Qatar Foundation Annual Research Conference Proceedings Volume 2014 Issue 1

THE USE OF WIRELESS SENSOR NETWORKS IN AGRICULTUTE A TOOL FOR A SUSTAINABLE FOOD SUPPLY IN THE ARAB WORLD In this paper some ideas of how to apply the technological advancement of the wireless sensor networks (WSN) in agriculture as a tool for food security is discussed. This will include some examples where the technology can be applied, what changes can this technology brings to the traditional farming, which can help within the solution of the Arab World food security problems. This will help the region to develop and be part of the global strategy for the World food security. WSN features of having a low power consummation nature with different options of using different energy sources will make it as the just technology suitable in a remote and less or without infrastructural bases environment for many countries within the region. The applications of WSN which are suitable for the purpose will be discussed. Keywords: WSN, Food Security, Agriculture in Arab region, WSN Farmer Kits Tool, Energy Sources. Introduction Arabic countries are naturally rich, many countries within the region have a wide virgin land. But unfortunately some of these countries have been a focus in term of food shortages for long time which cause by many factors like land degradation, water crisis, land deals, climate change, agricultural disease, governing system, wars, population growth, land use change, living style change, high prices and lack of technology. As technology has rational parts in solving the most difficult problems for today's society, WSN can be applied in agriculture to reduce or solve this problem. Use of WSN in Agriculture as a solution As traditional farming is the lead in the region, people use their own human sense to perceive the surrounding to investigate the soil and predict the weather. But the remote sensing of the WSN as an activity of recording, observing, perceiving objects or events, wirelessly these happenings are processes and analyzed in a real time. The idea of applying this technology is to be adopted in different applications shortly can be said here. *Soil Investigation by using the specialized soil test sensor detectors to determine the fertility of soil nutrient deficiencies, elements like Nitrogen is very important for plants. *Weather Prediction by using a web data from WSN can be transmitted enabling a remote online interactive retrieval access, and then these data can be shared with the farmers. *Detection of ground water using WSN the level and the amount of sufficient water can be detected before planting. *Using the WSN the water and the area can be controlled during irrigation which will help in reducing the energy consumption. *Food storage system will be advanced by the use of WSN in knowing usage validity time and the space of storing. *Knowing where how and when to deliver what kind of product by using WSN will help in the logistical distribution of crops. *Farming Dissemination by using an integrated WSN tool kit messages can be disseminated.

This paper describes our investigation into the effects of adding aromatic compounds to synthetic aviation fuels on the performance of these fuels. The work was done as an undergraduate research (UREP) project and was an extension to our group's previous studies which were aimed at characterizing blends of conventional and synthetic aviation fuels [1] and identifying optimum paraffinic building blocks for SPK [2]. Aromatics play a key role in aviation fuels as they enhance the density and elastomer swelling properties of these fuels. However, they are absent from synthetic gas-to-liquids (GTL) derived aviation fuels such as synthetic paraffinic kerosene (SPK) and thus must be added in from another source. In the first part of this study, standard analytical tests were conducted on blends of SPK and aromatic additives (styrene and Shell A150) in different concentrations from 0 to 25 % to measure certain fuel properties (i.e. density, flash point, freezing point, heat content and viscosity) using relevant ASTM procedures. The measured properties were then compared with the desired values for certification according to the ASTM D-1655 and D-7566 standards for conventional and hybrid (i.e. mixtures of oil-derived and synthetic fuels obtained from either natural gas or coal) jet fuels, respectively. In particular, ASTM D-7566 specifies the use of the 50-50 synthetic fuel blend with jet A-1; our group's efforts are aimed at increasing the workable synthetic ratio in the fuel. The experimental work was conducted in the Fuel Characterization Lab at Texas A&M University at Qatar. The data generated from these experiments was used to identify correlations between blend compositions and properties. In the second part of this study, small amounts (i.e. 1 vol %) of specialty aromatic compounds (such as benzaldehyde) were added to the blends from the first part of the study, specifically to enhance the elastomer swelling characteristics of these blends. This is a crucial property of aviation fuels as it ensures a tight seal in fuel tanks, thus preventing potentially catastrophic leakages. The added aromatic compounds were identified based on a Hansen solubility parameter analysis, and it was found that their addition favorably increased both the density and elastomer swelling characteristics of the SPK. Notably, three of the blends tested outperformed the elastomer swelling characteristics of conventional Jet A-1 by about a factor of 2. With respect to freezing point, viscosity, heat content, and flash point, the performance of all of the blends tested were in agreement with ASTM standards. These experimental results demonstrate the favorability our approach to synthetic fuel design i.e. the focused introduction of additives to improve the performance of synthetic fuels to standards at par with or, in some cases, surpassing those of conventional jet fuel.

Magnetic Particle Imaging (MPI) is a newly found imaging modality. It utilizes superparamagnetic materials as tracers in the blood stream to obtain very high resolutions. MPI promises to have high sensitivity, high spatial resolution and no radiation compared to other imaging modalities. Most commercially available MRI tracers (used for MPI for now) are all non-harmful when compared to Iodine (used for CT scan) and Gadolinium (used for MRI). MPI research is divided into three categories: MPI scanner development, superparamagnetic materials development, and image reconstruction techniques. In this project a small scale LabView-based system will be developed for use on small lab created phantoms, using 25 nm superparamagnetic iron oxide (SPIO) particles. At first a relaxometer will be developed, the imager will come as the next step. Transmitting and receiving signals will be implemented using LabView and a National Instruments PXI-1033 Chassis. Lab-built coils will be used to send the excitation signal and receive the signal induced by those SPIO's. The objective of this project is to be introduced to a new imaging modality that can have various applications and at the same time considered safe. The system being built is considered inexpensive and shows most of the aspects of how magnetic particle imaging works, starting with the physical phenomena, superparamagnetic nanoparticle properties and relaxation, signal generation and acquisition, and an introduction to the hardware of MPI. The system can be used to introduce engineers and engineering students to the MPI physical phenomena.

Recent rapid development in Qatar has brought awareness and recognition of the importance to catalogue, describe and preserve its biodiversity. Traditional methods of using morphological characteristics for species identification, although important, requires years of experience and is in need of complete specimens before identity is certain. Recent worldwide endeavor of DNA barcoding by using a segment of the mitochondrial gene cytochrome oxidase c 1 (CO1) to describe all species in the world, has gained recognition and popularity. In this student-centered research supported by Undergraduate Research Experience Program (UREP) of Qatar National Research Fund (QNRF), the objective is to sequence the barcoding gene CO1 of the lizards in Qatar and to compare the sequence among closely related species to facilitate future identification. The final results of this study will make available the barcode sequences of CO1 to be included in the GenBank database. Lizard species were collected across Qatar and photographs were taken for appropriated morphological identification. About 0.5 cm3 of muscle tissues were obtained from each specimen for DNA extraction. Currently between 8 to 12 different primer pairs suggested in literature and primer pair combinations were used for 7 species and a variety of programs of polymerase chain reaction (PCR) were employed in order to amplify the segment of gene of about 650 bp. Among the successfully amplified sequences from the 7 species currently analyzed, three species, Trachylepis septemtaeniata, Mesalina brevirostris, and Uromastyx aegyptia produced PCR products. To eliminate the presence of multiple sequences in the PCR product, PCR fragments were ligated to cloning vector in order to amplify one single sequence for each species. The current total success rate (<43%) based on the primer sequences obtained from publish results and from internal primers developed in this study further supports that the universal primers for reptiles are difficult to develop due to deep phylogenetic divergence. Future studies seeking universal primers should focus on candidate genes that evolve more slowly than CO1 gene to ensure higher homology of sequences among the reptilian species.

Objectives: Hereditary Hearing Loss (HHL) is a common genetic disorder accounting for at least 60% of prelingual deafness in children. The long tradition of consanguinity, which is widespread among populations of Arabian Peninsula, increases the prevalence of HHL. It is one of the most frequent causes for school failure in Qatar. GJB2 gene plays a worldwide major role in HHL recessive forms while in Qatar it has a minor role thus strongly suggesting the presence of additional causative genes. To overcome the remarkable genetic heterogeneity of HHL in Qatar population, an extremely powerful 2 steps "gene-identification strategy" was designed (Figure 1). STEP1 consists in a screening of 96 HHL genes by targeted re-sequencing (TS). Positive cases contribute to define an accurate molecular epidemiology picture while negative ones undergo STEP2, a combination of linkage studies and whole exome sequencing (WES) or directly to WES (depending on pedigree size). Methods: Ion Torrent (Life Technologies) (400X of mean target coverage and 581.000 Kb of targets size) was used for STEP1 and Illumina genotyping and Ion Proton (Life Technologies) (90X of mean coverage and 60Mb of target size) were used for STEP2. Sequencing variants were annotated/filtered according to standard pipelines. This strategy was applied to a first series of Qatari families. Results: STEP1 characterized 53% of Qatari families with HHL leading to the identification of 20 novel alleles in known HHL genes (i.e. GJB2, P2RX2, TECTA, TMPRSS3, LOXHD1, MYO15A, TMC1, TRIOBP, WFS1). STEP2 had already led to the discovery of 1 new gene (BDP1). The p*2625Gluext*11 mutation resulting in an elongation of 11 residues of the BDP1 protein was identified in a Qatari recessive family and its expression in the inner ear was confirmed by immunohistochemistry. Conclusion: This combined and powerful strategy proved to be very successful by explaining several HHL unsolved cases and by defining an accurate molecular epidemiology picture of Qatari genes/mutations. Moreover, this approach will be used for developing a "Qatari tailored" molecular diagnostic assay opening new important diagnostic perspectives for a such heterogeneous disorder as well as for defining targets for new possible therapeutic interventions

More than 30 years ago people have learned that exercise promotes oxidative damage in human tissues. Since then, our knowledge on exercise-induced free radical production and their effect has advanced markedly. In the beginning research has mainly focused on detrimental effects of exercise-induced free radical production (e.g. oxidation of macromolecules); however today a new era of redox biology exist that centers on the cell-signaling effects of exercise-induced free radicals, such as reactive oxygen species (ROS) that were shown to play a crucial role in muscle adaptation to exercise. Erythrocytes are rich in membrane polyunsaturated free fatty acid content and have high cellular concentrations of oxygen and haemoglobin that makes them susceptible to ROS induced damage. However, mild oxidative stress has beneficial effect by increasing endogenous antioxidant mechanisms. Thus, in the present work we have used sensitive mass spectrometry techniques to assess the potentially beneficial oxidative modifications of erythrocyte membrane proteins in response to exercise. We have recruited 3 healthy volunteers and their blood was drawn before exercise, immediately after and few hours after exercise. Erythrocyte membranes ("ghosts") were prepared and membrane proteins isolated. Proteins were then separated by 1-D gel electrophoresis, digested with trypsin and peptides analyzed by Orbitrap ELITE coupled with the Easy n-LC II for nano LC-MS/MS. The acquired data was searched with Proteome Discoverer 1.4 against Homo sapiens database to reveal the changes in the erythrocyte membrane proteome. Furthermore, data acquired was also searched through the database using the comprehensive workflow that included several dynamic modifications of peptides, including N-terminal carboxymethyl, C-terminal oxidation and terminal independent oxidation and trioxidation of peptides. The results obtained revealed several proteins that have translocated from the cytoplasm into the membrane following exercise. Moreover, numerous proteins showed exercise dependent modifications and up/down regulation. Exercise induced proteome changes were demonstrated to play an important role in several signaling pathways related to healthy living and lifestyle.

Traditional risk factors often fail to correlate with event incidence, thus there is a need for novel risk assessment in order to predict events and guide therapy in patients with acute coronary syndromes (ACS) following percutaneous coronary intervention (PCI). Peripheral endothelial dysfunction (PED) and obstructive sleep apnea (OSA) can both predict cardiovascular events, yet the prevalence of PED and OSA in patients hospitalized for ACS following PCI is unknown. Patients in the USA (n=65) and Qatar (n=352) were consented, enrolled following PCI for ACS, and underwent endothelial function testing (EndoPAT) on day 5 and home OSA testing (WatchPAT) following PCI. Baseline demographics at the time of patient admission showed only a modest prevalence of traditional CVD risk factors (Figure 1). The prevalence of PED (defined by EndoPAT<2.0) in this cohort was 73% (mean EndoPAT score of 1.8+0.5), and that of OSA 82% (Apnea Hypopnea Index>5; Figure 1). These functional, non-traditional risk factors were significantly more prevalent (p<0.0001) in this population than traditional risk factors, such as prior MI (6%), hypertension (52%), hyperlipidemia (47%), BMI>30 (43%), diabetes (36%), smoking (30%), CHF (1%), or family history of CVD (37%). Prevalence of both PED and OSA was present in 57% of participants. The current study demonstrated a higher prevalence of PED and OSA following ACS than the traditional CVD risk factors, underscoring their potential value for patient management. Detection and treatment of these functional risk factors may predict events and guide therapy in patients with ACS.

Background: Bicuspid aortic valve (BAV) is the most common cardiac malformation affecting 1-2% people worldwide. Despite its high prevalence, the pathogenesis of BAV is largely undetermined, although gene mutations leading to alterations in cell migration and signal transduction, in conjunction with non-genetic factors such as blood flow during valvulogenesis, may contribute to its formation prenatally. Objective: The determination of genetic factors contributing to the presentation of BAV in a family with three affected daughters. Methods: We applied next generation whole exome sequencing (>3Gigabases per individual) to high quality DNA from the blood samples of the three affected daughters and their unaffected parents. The >36.000.000 reads of each of the 5 individuals were analyzed with the bioinformatics tools Burrow-Wheeler Aligner, SOAPsnp, Sam tools, Varscan, and GATK to identify single nucleotide polymorphisms and insertions/deletions. Results: We identified over 38,000 SNPs and 3,400 Indels in each individual, of which >1,000 and >580, respectively, were novel. Forty one SNPs were detected in at least two of the affected siblings but neither parent, and only 3 of those were detected in all three BAV patients: HFM1 (ATP dependent DNA helicase), TSPAN2 (tetraspanin family member) and TTF2 (transcription termination factor, RNA polymerase II - pre-mRNA splicing regulator). All 3 genes carried exonic, non-synonymous SNVs, with highly significant pathogenicity prediction scores (SIFT, PhyloP, MutationTaster, LRT). Eight Indels were detected in at least two of the siblings, and only one of them was common across all three siblings: CCNL2 (cyclin L2). CCLN2 is a regulator of the pre-mRNA splicing process, as well as inducer of apoptosis, by modulating the expression of apoptotic and antiapoptotic proteins. In our patients it was found to carry a four base deletion affecting a splice site. None of the previously reported BAV-related genes were found to carry a common mutation across all, and unique to the BAV patients of this family. Conclusion: We have detected 4 genetic variants, shared by all three BAV patients but neither parent. These genes have not been associated with BAV to date. Of particular interest is the novel variant in TSPAN2, a gene of largely unexplored function, belonging to a transmembrane protein family known to mediate signal transduction events that play a role in the regulation of cell development, activation, growth, adhesion and motility.

Hematological Malignancies (e.g., leukemia and lymphoma) are among the top 5 causes of cancer death in the Middle Eastern Countries, including Qatar, Kuwait and Saudi Arabia. The monoclonal antibody rituximab, directed at the CD20 antigen, has become an essential drug for the treatment of Non Hodgkin Lymphoma (NHL). Although transient B cells depletion frequently occurs after rituximab treatment, it usually resolves after 6-9 months. Nevertheless, high frequency of non-neutropenic infections and persistent hypogammaglobulinaemia during follow-up period have been recently reported. However, impaired humoral response to the recall and primary antigens was found in NHL patients during (or few months after), rituximab treatment. Influenza vaccination is generally recommended in lymphoma patients, but few data are available about the activity of this vaccine after rituximab-containing regimens (RCR). It is presently unclear whether patients treated with RCR regain normal immunocompetence after achievement of complete remission. We present integrated data of 3 sequential studies conduced at our Institutions assessing the humoral response to seasonal influenza vaccination (2008/2009, 2009/2010 and 2011/2012 seasons; RIT-01, RIT-02, and RIT-03 studies, respectively) in NHL patients in complete remission (CR) for at least 6 months after treatment with rituximab-containing regimens (RCR). Overall, we found that patients treated with RCR have a significant lack of humoral response to both recall and naive influenza antigens as compared with HV and with cancer patients treated with chemotherapy not containing rituximab. This weakness was associated with depletion of CD27+ memory b cells. To determine early transcriptional changes predictive of immunoresponsiveness and to determine differences in innate immunity activation among patients treated with RCR, HV, and patients treated with chemotherapy without rituximab, PBMC were collected just before and 1 day after vaccination (RIT-03 study). Whole-genome gene expression analysis of these samples using microarray analysis reveals that the intradermal vaccination was associated with dramatic transcriptomic changes in PBMC, already detectable 24 hours after vaccination. These changes underlie modulation of innate response (eg, interferon stimulated genes, NK-releted transcripts) and differs according to the treatment administered (eg chemotherapy with or without rituximab). In conclusions: a) patients previously treated with RCR should be strictly monitored during influenza epidemic season; b) anti-neoplastic treatments containing rituximab result in prolonged and specific immune alterations.

Noncoding RNAs such as ribosomal RNAs (rRNA), transfer RNAs (tRNA) micro RNAs (miRNA), small interfering RNAs (siRNA) and long noncoding RNAs (lncRNA) are the dominant products of eukaryotic transcription and collectively represent more than 95% of total RNA of the cell. In addition to contributing as the core components of the translational machinery (rRNAs and tRNAs), these noncoding RNAs have been shown to be involved in a myriad of biological processes such as gene expression regulation and genome defence. Recently, a novel class of endogenously encoded species of RNA called circular RNAs (circRNA) has been shown to regulate gene expression in mammals by competing with miRNA targets under diverse scenarios. To investigate the role and regulatory potency of circRNAs in ovarian cancer, we performed paired-end RNA sequencing of 9 ovarian cancer samples from three patients at primary and metastatic stages and developed an in-house computational pipeline to identify and characterize the circRNA candidates. Our results show that circRNAs are widely expressed in ovarian cancer and oncogenic factors in cancer-associated pathways are particularly enriched for circRNAs. We also show that isoform diversity of circRNAs is comparable to that of the linear counterparts and a significant fraction of exons are preferentially expressed as circular forms compared to the canonical linear RNA form. Further, these candidate circRNAs are particularly enriched for miRNA seed matches and the hybridization energies of interaction favourably predicts formation of stable structural dimers between circRNAs and miRNA mature sequences. A large number of candidate circRNAs are also differentially expressed between primary and metastatic stages of ovarian cancer and show co-expression with their gene targets, implying a role for circRNAs in regulating expression of oncogenic factors. Taken together this study adds an important new dimension to the role of miRNAs vis-à-vis circRNAs in fine-tuning of gene expression and disease progression in ovarian cancer.