Abdullah Alawad

Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome.

Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants.

Synthesis, structural characterization, electrochemical behavior and anticancer activity of gold(III) complexes of meso-1,2-di(1-naphthyl)-1,2-diaminoethane and tetraphenylporphyrin

Three gold(III) complexes, [Au(npen)Cl2]Cl·2H2O (1), [Au(npen)2]Cl3 (2) and [Au(TPP)]Cl (3) (npen = meso-1,2-di(1-naphthyl)-1,2-diaminoethane, TPP = meso-tetraphenylporphyrin) have been synthesized and characterized using elemental analysis, IR and NMR spectroscopy, and one of them (1) by X-ray crystallography. The structure of 1 consists of a [Au(npen)Cl2] complex ion, a chloride counter ion and two water molecules. The gold atom in the complex ion adopts a distorted square planar geometry. The interactions of 1 and 2 with L-tyrosine, glutathione and lysozyme were studied electrochemically. The electrochemical measurements indicated that gold(III) remained stable and did not undergo reduction upon interaction with proteins. The in vitro cytotoxic properties of the complexes as well as of cisplatin were evaluated on three human cancer cell lines, A549 (lung cancer cells), MCF7 (breast cancer cells) and HCT15 (colon cancer cells) using MTT assay. The results indicated that the prepared gold(III) complexes were more potent than cisplatin in inhibiting the growth of the selected cancer cells. The IC50 data revealed that complex 3 was the most effective antiproliferative agent.

Generation of human iPS cell line SKiPSc1 from healthy Human Neonatal Foreskin Fibroblast cells.

The SKiPSc1 induced pluripotent stem (iPS) cell line was generated from Human Neonatal Foreskin Fibroblasts (HNFFs) obtained from a healthy donor infant that were reprogrammed using non-integrating Sendai viral vectors expressing Oct3/4, Sox2, c-Myc, and Klf4.

Sacasg and sacalg: new GFP-labelled camel skin and lung fibroblast cell lines

Camelids skin is claimed to respond differently under different physiological and pathological condition, however, there is no in vitro model with a reporter to investigate this claim. So generating camel fibroblast cell lines that expresses green fluorescent protein (GFP) would be important as a tool to monitor camel cell growth, migration and other processes. Hence, in this investigation, we created a GFP expressing fibroblast cell lines derived from a primary skin and lung fibroblast cell lines of the Arabian camel with a stable expression of GFP which was transfected using the pCAG-EGFP plasmid with CMV enhancer via Lipofectamine 2000 reagent. Stably transfected clones were selected by puromycin screening. The results revealed that camel fibroblasts can be efficiently transduced in vitro using pCAG-CMV-based vectors and that these vectors direct long-term transgene expression without evident toxicity, pathogenesis or alteration of native fibroblast morphology. Immunofluorescence staining showed no differences in the expression of fibroblast biomarkers between the transfected and non-transfected cell lines. The viability of thawed cells remained above 85% after cryopreservation in liquid nitrogen. The gene expression of the fibroblast markers was not different in the transfected cell lines. Taken together, we have established and fully characterised GFP expressing-fibroblast cell lines of Arabian camel. Based on our assays, we conclude that transfection of GFP into the Arabian camel skin and lung fibroblasts did not change their observed properties. The GFP-labelled cell lines may represent a new tool for convenient monitoring of live primary camel fibroblasts.

The Integrated Energy Decision Support System

In this paper we introduce a decision support system framework termed the Integrated Energy Decision Support System IEDSS. IEDSS was developed for energy planning at national and regional levels to inform energy planners at multiple levels of government. IEDSS employs system dynamics modeling to enable the rapid evaluation of the outcomes of different supply and demand policies at the national level. Agent-Based models are used to mimic the interactions between different entities when applying the framework at the regional level of government. Within the IEDSS framework policy makers specify a set of policy decisions and choose from a set of uncertain futures to investigate the performance of their policy decisions. Together these form a scenario for which IEDSS computes a set of output parameters that are used to evaluate the resulting outcome. As a model-driven DSS, IEDSS can be utilized in two ways. The first is as a single-user DSS that deploys a scenario-based planning approach which informs decision makers by mapping the solution space and the resultant effects caused by their policy choices. The second is as a group-based DSS that enhances communication and collaborative decision making between multiple entities. IEDSS is developed on a software platform that utilizes the front-end computation to handle templates, style sheets, and visualizations, while the backend is focused on data retrieval, models execution, and performance optimization. IEDSS was developed to address the power sector of the Kingdom of Saudi Arabia as a case study, but the framework and capabilities of its platform are applicable to any generalized case.

Molecular Modeling and Phylogeny of the Krüppel-like Factor 4 (cKLF4) Protein from the Arabian Camel, Camelus dromedarius

Krüppel-like factor 4 (KLF4) is a pluripotency transcription factor that helps in generating induced pluripotent stem cells (iPSCs). We sequenced for the first time the full coding sequence of Camelus dromedarius KLF4 (cKLF4), which is also known as the Arabian camel. Bioinformatics analysis revealed the molecular weight and the isoelectric point of cKLF4 protein to be 53.043 kDa and 8.74, respectively. The predicted cKLF4 protein sequence shows high identity with some other species as follows: 98% with Bactrian camel and 89% with alpaca KLF4 proteins. A three-dimensional (3D) structure was built based on the available crystal structure of the Mus musculus KLF4 (mKLF4) of 82 residues (PDB: 2 WBS) and by predicting 400 residues using bioinformatics software. The comparison confirms the presence of the zinc finger domains in cKLF4 protein. Phylogenetic analysis showed that KLF4 from the Arabian camel is grouped with the Bactrian camel, alpaca, cattle, and pig. This study will help in the annotation of KLF4 protein and in generating camel-induced pluripotent stem cells (CiPSCs).

Phylogenetic and Structural Analysis of the Pluripotency Factor Sex-Determining Region Y box2 Gene of Camelus dromedarius (cSox2)

Although the sequencing information of Sox2 cDNA for many mammalian is available, the Sox2 cDNA of Camelus dromedaries has not yet been characterized. The objective of this study was to sequence and characterize Sox2 cDNA from the brain of C. dromedarius (also known as Arabian camel). A full coding sequence of the Sox2 gene from the brain of C. dromedarius was amplified by reverse transcription PCRjmc and then sequenced using the 3730XL series platform Sequencer (Applied Biosystem) for the first time. The cDNA sequence displayed an open reading frame of 822 nucleotides, encoding a protein of 273 amino acids. The molecular weight and the isoelectric point of the translated protein were calculated as 29.825 kDa and 10.11, respectively, using bioinformatics analysis. The predicted cSox2 protein sequence exhibited high identity: 99% for Homo sapiens, Mus musculus, Bos taurus, and Vicugna pacos; 98% for Sus scrofa and 93% for Camelus ferus. A 3D structure was built based on the available crystal structure of the HMG-box domain of human stem cell transcription factor Sox2 (PDB: 2 LE4) with 81 residues and predicting bioinformatics software for 273 amino acid residues. The comparison confirms the presence of the HMG-box domain in the cSox2 protein. The orthologous phylogenetic analysis showed that the Sox2 isoform from C. dromedarius was grouped with humans, alpacas, cattle, and pigs. We believe that this genetic and structural information will be a helpful source for the annotation. Furthermore, Sox2 is one of the transcription factors that contributes to the generation-induced pluripotent stem cells (iPSCs), which in turn will probably help generate camel induced pluripotent stem cells (CiPSCs).