Detection and quantification of microbial DNA sequences in soil by Southern and dot/slot blot hybridization

Author(s):  
Carsten S. Jacobsen
Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 944-953 ◽  
Author(s):  
Xinping Zhao ◽  
Gary Kochert

We have characterized a repeated DNA sequence (RTL 122) from rice (Oryza sauva L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL 122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15–20 kb. We characterized three bacteriophage lambda clones that contained the RTL 122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.Key words: rice, Oryza, repeated sequences, DNA fingerprinting, coordinated evolution.


Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 428-432 ◽  
Author(s):  
P. Besse ◽  
C. L. McIntyre ◽  
D. M. Burner ◽  
C. G. de Almeida

The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum × Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum × Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.Key words: slot blot, Erianthus, genomic DNA, Saccharum, sugarcane.


BioTechniques ◽  
2001 ◽  
Vol 30 (3) ◽  
pp. 680-685 ◽  
Author(s):  
Bruce Budowle ◽  
William R. Hudlow ◽  
Steven B. Lee ◽  
Leonard Klevan

1995 ◽  
Vol 7 (5) ◽  
pp. 1053 ◽  
Author(s):  
TE Spencer ◽  
GH Graf ◽  
FW Bazer

This study determined effects of day of oestrous cycle and early pregnancy on sulfated glycoprotein-1 (SGP-1) expression in ovine endometrium. A 364-bp clone of the ovine SGP-1 mRNA was amplified from reverse transcribed Day-15 cyclic endometrial mRNA using the polymerase chain reaction (PCR) and primers specific for the rat SGP-1 mRNA sequence. Nucleotide sequence of the ovine SGP-1 cDNA shared significant identity with rat SGP-1 and human prosaposin. Ewes (n = 40) were hysterectomized on either Day 1, 6, 11, 13 or 15 of the oestrous cycle or on Day 11, 13, 15, 17 or 25 of early pregnancy. Total cellular RNA was isolated from endometrium and subjected to Northern and slot blot hybridization analyses using an antisense cRNA probe transcribed from the ovine SGP-1 cDNA clone. A single 2.6-kb mRNA transcript was detected by Northern hybridization analyses. Slot blot hybridization analyses indicated that steady-state levels of endometrial SGP-1 mRNA varied during the oestrous cycle (cubic, P < 0.02) and increased between Day 11 and Day 25 of early pregnancy (linear, P < 0.01). On Days 11, 13 and 15, endometrial SGP-1 mRNA levels were greater in pregnant ewes than in cyclic ewes (day x pregnancy status, P < 0.01). Immunohistochemical localization of SGP-1 in uterine tissues with rabbit anti-rat SGP-1 antibody revealed intense immunoreactivity associated primarily with the endometrial epithelium. These results indicate that the ovine endometrium expresses SGP-1, a prosaposin, and that SGP-1 expression varies during the oestrous cycle and is enhanced by the conceptus. The presence of SGP-1 in the endometrium suggests intracellular and extracellular roles for this protein in glycosphingolipid metabolism or transport in the uterine environment.


2000 ◽  
Vol 38 (4) ◽  
pp. 207-212 ◽  
Author(s):  
Juergen Loeffler ◽  
Holger Hebart ◽  
Stella Magga ◽  
Diethard Schmidt ◽  
Lena Klingspor ◽  
...  

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