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

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

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

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

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

Irrigation and drainage in the new millennium

Presented at the 2000 USCID international conference, Challenges facing irrigation and drainage in the new millennium on June 20-24 in Fort Collins, Colorado.Includes bibliographical references.A field study was conducted at Mashtul Pilot Area MPA (260 feddans' 1 feddan = 4200 m2) situated at north Zagazig to evaluate the performance of the long term constructed subsurface drainage system. The evaluation of grades, alignment and clogging of drain lines can give an indication of the system performance and efficiency. Three drainage units served by the same collector were selected. Four 30 m interval PVC lateral pipes were installed at different depths. The results revealed that, the collector drain slopes were either steep or flat while the overall slope of the collector drain was considered steep for about 45.50% of the sections and flat for the rest. On the other hand, some sections showed an inverse slope which can cause a decrease in the discharge rate. The regularity was classified as good for about 82% of the sections and moderate for the rest. The slope of the lateral drains was correct for 41.7% of those under study (12 lateral drains), steep for 16.60%, and flat for the rest, and the regularity was classified as poor except lateral number 71 which had moderate regularity in the first approach while, in the second approach 41.67% had moderate regularity and poor for the rest. Also the deviation of the drain pipes from the straight line was generally larger than pipe diameter. Consequently, air entrapment and sedimentation resulted. The results also indicated that, the average height of sedimentation inside lateral drains was 12.70 mm (618.30 gm/m drain length) while for collector drains, sediment was in 22.88% of pipe diameter. The average reduction in discharge capacity due to sedimentation for laterals and collectors upstream and downstream parts were 17.17%, 32.80% and 17.60% respectively. Also using Manning, Visser and Wesseling equations leads to different safety factors

STRUCTURAL OF SUPRAMOLECULAR HYDROGEN BONDING DIOXOURANIUM (VI) COMPLEXES

The azodye ligands were synthesized from the coupling of 3-methyl-1-phenyl-1H-pyrazol-5(4H)-one with aniline derivatives and characterized by elemental analyses, IR and NMR spectroscopy. Dioxouranium (VI) complexes of the prepared ligands were characterized by elemental analyses, conductance, thermal analysis and spectral (UV, IR and NMR) results. IR spectra show that the ligands behave as a monobasic bidentate coordinating via the hydrazo nitrogen atom and CO of the pyrazole ring. Thermal studies to verify the status of water molecules inside or outside the coordination sphere of the central metal ion. The optimized bond lengths, bond angles and the calculated quantum chemical parameters for the ligands were investigated. The coordination geometries and electronic structures are determined from a framework for the modeling of the complexes. The force constants, FUO (10-8 N/Ao) and the bond lengths, RUO (Ao) have been calculated from an asymmetric stretching frequency of O-U-Ogroup

Relative Rate Observer Self-Tuning of Fuzzy PID Virtual Inertia Control for An Islanded microgrid

Expanding the usage of renewable energy in islanded microgrids leads to a reduction in its total inertia. Low inertia microgrids have difficulties in voltage and frequency control. That affected saving its stability and preventing a blackout. To improve low inertia islanded microgrids\u27 dynamic response and save their stability, this paper presented relative rate observer self-tuning fuzzy PID (RROSTF-PID) based on virtual inertia control (VIC) for an islanded microgrid with a high renewable energy sources (RESs) contribution. RROSTF-PID based on VIC\u27s success in showing remarkable improvement in the microgrid\u27s dynamic response and enhancement of its stability. Moreover, it handles different contingency conditions successfully by giving the desired frequency support. Ant colony optimization (ACO) technique is used to find the optimal values of the RROSTF-PID based on VIC parameters. Furthermore, using MATLAB TM/Simulink, RROSTF-PID based on VIC response is compared to Optimal Fuzzy PID (OF-PID) based VIC, Fuzzy PID (F-PID) based VIC, PID-based VIC, conventional VIC responses, and the microgrid without VIC response under different operation conditions

Effect of Shape, Orientation and Aging of a Plastic Greenhouse Cover on the Degradation Rate of the Optical Properties in Arid Climates

In arid climates, the optical properties of plastic-covered greenhouses deteriorate very quickly. To examine the effect of greenhouse shape and orientation on the degradation rate of cover optical properties, four greenhouse prototypes were constructed in two shapes (duo-pitched roof and tunnel), covered with a 200  m thick low-density polyethylene film. Two types were oriented in the North–South direction, the other two in the East–West direction, and all were exposed for one year to an arid climate. Samples were taken from the different surfaces of each cover for testing. The total transmittance (Ts) and reflectance (Rs) of the samples were measured and averaged to obtain the whole cover properties (T and R). Measurements were carried out periodically every 30 days for the four prototypes. The degradation behavior of the optical properties of each cover surface (Ts, Rs) and the whole cover (T, R) was investigated for the four film covers during the exposure time. Results show that the degradation rate of Ts depends on the surface location and the cover orientation. Among the different surfaces of the four prototype covers, the maximum difference in the Ts value between the E and N surfaces for the tunnel cover oriented in the N–S direction was 15.5%. Although the variation of the Ts value among the different cover surfaces was found, the time dependences of the whole cover transmittance (T) for the four covers tested were almost similar. Accordingly, the shape and orientation of the small size greenhouses did not significantly affect the degradation rate of the cover optical properties. In the four covers tested, the reduction in the global solar radiation transmittance (T) was 27–31% after one-year exposure compared to the new film. Nonlinear correlation was developed to predict the degradation rate of the cover transmittance as a function of the accumulated solar irradiance