African
Journals On-line
African Journal of Biotechnology
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.
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