Papers by Waleed M . M . El-Sayed
Journal of Genetic Engineering and Biotechnology
Exopolysaccharides (EPSs) from microorganisms are essential harmless natural biopolymers used in ... more Exopolysaccharides (EPSs) from microorganisms are essential harmless natural biopolymers used in applications including medications, nutraceuticals and functional foods, cosmetics, and insecticides. Several microbes can synthesize and excrete EPSs with chemical properties and structures that make them suitable for several important applications. Microbes secrete EPSs outside their cell walls, as slime or as a “jelly” into the extracellular medium. These EPS-producing microbes are ubiquitous and can be isolated from aquatic and terrestrial environments, such as freshwater, marine water, wastewater, and soils. They have also been isolated from extreme niches like hot springs, cold waters, halophilic environments, and salt marshes. Recently, microbial EPSs have attracted interest for their applications such as environmental bio-flocculants because they are degradable and nontoxic. However, further efforts are required for the cost-effective and industrial-scale commercial production of...
Marine Biomaterials: Resources, Categories, and Applications
Marine Biomaterials, 2022
Journal of Biotechnology & Biomaterials, 2016
Ulva lactuca acts a vital potential marine energy crop. Reducing sugars from U. lactuca were obta... more Ulva lactuca acts a vital potential marine energy crop. Reducing sugars from U. lactuca were obtained and evaluated for the bioethanol production by Saccharomyces cerevisiae. The optimization process was investigated by Plackett-Burman experimental design followed by immobilization technique on supported solid materials. Results show that the sugar concentration, pH level and the inoculums size have a significant effect on the bioethanol production by S. cerevisiae to give concentration (12 ± 0.5 g/g of sugar/l) with conversion efficiency (47.1%). The immobilization of yeast cells upon luffa pulp shows the highest bioethanol productivity (13.3 g/g of sugar/l) with conversion efficiency (52%). Therefore, the immobilized yeast upon luffa pulp was recommended in the current work. Moreover, the supportive luffa pulp was efficiently used and recycled for several times in the bioethanol production.
Environmental influence on rotenone performance as an algal crop protective agent to prevent pond crashes for biofuel production
Rotenone as an algal crop protective agent has the potential to be a promising, inexpensive tool ... more Rotenone as an algal crop protective agent has the potential to be a promising, inexpensive tool for algal biofuel productivity enhancement due to its ability to inhibit zooplankton in algaculture. This study focuses on the potential impact of various physical and chemical factors affecting rotenone persistence during algal cultivation for biofuel production. The roles of light, temperature, pH, cultivation medium and adsorption to algal biomass were evaluated. Chlorella kessleri was used as the model oleaginous microalgae in this study. Temperature increased the rate of rotenone degradation, with average degradation rates ranging from 1 ± 0.8 mg/L-h to 3.6 ± 1.5 mg/L-h as the temperature increased from 15 °C to 35 °C. Increased pH also raised the rate of degradation from 1.0 ± 0.9 to 3.4 ± 1.7 mg/L-h as the pH increased from 7 to 10. In contrast, light had little effect on rotenone degradation compared to dark conditions ( p = 0.324). BG-11 medium also increased rotenone degradati...
Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii
bioRxiv, 2020
Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in... more Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genomic DNA of cells. The distribution of rNMPs in DNA has been studied only in limited genomes, such as yeast nuclear and mitochondrial DNA, as well as human mitochondrial DNA. In this study, we used the ribose-seq protocol and the Ribose-Map bioinformatics toolkit to reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. The study presents the discovery of a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the nucleotide content of these C. reinhardtii genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. In addition, we reveal specific rNMP biases and patterns in the mitochondrial, chloroplast and nuclear DNA of C. reinhardtii.
Capture of Ribonucleotides in Yeast Genomic DNA Using Ribose-Seq
Methods in Molecular Biology
Experiments conducted in yeast cells have recently shown abundant presence of ribonucleotides (rN... more Experiments conducted in yeast cells have recently shown abundant presence of ribonucleotides (rNMPs) embedded both in nuclear and mitochondrial DNA. Indeed, rNMPs are the most frequent, nonstandard nucleotides found in cellular DNA. rNMPs have a highly reactive 2'-hydroxyl group in the ribose sugar that gives rise to genome instability by altering the structure, function, and properties of DNA. In order to profile rNMPs embedded in yeast genomic DNA, as well as any other genomic DNA of interest, we developed "ribose-seq." Ribose-seq utilizes Arabidopsis thaliana tRNA ligase (AtRNL), which enables ligation of 2'-phosphate termini of DNA molecules terminating with an rNMP to the 5'-phosphate end of the same DNA molecules. Thus, a unique feature of ribose-seq is its capacity to specifically and directly capture the rNMPs present in DNA. Here we describe how ribose-seq is applied to yeast Saccharomyces cerevisiae DNA to capture rNMPs that are incorporated in the yeast genome and build libraries of rNMP incorporation for high-throughput sequencing. We also provide the advancements over our original ribose-seq protocol at the end of Subheading 1, and the specific details are provided in the methods part of this chapter.
Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporatio... more Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporation remain poorly characterized. Here, by using ribose-seq and Ribose-Map techniques, we built and analyzed high-throughput sequencing libraries of rNMPs derived from mitochondrial and nuclear DNA of budding and fission yeast. We reveal both common and unique features of rNMP sites among yeast species and strains, and between wild type and different ribonuclease H-mutant genotypes. We demonstrate that the rNMPs are not randomly incorporated in DNA. We highlight signatures and patterns of rNMPs, including sites within trinucleotide-repeat tracts. Our results uncover that the deoxyribonucleotide immediately upstream of the rNMPs has a strong influence on rNMP distribution, suggesting a mechanism of rNMP accommodation by DNA polymerases as a driving force of rNMP incorporation. Consistently, we find deoxyadenosine upstream from the most abundant genomic rCMPs and rGMPs. This study establishes a framework to better understand mechanisms of rNMP incorporation in DNA.
Nature Communications
Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporatio... more Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporation remain poorly characterized. Here, by using ribose-seq and Ribose-Map techniques, we built and analyzed high-throughput sequencing libraries of rNMPs derived from mitochondrial and nuclear DNA of budding and fission yeast. We reveal both common and unique features of rNMP sites among yeast species and strains, and between wild type and different ribonuclease H-mutant genotypes. We demonstrate that the rNMPs are not randomly incorporated in DNA. We highlight signatures and patterns of rNMPs, including sites within trinucleotide-repeat tracts. Our results uncover that the deoxyribonucleotide immediately upstream of the rNMPs has a strong influence on rNMP distribution, suggesting a mechanism of rNMP accommodation by DNA polymerases as a driving force of rNMP incorporation. Consistently, we find deoxyadenosine upstream from the most abundant genomic rCMPs and rGMPs. This study establishes...
All fiber on-axis coupling scheme between single mode fiber and GRIN fiber
Http Dx Doi Org 10 1080 09500340701558542, Apr 10, 2008
Page 1. Journal of Modern Optics Vol. 55, No. 7, 10 April 2008, 10331049 All fiber on-axis coupl... more Page 1. Journal of Modern Optics Vol. 55, No. 7, 10 April 2008, 10331049 All fiber on-axis coupling scheme between single mode fiber and GRIN fiber Waleed S. Mohammeda*, Xija Gub, Joachim Meiera and Peter WE Smitha ...
Applied Optics, 2009
Laser beam shaping is an important subject for industrial and medical applications since differen... more Laser beam shaping is an important subject for industrial and medical applications since different applications may require different laser intensity distributions. We present an all-fiber beam-shaping device that could transform a Gaussian-shaped laser beam into an intensity uniform beam in the 1:0 μm wavelength region using a long-period grating (LPG). The device can be used to shape the beam of a Yb-doped high-power fiber laser. The mode structure of the LPGs made of HI1060 fiber is analyzed. The design parameters that affect the beam shaping are discussed, and the results of the beam shaping using two cladding modes, LP 03 and LP 04 , are presented.
All-fiber multimode interference bandpass filter
Optics Letters, Sep 1, 2006
A novel design for an all-fiber bandpass filter based on a multimode interference reimaging pheno... more A novel design for an all-fiber bandpass filter based on a multimode interference reimaging phenomenon is presented. The filter has achieved low insertion loss with adequate bandwidth and isolation for coarse wavelength-division multiplexing. The filter can easily be made with any central wavelength that is compatible with the single-mode fiber used for its construction. The measured filter performance matches the theoretical predictions well. The filter can have broad applications in fiber-optic telecommunications, spectroscopy, and sensing.
Study of Localized Surface Plasmon properties on metallic nano-rods towards optical antennas
2014 International Electrical Engineering Congress, Mar 1, 2014
Proceedings of Spie the International Society For Optical Engineering, 2008
We present three new interferometric techniques for dispersion characterization covering from mil... more We present three new interferometric techniques for dispersion characterization covering from millimeter waveguides to kilometers of fibers. The first is a Frequency-Shifted Interferometer (FSI) that measures fibers from meters to tens of kilometers. The second is a three-wave Single-Arm Interferometer (SAI), where the envelope of a three-wave interference pattern yields the second-order dispersion directly. It is suitable for fibers from centimeters to >1m. The third is a Common-Path Interferometer (CPI) that measures dispersion of millimeter-long fibers/waveguides. These techniques offer high precision in their respective ranges, and are all "single-arm" interferometers: the two interfering beams go through the same arm of the interferometer. They are simple, low-cost, and more resilient to phase and polarization instabilities than conventional interferometric techniques for dispersion measurement.
Demonstration of visible light communications using RGB LEDs in an indoor environment
Ecti Con2010 the 2010 Ecti International Confernce on Electrical Engineering Electronics Computer Telecommunications and Information Technology, 2010
Page 1. Demonstration of Visible Light Communications Using RGB LEDs in an Indoor Environment Nat... more Page 1. Demonstration of Visible Light Communications Using RGB LEDs in an Indoor Environment Natasha Shrestha1, Muhammad Sohail1, Charusluk Viphavakit2, Poompat Saengudomlert1 and Waleed S. Mohammed2 ...
Opt Express, 2007
We investigated the dispersion characteristics of submicron sized AlGaAs waveguides. Numerical si... more We investigated the dispersion characteristics of submicron sized AlGaAs waveguides. Numerical simulations shows that the tight confinement of the optical waves in such nanowires leads to strong variations of the dispersion characteristics compared to classic, weakly guided waveguides of the same material system. We found numerically that the investigated structure has negative GVD for the TE mode provided the waveguide width is between 670 nm and 280 nm. Experimental data obtained from 300 μm -1 mm long wires confirms the numerical results.
All-Fiber Laser Beam Shaping at 1.0 μm Wavelength Region in a Single-mode Fiber
Proceedings of Spie the International Society For Optical Engineering, 2008
Laser beam shaping is an important subject in industrial and medical applications of lasers since... more Laser beam shaping is an important subject in industrial and medical applications of lasers since different applications may require different laser intensity distributions. Recently we demonstrated successfully an all-fiber laser beam shaping device that could transform a Gaussian ...
Monolithic integration of dual layer optics on broad area semiconductor lasers
Conference on Lasers and Electro Optics 2003 Cleo 03, Jun 6, 2003
A broad area InGaAs semiconductor laser diode with two monolithically integrated optical elements... more A broad area InGaAs semiconductor laser diode with two monolithically integrated optical elements, a 275 nm period diffraction grating and multilevel refractive lens, is presented. We discuss the potential of dual optics integration for beam shaping of high power lasers and amplifiers.
Measurement of aluminium oxide film by fabry‐perot interferometry and scanning electron microscopy
Journal of Saudi Chemical Society, 2016
System and Method to Determine Chromatic Dispersion in Short Lengths of Waveguides Using a 3-WAVE Interference Pattern and a Single-Arm Interferometer
System and method to determine chromatic dispersion in short lengths of waveguides using a common path interferometer
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Papers by Waleed M . M . El-Sayed