin I gene family of Dictyostelium discoideum is linked to genes regulating its expression.

Genetics ◽  
1988 ◽  
Vol 119 (3) ◽  
pp. 571-578
Author(s):  
D L Welker
Keyword(s):  
Linkage Group ◽  
Gene Family ◽  
Dictyostelium Discoideum ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Regulatory Element ◽  
Cellular Slime Mold ◽  
Regulatory Loci ◽  
Group Ii ◽  
Restriction Fragment Length

Abstract The discoidin I protein has been studied extensively as a marker of early development in the cellular slime mold Dictyostelium discoideum. However, like most other developmentally regulated proteins in this system, no reliable information was available on the linkage of the discoidin genes to other known genes. Analysis of the linkage of the discoidin I genes by use of restriction fragment length polymorphisms revealed that all three discoidin I genes as well as a pseudogene are located on linkage group II. This evidence is consistent with the discoidin I genes forming a gene cluster that may be under the control of a single regulatory element. The discoidin I genes are linked to three genetic loci (disA, motA, daxA) that affect the expression of the discoidin I protein. Linkage of the gene family members to regulatory loci may be important in the coordinate maintenance of the gene family and regulatory loci. A duplication affecting the entire discoidin gene family is also linked to group II; this appears to be a small tandem duplication. This duplication was mapped using a DNA polymorphism generated by insertion of the Tdd-3 mobile genetic element into a Tdd-2 element flanking the gamma gene. A probe for Tdd-2 identified a restriction fragment length polymorphism in strain AX3K that was consistent with generation by a previously proposed Tdd-3 insertion event. A putative duplication or rearrangement of a second Tdd-2 element on linkage group IV of strain AX3K was also identified. This is the first linkage information available for mobile genetic elements in D. discoideum.

scholarly journals Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis

2004 ◽  
Vol 70 (11) ◽  
pp. 6580-6586 ◽  
Author(s):  
Takuya Miyamoto ◽  
Makoto Kawahara ◽  
Kiwamu Minamisawa
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Miscanthus Sinensis ◽  
Nitrogen Fixing ◽  
Probable Number ◽  
Group Ii ◽  
Restriction Fragment Length

ABSTRACT Anaerobic nitrogen-fixing consortia consisting of N2-fixing clostridia and diverse nondiazotrophic bacteria were previously isolated from various gramineous plants (K. Minamisawa, K. Nishioka, T. Miyaki, B. Ye, T. Miyamoto, M. You, A. Saito, M. Saito, W. Barraquio, N. Teaumroong, T. Sein, and T. Tadashi, Appl. Environ. Microbiol. 70:3096-3102, 2004). For this work, clostridial populations and their phylogenetic structures in a stand of the grass Miscanthus sinensis in Japan were assessed by a 16S rRNA gene-targeted terminal restriction fragment length polymorphism (TRFLP) analysis combined with most-probable-number (MPN) counts. PCR primers and restriction enzymes were optimized for analyses of the plant clostridia. Clostridia were detected in strongly surface-sterilized leaves, stems, and roots of the plants at approximately 104 to 105 cells/g of fresh weight; they made up a large proportion of N2-fixing bacterial populations, as determined by MPN counts associated with an acetylene reduction assay. Phylogenetic grouping by MPN-TRFLP analysis revealed that the clostridial populations belonged to group II of cluster XIVa and groups IV and V of cluster I; this result was supported by a culture-independent TRFLP analysis using direct DNA extraction from plants. When phylogenetic populations from M. sinensis and the soil around the plants were compared, group II clostridia were found to exist exclusively in M. sinensis.

scholarly journals Rapid Identification and Differentiation of the Soft Rot Erwinias by 16S-23S Intergenic Transcribed Spacer-PCR and Restriction Fragment Length Polymorphism Analyses

2001 ◽  
Vol 67 (9) ◽  
pp. 4070-4076 ◽  
Author(s):  
I. K. Toth ◽  
A. O. Avrova ◽  
L. J. Hyman
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Soft Rot ◽  
Group Iii ◽  
Group I ◽  
Its Pcr ◽  
Restriction Fragment Length

ABSTRACT Current identification methods for the soft rot erwinias are both imprecise and time-consuming. We have used the 16S-23S rRNA intergenic transcribed spacer (ITS) to aid in their identification. Analysis by ITS-PCR and ITS-restriction fragment length polymorphism was found to be a simple, precise, and rapid method compared to current molecular and phenotypic techniques. The ITS was amplified fromErwinia and other genera using universal PCR primers. After PCR, the banding patterns generated allowed the soft rot erwinias to be differentiated from all other Erwinia and non-Erwinia species and placed into one of three groups (I to III). Group I comprised all Erwinia carotovorasubsp. atroseptica and subsp.betavasculorum isolates. Group II comprised allE. carotovora subsp. carotovora,subsp. odorifera, and subsp. wasabiae andE. cacticida isolates, and group III comprised allE. chrysanthemi isolates. To increase the level of discrimination further, the ITS-PCR products were digested with one of two restriction enzymes. Digestion with CfoI identified E. carotovora subsp.atroseptica and subsp. betavasculorum(group I) and E. chrysanthemi (group III) isolates, while digestion with RsaI identified E. carotovora subsp. wasabiae, subsp. carotovora, and subsp.odorifera/carotovora and E. cacticida isolates (group II). In the latter case, it was necessary to distinguishE. carotovora subsp. odorifera and subsp. carotovora using the α-methyl glucoside test. Sixty suspected soft rot erwinia isolates from Australia were identified as E. carotovora subsp.atroseptica, E. chrysanthemi,E. carotovora subsp. carotovora, and non-soft rot species. Ten “atypical” E. carotovora subsp. atroseptica isolates were identified as E. carotovora subsp.atroseptica, subsp. carotovora, and subsp. betavasculorum and non-soft rot species, and two “atypical” E. carotovora subsp.carotovora isolates were identified as E. carotovora subsp. carotovora and subsp.atroseptica.

Mapping flagellar genes in Chlamydomonas using restriction fragment length polymorphisms.

Genetics ◽  
1988 ◽  
Vol 120 (1) ◽  
pp. 109-122
Author(s):  
L P Ranum ◽  
M D Thompson ◽  
J A Schloss ◽  
P A Lefebvre ◽  
C D Silflow
Keyword(s):  
Molecular Markers ◽  
Linkage Group ◽  
Restriction Fragment ◽  
Cdna Clone ◽  
Fragment Length ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Gene Maps ◽  
Flagellar Genes ◽  
Restriction Fragment Length

Abstract To correlate cloned nuclear DNA sequences with previously characterized mutations in Chlamydomonas and, to gain insight into the organization of its nuclear genome, we have begun to map molecular markers using restriction fragment length polymorphisms (RFLPs). A Chlamydomonas reinhardtii strain (CC-29) containing phenotypic markers on nine of the 19 linkage groups was crossed to the interfertile species Chlamydomonas smithii. DNA from each member of 22 randomly selected tetrads was analyzed for the segregation of RFLPs associated with cloned genes detected by hybridization with radioactive DNA probes. The current set of markers allows the detection of linkage to new molecular markers over approximately 54% of the existing genetic map. This study focused on mapping cloned flagellar genes and genes whose transcripts accumulate after deflagellation. Twelve different molecular clones have been assigned to seven linkage groups. The alpha-1 tubulin gene maps to linkage group III and is linked to the genomic sequence homologous to pcf6-100, a cDNA clone whose corresponding transcript accumulates after deflagellation. The alpha-2 tubulin gene maps to linkage group IV. The two beta-tubulin genes are linked, with the beta-1 gene being approximately 12 cM more distal from the centromere than the beta-2 gene. A clone corresponding to a 73-kD dynein protein maps to the opposite arm of the same linkage group. The gene corresponding to the cDNA clone pcf6-187, whose mRNA accumulates after deflagellation, maps very close to the tightly linked pf-26 and pf-1 mutations on linkage group V.

Adenomyosis: genetics of estrogen metabolism

2019 ◽  
Vol 37 (2) ◽  
Author(s):  
Natalia Artymuk ◽  
Olga Zotova ◽  
Lyudmila Gulyaeva
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Estrogen Metabolism ◽  
Control Group ◽  
Inclusion Criteria ◽  
Group I ◽  
Restriction Fragment Length

Abstract Background To analyze the allelic variants of genes of enzymes involved in estrogen metabolism: CYP1A1, CYP1A2, CYP19 and SULT1A1 using polymerase chain reaction-restriction fragment length polymorphism-restriction fragment length polymorphism (PCR-RFLP) analysis of women with histologically confirmed adenomyosis and women without proliferative diseases of pelvic organs was performed. We studied the following polymorphisms: CYP1A1 M1, T264 → C transition in the 3′-noncoding region; CYP1A2*1F, C734 → A transversion in CYP1A2 gene; C → T transition (Arg264Cys) in exon 7 of CYP19; SULT1A1*2, G638 → A transition (Arg213His) in the SULT1A1 gene. Materials and methods The study included 804 patients. Group I (experimental group) consisted of 268 women with adenomyosis. Inclusion criteria were: histological verification of adenomyosis, consent of patients to participate in the study. Group II (control group) – 536 women without proliferative diseases of the uterus. Inclusion criteria were: lack of proliferative processes of the uterus histologically confirmed by ultrasound examination, patient’s consent to participate in the study. Results We found the significant association of C allele, T/C and C/C genotypes of the CYP1A1 gene (CYP1A1 M1 polymorphism), A allele, C/A and A/A genotypes of the CYP1A2 gene (CYP1A2*1F polymorphism) and the T allele, C/T and C/C genotypes of the CYP19 (Arg264Cys polymorphism) gene with the risk for adenomyosis. Conclusions Patients with adenomyosis had increased frequency of C allele, T/C and C/C genotypes of the CYP1A1 gene, A allele, C/A and A/A genotypes of the CYP1A2 gene and T allele and C/T and C/C genotypes of the CYP19 gene and, on the contrary, decreased frequency of the mutant allele and heterozygous and mutant homozygous genotype of the CYP1A2 gene compared to women without proliferative diseases of the uterus.

A Consensus Linkage Map for Sugi (Cryptomeria japonica) From Two Pedigrees, Based on Microsatellites and Expressed Sequence Tags

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1551-1568 ◽  
Author(s):  
Naoki Tani ◽  
Tomokazu Takahashi ◽  
Hiroyoshi Iwata ◽  
Yuzuru Mukai ◽  
Tokuko Ujino-Ihara ◽  
...  
Keyword(s):  
Linkage Group ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Dna Markers ◽  
Cryptomeria Japonica ◽  
Linkage Groups ◽  
Consensus Map ◽  
Length Polymorphisms ◽  
Cleaved Amplified Polymorphic Sequences ◽  
Restriction Fragment Length

Abstract A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.

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