Complementary DNA – 25S ribosomal RNA hybridization: an improved method for phylogenetic studies

1983 ◽  
Vol 29 (5) ◽  
pp. 546-551 ◽  
Author(s):  
Siavash Baharaeen ◽  
Ulrich Melcher ◽  
Helen S. Vishniac

In a new combination of techniques for ribosomal RNA hybridization, complementary DNA is synthesized on 25S ribosomal RNA fragments generated by mild alkali treatment, by the enzymatic addition of polyadenylic acid tails, hybridization of these tails with oligo deoxyribosylthymine, and reverse transcription in the presence of tritiated TTP. Hybridization reactions are performed in solution. Heteroduplexes are collected on diethylaminoethylcellulose filter discs after treatment with S1 nuclease. The problems presented by secondary rRNA structure are avoided by denaturation before reverse transcription and before hybridization. The high percentage of duplex formation (78–87%), the low standard deviation of relative binding (averaging ± 1.00330% relative binding), and small differences in reciprocal hybridizations (1.71–5.18% relative binding), as well as the elimination of complications resulting from differences in the number of rRNA cistrons in nuclear DNA, make this method preferable to the membrane-filter technique commonly used in phylogenetic classifications based on the homology of large rRNAs.

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4171-4171 ◽  
Author(s):  
Rashidah M. Green ◽  
John F. Tisdale ◽  
Naoya Uchida

Abstract Abstract 4171 Hematopoietic stem cell (HSC)-targeted gene therapy approaches utilizing HIV1-based lentiviral vectors is a promising modality for a number of inherited and acquired disorders affecting the blood. Unlike cell lines and murine HSCs, human HSCs demonstrate lower transduction efficiency with HIV1 vectors, potentially limiting this approach. Lentiviral transduction requires four essential steps: (1) internalization, (2) reverse transcription, (3) nuclear transport, and (4) integration into genomic DNA. In this study, we sought to evaluate which step limits transduction of human CD34+ cells with HIV1 vectors. We transduced HeLa cells and human CD34+ cells with a self-inactivating-HIV1 vector at low and a 10-fold-higher multiplicity of infection (MOI) (MOI 0.5 vs. MOI 5 for HeLa cells and MOI 5 vs. MOI 50 in CD34+ cells, respectively) and assayed each of the four steps based upon the rationale that if a given step was not rate limiting, a 10-fold-greater value would be obtained at the 10-fold-higher MOI. Amounts of the vectors were determined by real time PCR using RNA and DNA samples extracted from the transduced cells over time. The ratios of vector genome amounts at high MOI to amounts at low MOI were compared between CD34+ cells and HeLa cells to determine whether there was a limiting step for CD34+ cell transduction. To evaluate RNA internalization, we determined relative amounts of vector RNA in the cells at 5 min, 10 min, 30 min, and 60 min after transduction. Among HeLa cells, relative amounts of vector RNA showed a rapid increase and then plateaued at 30 min after transduction, while in the CD34+ cells, relative amounts of vector RNA increased gradually over 60 min. When we calculated the ratios of vector RNA amounts at high MOI to low MOI for each type of cell, we observed similar ratios when comparing HeLa to CD34+ cells at 60 min after transduction. These data suggest that despite slower internalization of vector RNA in CD34+ cells, it is not a limiting step in lentiviral transduction. To evaluate reverse transcription, nuclear transport, and integration; we determined relative amounts of vector DNA at 2 hrs, 4 hrs, 6 hrs, 12 hrs, 24 hrs, 2 days, 3 days, 6 days, and 10 days after transduction. We detected similar patterns of relative vector DNA in both Hela and CD34+ cells: as their relative amounts increased, they reached a peak at 24 hrs (reverse transcription), decreased, and then reached a plateau at 2–3 days after transduction (nuclear transport and integration). CD34+ cells showed higher ratios of vector DNA at high MOI to low MOI at 2–24 hrs, similar ratios at 2 days, and lower ratios at 3–10 days, compared to HeLa cells (Figure). These data suggest that transduction of human CD34+ cells has a limitation around 2 days after vector exposure corresponding to nuclear transport or integration. To evaluate nuclear transport for both types of cells, we compared the relative amounts of vector DNA to total DNA and nuclear DNA. Nuclear DNA was extracted from the nuclear fractions of transduced cells which had been isolated by a sucrose gradient. In both cells, the nuclear DNA had tendencies to show lower amounts of vector DNA at 6–48 hrs after transduction and similar or higher amounts of vector DNA at 2–7 days, compared to the total DNA. These data suggest that vector DNA is transported to the nucleus in about 2–3 days. Taken together, these data suggest that nuclear transport is a limiting step in lentiviral transduction of human CD34+ cells. We hypothesized that transduction efficiency for human CD34+ cells might increase under conditions that induce greater cell expansion, since dividing cells do not have intact nuclear membranes. We compared relative amounts of vector DNA in human CD34+ cells transduced in X-VIVO10 medium (standard) and StemlineII medium (greater expansion) at 12 hrs, 24 hrs, 2 days, 3 days, 5 days, and 7 days after transduction. StemlineII exposed cells showed higher amounts of vector DNA, compared to X-VIVO10, at all time points except 24 hrs. The data suggest that StemlineII increases transduction efficiency for human CD34+ cells by increasing nuclear transport. In summary, we demonstrate that nuclear transport is a limiting step in lentiviral transduction of human CD34+ cells and that StemlineII medium could increase transduction efficiency. These data are helpful for the design of strategies to improve upon lentiviral transduction for human CD34+ cells by improving nuclear transport. Disclosures: No relevant conflicts of interest to declare.


1978 ◽  
Vol 31 (1) ◽  
pp. 25 ◽  
Author(s):  
Robert H Symons

The requirement for purified plant viral RNAs for sequence characterization by hybridization analysis using complementary DNA led to the development of a routine two-step procedure for their purification. The method was worked out using Escherichia coli ribosomal RNAs and then applied to four plant viral RNAs, all of which contain four major RNA components. The first of the two steps involves the electrophoresis of native RNA on 2�8 % polyacrylamide slab gels, the location of the RNA bands by brief staining and the recovery of the RNA from each gel band by electrophoretic elution. The eluted RNA, concentrated by ethanol precipitation, was then run on a second gel after a denaturation step to release nicked and aggregated RNA fragments. Each RNA band was again located by staining and recovered by electrophoretic elution and ethanol precipitation. The 16-S and 23-S ribosomal RNAs and the plant viral RNAs were obtained in overall yields of 40 and 8-16 % respectively. RNAs so purified have been successfully used for the preparation of complementary DNA by two different methods.


MycoKeys ◽  
2020 ◽  
Vol 68 ◽  
pp. 115-135
Author(s):  
Rui Du ◽  
Fang Wu ◽  
Genevieve M. Gate ◽  
Yu-Cheng Dai ◽  
Xue-Mei Tian

Sidera is a polypore genus with white to cream or buff basidiomata, whose species in Hymenochaetales are poorly known. We study the phylogeny and diversity of Sidera based on our recent collections from tropic and subtropic Asian-Pacific regions. Phylogenetic analyses based on the internal transcribed spacer (ITS) and nuclear large subunit (nLSU) ribosomal RNA gene regions indicate that ten terminal lineages are well supported within Sidera. Based on morphological examination and phylogeny, four new species, viz. Sidera minutissima, S. parallela, S. srilankensis and S. tenuis are described, and a new combination, Sidera minutipora, is proposed. All these species are illustrated. Sidera minutissima is characterized by tiny basidiomata with bluish pores when fresh, generative hyphae dominating at the dissepiment edges, the presence of cystidioles, and allantoid basidiospores measuring 3.8–4.4 × 0.9–1.3 μm. Sidera parallela differs from other poroid species in the genus by having parallel tramal hyphae in combination with lunate basidiospores measuring 2.8–3.3 × 0.9–1.2 μm. Sidera srilankensis have generative and skeletal hyphae co-dominating at the dissepiment edges, and lunate basidiospores measuring 3.5–4 × 1–1.3 μm. Sidera tenuis is distinguished by small pores (8–10 per mm) and relatively long allantoid basidiospores measuring 4.2–5 × 0.8–1 μm. Sidera minutipora is characterized by buff to olivaceous buff basidiomata when dry, 5–7 pores per mm, rosette-like crystals rare, and allantoid basidiospores measuring 3.7–4.3 × 1–1.3 μm. An identification key to all accepted species is provided.


Phytotaxa ◽  
2018 ◽  
Vol 355 (1) ◽  
pp. 1 ◽  
Author(s):  
CHUN L. LI ◽  
ANDRZEJ WITKOWSKI ◽  
MATT P. ASHWORTH ◽  
PRZEMYSŁAW DĄBEK ◽  
SHINYA SATO ◽  
...  

Dozens of monoclonal cultures of small-celled araphid diatoms from brackish or marine habitats worldwide were analyzed using morphological observations (light and electron microscopy) and molecular data (nuclear-encoded small subunit ribosomal RNA and chloroplast encoded rbcL and psbC). As a result, we established one new genus Gedaniella, distinguished by a shared morphological character (occlusions of branched volae, projecting from the apical sides of the areolae) and some molecular data, including five new species: G. alfred-wegeneri, G. arenaria, G. boltonii, G. panicellus, G. paucistriata and three new combinations: G. flavovirens, G. guenter-grassii and G. mutabilis. Additionally we describe eleven novel species within the existing genus Serratifera: S. andersonii, S. brevis, S. clavata, S. corallina, S. namibica, S. nosybeana, S. parkii, S. punctata, S. rhombica, S. sourniae, S. takanoi and one new combination S. opephoroides. Furthermore, five new taxa or combinations were described within other genera: such as Cratericulifera crinigera, Nanofrustulum wachnickianum, Plagiostriata baltica, Pseudostaurosira madagascariensis and Stauroforma rinceana. Detailed descriptions for established species are also provided: Nanofrustulum shiloi, Opephora pacifica and Pseudostaurosira elliptica. This study strongly suggests that the complete biodiversity of small-celled araphids is still far from known, and many species currently placed in Opephora and Pseudostaurosira need to be further re-investigated.


Virology ◽  
2019 ◽  
Vol 528 ◽  
pp. 181-197 ◽  
Author(s):  
Joseph R. Fauver ◽  
Shamima Akter ◽  
Aldo Ivan Ortega Morales ◽  
William C. Black ◽  
Americo D. Rodriguez ◽  
...  

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