African Journals On-line
African Journal of Biotechnology

Issues Available About the Journal

Volume 2, Number 5, May 2003
Contents

ABSTRACTS

 

Bioinformatic tools and guideline for PCR primer design

Kamel A. Abd-Elsalam

Molecular Markers Lab., Plant Pathology Research Institute, Agricultural Research Center, Orman 12619, Giza, Egypt

Corresponding author; Tel: 002 02 5724893, Fax: 002 02 4723146, E-mail: [email protected]

Accepted 28 April 2003

Abstract

Abstract: Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no product due to non-specific amplification and/or primer-dimer formation, which can become competitive enough to suppress product formation. There are several online tools devoted to serving molecular biologist design effective PCR primers. This review intends to provide a guide to choosing the most efficient way to design a new specific-primer by applying current publicly available links and Web services. Also, the purpose here is to provide general recommendations for the design and use of PCR primers.

Key words: Bio-computing, primer design, web-based resources.

 

 

Substrate Channelling and Energetics of Saccharomyces cerevisiae DSM 2155 Grown on Glucose in Fed-Batch Fermentation Process

Olusegun Peter Akinyemi1, Eriola Betiku2+*, and Bamidele Ogbe Solomon2

1Chemical and Polymer Engineering Department, Lagos State University, Lagos State, Nigeria.

2Chemical Engineering Department, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria.

*Corresponding author: E-mail: [email protected], Tel.: +49-531-6181-183, Fax: +49-531-6181-111

+Present address: German Research Centre for Biotechnology, Biochemical Engineering Division, Mascheroder Weg 1, D-38124, Braunschweig, Germany

Accepted 10 April, 2003.

Abstract

Abstract: Data collected during the high-cell-density cultivation of Saccharomyces cerevisiae DSM 2155 on glucose in a simulated five-phase feeding strategy of fed-batch process, executed on the Universal BIoprocess CONtrol (UBICON) system using 150L bioreactor over a period of 24h have been analysed. The consistency of the data set was checked using both the available electron and carbon balances. Estimates of the true energetic yields and cell maintenance requirements were obtained through the application of a multivariate statistical procedure known as covariate adjustment technique. A low value of maintenance coefficient, me = 0.004h-1, and a high average value of the true biomass energetic yield, hmax = 0.745, were obtained for the bioreactor system, which showed that the organism was in no danger of ethanol produced during this cultivation. A simple model for estimating the distribution of substrate consumed between the fermentative and the respiratory pathways in the oxido-reductive process was developed based on the respiratory quotient (RQ) values. The fraction of substrate consumed for respiratory metabolic activities (qsresp/qs) was virtually 1.0 for the first three phases of the feeding strategy, which accounted for the first sixteen hours of the 24h operation. This was an indication that ethanol formation was avoided during this period.

Key Words: Saccharomyces cerevisiae DSM 2155, available electron and carbon balances, fed-batch, respiratory quotient, true energetic yields, maintenance requirement.

 

 

Biodegradation of Bonny light crude oil in soil microcosm by some bacterial strains isolated from crude oil flow stations saver pits in Nigeria

A. I. Okoh

Department of Microbiology, Obafemi Awolowo University, Ile – Ife, Nigeria. E-mail: [email protected]; Tel: 234-803-7145687

Accepted 21 April 2003

Abstract

Abstract: In an effort at developing an active indigenous bacterial consortium that could be of relevance in bioremediation of petroleum contaminated systems in Nigeria, four hydrocarbon degrading bacteria strains were isolated. Partial sequencing of the 16S rDNA of the isolates suggests that they are all strains of Pseudomonas aeruginosa. Axenic cultures of the isolates biodegraded Bonny light crude oil in soil microcosm. Amount of crude oil biodegraded in 15 days ranged significantly (P < 0.05) from 4.9% to 29.6%. Degradation rates and specific growth rates varied significantly (P < 0.05) between 0.049 and 0.351 day-1 and 0.017 and 0.028 hour-1 respectively. Major peak components of the oil were reduced by between 6.5% and 70.6%. It would appear that oil degradation capability of axenic cultures of at least three of these isolates was not different from that of their consortium. Also, the multiple antibiotic resistance observed in the isolates is an important factor to consider in their eventual use in bioremediation exercises.

Key words: Crude oil, soil microcosm, biodegradation.

 

Genetic affinities of Fusarim spp. and their correlation with origin and pathogenicity

Mohmed S. Khalil1, Mohmed A. Abdel-Sattar2, Ibrahim N. Aly2, Kamel A. Abd-Elsalam1,3* and Joseph A. Verreet3

1Agricultural Research Center, Plant Pathology Research Institute, Giza, Egypt.

2Suez Canal University, Faculty of Agriculture, Ismailia, Egypt.

3Christian Albrechts Universität zu Kiel, Institut für Phytopathologie, Kiel, Germany

*Corresponding author; phone: (49 431) 880 2993, fax: (49 431) 880 1583, e-mail: [email protected]

Accepted 14 April, 2003

Abstract

Abstract: Random amplified polymorphic DNA (RAPD) analyses was used in combination with pathogenicity assays to study the taxonomic kinships among five Fusarium species. A total of 46 isolates of Fusarium spp. obtained from diseased cotton seedlings showing typical root rot and dampping-off symptoms were characterized. Of 10 primers tested, four primers produced polymorphic amplification patterns with taxon-specific bands, in addition to individual-specific bands. Genetic analysis indicated into 2 main clusters, with the minor cluster included all F. moniliforme and F. solani at the genetic similarity of GS=57.82%. The major cluster consisted of all F. oxysporum, F. avenaceum and F. chlamydosporum clustered at 71% similarity. There was no clear-cut relationship between clustering in the RAPD dendrogram, pathogenicity test and geographic origin of tested isolates. The results suggest that RAPD-PCR is a useful method for analysing genetic variation within and between Fusarium spp.

Key words: DNA-fingerprinting, Fusarium chlamydosporum, genetic homology, RAPD-PCR.  

 

 

Four gene introduction methods affect the shoot regeneration and localization of transgene expression in greenhouse stem explants and in vitro-grown chrysanthemum stem thin cell layers

J. A. Teixeira da Silva* and S. Fukai

Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, 761-0795, Japan

*Corresponding Author; E-mail: [email protected], Telfax: +81878910747

Accepted 18 April, 2003

Abstract

Abstract: Gene introduction method (GIM) affected shoot regeneration capacity (SRC) in standard and spray-type chrysanthemums. SRC was both cultivar and GIM-dependent in both in vitro and greenhouse stem explants, the former significantly higher than the latter. Sonication had an SRC-stimulating effect on in vitro explants. Other GIMs (Agrobacterium, biolistics, Agrolistics) had an SRC-inhibiting effect on greenhouse explants. Genotype-dependence of SRC was observed in both in vitro and greenhouse material. SRC is influenced by the explant and regeneration media, which should be modified if altered by the GIM. Shoots derived from all GIM treatments showed normal growth under in vitro and greenhouse conditions, and flowered normally. In addition, this study further shows that explant origin (in vitro versus greenhouse) and cultivar significantly affect the regeneration process, even when an optimized medium is utilized. The integration of the GUS transgene is also GIM-dependent, but in all cases is shown to occur in the venation.

Keywords: Agroinfection, biolistics, explant survival, regeneration, sonication.  

 

 

Molecular distribution of gypsy-like retrotransposons in cotton Gossypium Spp.

Essam A. Zaki1,y,* and Abdel Ghany A. Abdel Ghany2

1Genetic Engineering and Biotechnology Research Institute, GEBRI, Research Area, Borg El Arab, Post Code 21934, Alexandria

2Institute of Efficient Productivity, Zagazig University, Zagazig, Egypt.

*Corresponding author: Phone (765) 494-9837, Fax: (765) 496-1496, E-mail: [email protected].

yCurrent Address: Department of Biological Sciences, 1392 Lilly Hall of Life Sciences, West Lafayette, IN 47907-1392, USA.

Accepted 18 April, 2003

Abstract

Abstract: PCR primers specific for conserved domains of the reverse transcriptase (RT) genes of gypsy-like retrotransposons amplified their corresponding gene in two Gossypium barbadense cultivars. Analysis with the FASTA software showed a high DNA sequence homology to pine, gypsy LTR-retrotransposon. Using the PCR product as a hybridization probe, gypsy-like retrotransposons were detected in wild type species of Gossypium, suggesting that gypsy-like retrotransposons are present in the Gossypium genome. This supports the view that gypsy-like retrotransposons are major components of plant genomes. Our results suggest gypsy-like retrotransposons have played a fundamental role in the shaping and evolution of the Gossypium genome.

Key words: Gossypium, gypsy, polyploidy, retroelements, retrotransposons, retroviruses, reverse transcriptase.

 

 

DNA Sequences of RAPD Fragments in the Egyptian cotton Gossypium barbadense

Abdel Ghany A. Abdel Ghany1 and Essam A. Zaki2,y,*

1Institute of Efficient Productivity, Zagazig University, Zagazig, Egypt.

2Genetic Engineering and Biotechnology Research Institute, GEBRI, Research Area, Borg El Arab, Post Code 21934, Alexandria, Egypt.

*Corresponding author: Phone (765) 494-9837, Fax: (765) 496-1496, E-mail: [email protected].

yCurrent Address: Department of Biological Sciences, 1392 Lilly Hall of Life Sciences, West Lafayette, IN 47907-1392, USA.

Accepted 4 April, 2003

Abstract

Abstract: Random Amplified Polymorphic DNAs (RAPDs) is a DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. Despite the fact that the RAPD technique has become a very powerful tool and has found use in numerous applications, yet, the nature of molecular variation(s) uncovered by the RAPD technique is still unclear. The aim of the following study, therefore, was to investigate the molecular nature of RAPD DNA fragments in four Gossypium barbadense cultivars. Five RAPD DNA fragments, generated by improved RAPD-PCR technique, and representing polymorphic and nonpolymorphic bands were analyzed at the molecular level using DNA sequence analysis. Nonpolymorphic RAPD DNA fragments showed homologies to previously characterized plant structural genes. Comparative nucleotide sequence analysis of two comigrating nonpolymorphic fragments revealed that these two DNA sequences are highly similar to each other, indicating that similarity of fragment size is a good predicator of homology. Polymorphic RAPD DNA fragments, on the other hand, showed homologies to middle and high-repetitive DNA sequences. These results promote the initiative to integrate these RAPD markers in cotton breeding applications, and DNA fingerprinting.

Key words: Gossypium, MITEs, RAPD-PCR, repetitive DNA, sequence similarity, retrotransposons.

 

 

Effect of salt and drought stress on acid phosphatase activities in alfalfa (Medicago sativa L.) explants under in vitro culture

A. A. Ehsanpour* and F. Amini

Dept. of Biology, Esfahan University, Esfahan, Iran *Corresponding author: E-mail: [email protected]

Accepted 4 April 2003

Abstract

Abstract: Acid phosphatase is wildly found in plants. This enzyme has intra and extra cellular activity. For instance, it dephosphorylase organic phosphate and change it to inorganic phosphate. However, acid phosphatase activity is increased by salt and osmotic stress. In this experiments, calluses were produced from invitro grown explants of Medicago sativa cv. Yazdi and cv. Hamedani under aseptic condition on MS medium containing NAA, 2,4-D. Then calluses and seedling were transferred to the same medium containing 0,0.2, 0.4, 0.6, 0.8, 1% NaCl and 0, 2, 4, 6, 8, 10% Mannitol as osmotic stress. After 2 weeks acid phosphatse activities were measured and data statistically analyzed. Clearly acid phosphatase activities was increased by salt and drought stress in both cultivars, and the difference between two genotype indicating that the acid phosphatase activity is highly genotype dependent.

Key words: Acid phosphatase, Medicago sativa, osmotic, salt, drought, stress.

AJOL Home Page How to order photocopies Order Form INASP Home Page