DNA Sequences of RAPD Fragments in the Egyptian cotton Gossypium barbadense

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. (African Journal of Biotechnology: 2003 2(5): 129-132

Phylogenetic and molecular evolutionary analyses of gypsy group retrotransposon families in the Egyptian cotton Gossypium barbadense

Gypsy group retrotransposons in the Egyptian cotton, Gossypium barbadense, was examined by phylogenetic and molecular evolutionary analyses. DNA sequences of gypsy group retrotransposons in two G. barbadense cultivars revealed that these sequences are heterogeneous and represent two distinct families. Sequence variation between these families seems to preserve coding information of the reverse transcriptase domain. The high ratio of synonymous to nonsynonymous changes indicates that the reverse transcriptase domain of these families is evolving under purifying selection. Our phylogenetic analysis revealed that the closest relatives of cotton retroelements are found in other plants gypsy group retrotransposons. Cotton retroelements-encoded transcripts were detected in their related respective young seedlings using RNA slot-blot hybridization, suggesting their transcriptional activity. The wide distribution of gypsy group retrotransposons and the detection of their encoded transcripts illustrate their active role in the Gossypium genome. Key words: Evolution, Gossypium, gypsy, retrotransposons, reverse transcriptase, substitution rates, transcription. African Journal of Biotechnology Vol.2(9) 2003: 271-27

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

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. (African Journal of Biotechnology: 2003 2(5): 124-128

Sequence heterogeneity of the envelope-like domain in the Egyptian cotton Gossypium barbadense

Abbreviations; LTR: long terminal repeat, ORF: open-reading frame, PCR: polymerase chain reaction, RT: reverse transcriptase gene. The current study aimed to investigate the evolution of env-like sequences in the Egyptian cotton Gossypium barbadense. DNA sequence determination and analysis of env -like sequences revealed that these sequences are heterogeneous in G. barbadense. The observed sequence diversity, however, seems to preserve the coding information. Phylogenetic analysis demonstrated that plant env -like sequences group together, suggesting their monophyletic origin. Gossypium env-like sequences are, however, more closely related to elements present in other plant species. Our result suggests that env -like sequences in cotton have evolved under functional constraint and likely to play a role in the life cycle of these elements. Key words: Envelope, Gossypium, gypsy, plant retroviruses, retrotransposons, retroviruses, reverse transcriptase. African Journal of Biotechnology Vol.2(10) 2003: 341-34

Stachybotrys chartarum: A Novel Biological Agent for The Extracellular Synthesis of Silver Nanoparticles and Their Antimicrobial Activity

Microbial assisted biosynthesis of nanoparticles is a rapidly progressing area of nanobiotechnology. Inthis paper Stachybotrys chartarum assisted extracellular synthesis of silver nanoparticles (AgNPs) is reportedwhen challenged with 1mM silver nitrate (AgNO3). The characterization of AgNPs was carried out visualobservation and UV-Vis spectrophotometry. Further analysis carried out by Fourier Transform InfraredSpectroscopy (FTIR), provides evidence for the presence of proteins as capping agent, which helps in increasingthe stability of the synthesized AgNPs. Transmission Electron Microscopy (TEM) investigations confi rmedthat AgNPs were formed. The synthesized silver nanoparticles were found in the range of 65-108 nm. Finally,the antimicrobial susceptibility of AgNPs synthesized was investigated which exhibited more potent activityagainst bacteria than fungi compared with using silver nitrate at concentration 1mM. Keywords: Antimicrobial activity, Stachybotrys chartarum, Silver nanoparticle

Responses of plastic shading nets to global and diffuse PAR transfer: Optical properties and evaluation

AbstractTo cover agricultural structures for protecting plants from high solar radiation in hot and sunny regions different types of shading nets are used. In summer, the amount of photosynthetically active radiation (PAR) transmitted through these nets usually fulfils plant growth requirements. However, their applicability in winter is still unknown. So far, the choice of nets has mostly been empirical, because technical data such as the radiometric properties that are used to characterize the different types of nets are not available. This paper presents a simple method for measuring the radiometric properties related to global and diffuse PAR of seven types of shading nets including nets with colours and shading rates that are commonly used in hot regions. A shading system was developed to simulate the diffuse PAR under cloudy conditions. The results show that under clear sunny and cloudy conditions the radiometric properties depended on both net porosity and colour. Net reflectance strongly depended on net colour. Net transmittance and absorptance depended primarily on colour and secondarily on porosity. The radiometric properties of nets under global and diffuse PAR conditions tended to be similar to those of translucent materials so that a plastic net can be considered as translucent material when investigating the equivalent optical parameters (refractive index and absorption coefficient). This can help to predict the radiometric properties of the net without the need of measurements. Under the sunny conditions of winter seasons, the structures covered with the tested nets are suitable for growing crops that can grow at PAR less than 150Wm−2. However, under cloudy conditions very few plants will grow that can grow at PAR less than 30Wm−2

Isolation, characterization, and phylogenetic analysis of copia-like retrotransposons in the Egyptian cotton Gossypium barbadense and its progenitors

We have used the polymerase chain reaction to analyze copia-like retrotransposons in the Egyptian cotton and its progenitors. All three cotton species studied contain reverse transcriptase fragments from copia-like retrotransposons. Sequence analysis of these reverse transcriptase fragments reveals that each is different from the others, with predicted amino acid diversities between 9 and 94%. The detection of stop codons and insertions/deletions in the derived amino acid sequences of the Gossypium RT clones, suggests that these clones represent defective retrotransposons. The presence of these sequences in G. barbadense progenitors, however, suggests the presence of active retrotransposons capable of producing new functional copies at an appropriate rate to compensate for the mutational loss of old ones. Phylogenetic analysis provided strong bootstrap support for a monophyletic origin of plant copia-like retrotransposons, yet showed high diversity within all species. Our results suggest that both vertical transmission of copia-like retrotransposons within G. barbadense lineages, and horizontal transmission between G. barbadense and its progenitors have played major roles in the evolution of copia-like retrotransposons in Gossypium. Keywords: Genome structure, Gossypium, repetitive DNA, polyploidy, sequence diversity, retrotransposons. (African Journal of Biotechnology: 2003 2(6): 165-168