Project Title: Microbial Enhanced Oil Recovery (MEOR) (ongoing)
Project Code: SR/SCI/BIOL/08/01
Investigators Elshafie, A.E.  ( Biology, COS, SQU); Al-Bahry, S.N. (Biology, COS, SQU)                                                                                
Collaborator (s) (Name & affiliation): Al-Wahaibi, Y. (Engineering, SQU), Al-Siyabi, Z. (Min. of Oil & Gas), Mandhari, M. (PDO)
Duration: 3 years
Budget: 90000
Year: Third
Summary:
Microbial Enhanced Oil Recovery (MEOR) has started at SQU in 2008 with very clear objectives of building scientific capacity, set up protocols for isolating and identifying indigenous microorganisms in Wafra Oil Field (PDO) and study the characteristics of these microorganisms. All these with the aim of supporting MEOR field application in Oman for the increase of oil production in Wafra Oil wells. Microorganisms will be isolated, characterized morphologically and culturally using Denaturation Gradient Gelelectrophorosis (DGGE), PCR and DNA sequencing. The abilities of the anaerobic isolates and consortia to grow at 60oC and produce gases, acids, biosurfactants and biopolymers in different media will be assessed, identified and quantified. Microflora map of the Wafra Oil wells will be constructed and correlated with the geological, chemical and petrophysical map of Wafra Oil wells. Core flooding experiments will be carried out to assess the abilities of the anaerobic microbial consortia to release oil from core.

Project Title: Bioremediation of oil polluted ecosystems in the Sultanate of Oman (Awarded)
Project Code: RC/SCI/BIOL/11/01
Investigators
Abed, R. Biology, SQU; Al Waihabi, Y., (Petroleum engineering, SQU); Dobretsov, S., (CAMS, SQU)., Al Bahry, S., (Biology, SQU); Al Harthy, A. (PDO, Oman); Al Sabahi, J. (CAMS, SQU)
Collaborator (s) (name & affiliation):
Duration: 3 years
Budget: 133,000
Year: 2011
Summary: Frequent incidences of oil pollutions have been reported in Oman, some of high magnitude that caused severe impacts on terrestrial and marine environments. Oil pollution poses serious threats for the Sultanate’s economy, fishing industry, public health, water desalination plants, underground water, agriculture soils and tourism. So far, there are very few national projects that deal with oil spills and ways to treat them. This project aims at testing various bioremediation approaches (mainly biostimulation and bioaugmentation) for the cleanup of oil pollution using indigenous bacteria under the extreme environmental conditions of the Gulf region. We will investigate the use of oil-polluted cyanobacterial mats and isolated cyanobacterial consortia for bioremediation. We hypothesize that the oil-polluted ecosystems of Oman are rich in novel halophilic and thermophilic oil-degrading bacteria, whose biodegradation activity can be increased by the addition of limited nutrients and optimizing environmental conditions. The presence of cyanobacteria in cyanobacterial consortia will facilitate degradation processes by fueling the oil-degrading bacteria with necessary oxygen, nitrogen and organics via their nitrogen fixation, photosynthesis and fermentation processes, thus circumventing the expensive use of fertilizers and chemicals normally used in the cleanup of oil pollution. In the proposed work, biostimulation of indigenous bacteria through optimization of environmental conditions and the addition of inorganic and organic fertilizers will be compared. Bioaugmentation, which involves the addition of bacteria, will be carried out after isolation and characterization of halophilic and thermophilic oil-degrading bacterial consortia. The response of indigenous microbial communities to treatments will be monitored using state-of-art molecular techniques such as denaturing gradient gel electrophoresis (DGGE), automated rRNA intergenic spacer analysis (ARISA), fluorescent in situ hybridization (FISH) and 16S rRNA cloning. Bacterial consortia that are relevant to oil biodegradation will be tested for their ability to bioremediate polluted areas under in situ conditions. The proposed research will enable us to gain a better fundemental understanding of polluted ecosystems in Oman and bacterial diversity and activity under multiple extreme coditions. The project will lay the foundation for bioremediation of oil polluted ecosystems in Oman, help in capacity building and training of Omani students and contribute to the establishment of a bioremediation research nucleus at Sultan Qaboos University with most modern techniques.

Project Title: A Community Genomic Study of Inherited Neurological Disorders in Oman (Awarded)
Project Code: RC/SCI/BIOL/10/01
Investigators
Alkhayat AlShehi, A. , Biology, SQU; Koul, R., (Child Health, SQUH); Alfetaisi, A., (Child Health, SQUH); Alasmi, A., (Neurology, Medicine, SQU); Ramachandiran N., (Neurology, Medicine, SQU); Gujjar, A. R.,  (Neurology, Medicine, SQU); AlRasbi, S., (Neurology, Medicine, SQU)
Collaborator (s) (name & affiliation): Crosby, A.H., (St Georges University of London, London, UK)
Duration: 3 years
Budget: 124,750
Year: 2010
Summary: This projects studies inherited neurological autosomal recessive diseases are in the Omani community. The overall objective of this project is to identify the genes responsible for these disorders using the method of Homozygosity Mapping. We use Affymetrix Microarray platform to perform the 10K and the 250K SNP chip arrays genotyping for the affected patients and compare them to their parents and their no affected siblings. Regions of shared homozygosity are analyzed by Bioinformatics tools in order to initiate the process of candidate gene prioritization and sequencing.

Project Title: The ecological role of nutrients in Omani wadis (ongoing)
Project Code: IG/SCI/BIOL/09/01
Investigators: Barry, M. J., (Biology, SQU); Abed, R. M. M. (Biology, SQU)
Duration: 2 years
Budget: 7000 OR
Year: 2009
Summary:
This project aimed to study ecological processes in wadis and natural and anthropogenic factors that could affect them. In the first part of the project cyanobacterial communities in Wadi Al Khoud were studied using  microscopic, pigment, and molecular techniques. The effects of environmental conditions on community structure were measured.  Additionally the ability of the cyanobacterial communities to fix atmospheric nitrogen was measured. Following flooding, the recovery of communities was also recorded. We found that communities varied significantly between sites and that flooding had a major effect on community composition and rates of nitrogen fixation. These findings were discussed in light of different models of community recovery. In the second part of the study we investigated impact of human disturbance on a key wadi grazer the Arabian toad (Bufo arabicus). The effects of predators and heavy metal pollution were measured on this species. We found that the tadpoles respond to invertebrate predators by changing their shape and growth pattern and that exposure to pollutants can inhibit these responses.

Project Title: Bioremediation of oil-polluted sites under extreme environmental conditions (ongoing)
Project Code: IG/SCI/BIOL/09/02
Investigators: Abed, R. (Biology, COS, SQU); Al-Bahry, S. (Biology, COS, SQU)
Collaborator (s):
Duration: 2 years
Budget: 4500 OR
Year: 2009
Summary:
Oil pollution of the marine environment poses serious threats for the economy and tourism in Oman. The project aims at designing a bioremediation approach based on the use of indigenous oil-degrading bacteria, which dominate oil-polluted coastal sediments. We hypothesize that the presence of these consortia will facilitate degradation processes and circumvent the expensive use of fertilizers. On the other hand, polluted sediments of Oman (Wadi Al Milh-Qurieat and oil-wells in Dakhleia) are expected to be rich in novel halophilic and thermophilic oil-degrading bacteria, which will efficiently degrade oil components under the harsh local environmental conditions. In the proposed work, we will identify and characterize oil-degrading aerobic chemotrophs from different polluted sites using cultivation as well as molecular techniques such as denaturing gradient gel electrophoresis (DGGE). Bacterial consortia that are relevant to oil biodegradation will be isolated in cultures and then tested for their ability to bioremediate polluted areas. The proposed research will enable us to gain a better understanding of marine ecosystems in Oman, explore the diversity of biotechnologically-significant novel bacteria, clean polluted coasts and setting up a unit for microbial ecology research at the SQU with most modern molecular techniques.

Project Title: Gene gun mediated gene transfer in somatic cells in date palm (awarded)
Project Code: IG/SCI/BIOL/10/02
Investigators Sardar, A. F. (Biology, SQU); Al-Rawahy, S. (Biology, SQU)
Duration: 3 years
Budget: 5500
Year: 2010
Summary:
Date palm (Phoenix dactylifera) is an important fruit tree crop of Oman. So far there is no research conducted on the genetic engineering of date palm anywhere in the world. The present proposal deals with the genetic transformation in the callus cells of date palm using gene gun device. Gene gun uses particle bombardment for cell transformation in which high density, sub-cellular sized gold particles coated with DNA are accelerated to high velocity to deliver genes into living cells. The proposed project aims to standardize the protocols for the biolistic gene transfer and the expression of the genes in the cells. It is proposed to use pUC19 vector with luciferase (LUC) and glucuronidase (GUS) reporters. After bombardment the callus will be cultured for 1 week before assaying the enzyme activities of GUS and LUC.

Project Title: Expression of gonadal progesterone receptors and plasma estradiol during embryonic development of the green turtle, Chelonia mydas, eggs under various incubation temperature.
Project Code: IG/SCI/BIOL/10/01
Investigators:  Al-Bahry, S., Mahmoud, I., Al-Amri, I., Al-Azkawi, A., Bakheit, C., Yaish, M.
Duration:  3 years
Budget: 9200
Year: 2009-2012
Summary:

Fresh green turtle eggs will be collected at random from different nests immediately after egg laying in green turtles at Ras Al Hadd Reserve during peak nesting period. Immediately after collection, the eggs will be brought to SQU and placed in three different incubators with 40-45 eggs in each incubator – set at constant temperature throughout the incubation period. Incubator one will be set at 30oC, to produce female hatchlings; the second will be st at 26oC to produce mixed sexes. Higher nest temperature 30-31oC always produces female while temperature at 26-27oC always produces males and in between temperature mixes sexes are produced. Under these incubation temperatures different embryonic stages will be examined to determine the presence of progesterone receptors (PGRs) using immunogold techniques which is the most important indicator of the gonadal differentiation in females. The localization of PGRs will be determined using the immunogold and transmission electron microscope (TEM) technique. Scanning electron microscope (SEM) and the routine light histological preparations of gonadal tissues will be used to examine the sex of the embryo especially after the critical period (21-27 days) of incubation in which gonadal differentiation takes place in the sea turtles. Plasma estradiol (E2) levels using HPLC MS/MS will also be monitored at different stages of development. The detectable plasma levels in the embryo, is an important indicator for the presence of PGRs since E2 is the main primer of PGRs. During the developmental stages many changes of plasma protein are linked to the appearance of PGRs and E2.  Expression of the proteins will be analyzed by SDS gel electrophoresis (SDS-PAGE) and the 2-dimensional gel electrophoresis (2DGE). The PGRs, E2 and detection of plasma proteins in this study will be the first in the sea turtles which would be an important tool in analyzing the effect of incubation temperatures on gonadal differentiation in sea turtles.

Project Title: Bio-monitoring of metals, hydrocarbons and dioxins in sea water, sediment and marine organisms from the Arabian Sea and Gulf of Oman (ongoing)
Project Code: EU/LPool/336/2009
Investigators: Al-Rawahy, S. H. (Biology, COS, SQU)
Collaborator (s) (name & affiliation): Van den Berg, S. C. (School of Environmental Science, University of Liverpool, U.K.)
Duration: 3 years.
Budget: 12,500 OR
Year: 2009-2012
Summary:
Identification of inorganic and organic pollutants has become an important environmental issue in the Arabian Gulf Region within the past few years. Several studies conducted in the Arabian Sea indicated ubiquity of heavy metals and organic pollutants in different marine matrices. Elevated concentrations of contaminants in seawater, sediment and biota indicate an alarming environmental signal of possible toxicological effects for the marine organisms and growing risk for human. For Oman, marine products (fish and shellfish) are essential diet items for people and represent important commercial exported goods. Therefore, monitoring of pollutants should be developed to protect human health and conserve the environment. Concerning marine contamination, previous investigations conducted so far are characterized by notable shortcomings. For example, few commercial fish species were included and limited number of specimens/pollutants was analyzed. They did lack temporal trends in the contaminant concentrations and were spatially-scattered along provincial coastlines. This project intends to compensate for temporal changes in contaminants levels in commercially-valuable fish species in Omani water of the Arabian Sea. Recent massive kills in fish and green turtle populations in the Arabian Sea indicate an alarming environmental signal of underlying problems. These problems can have a long-ranging impact on the economic vitality of the region, especially marine life and tourism. The aim of this study, therefore, is to investigate the accumulation and effects of these environmental pollutants on important commercial fish species in the Arabian Sea and Gulf of Oman. The study will also monitor and examine the accumulation of these pollutants in the green turtle population during nesting activity in Ras Al-Hadd Turtle Reserve using trace metal indices as a guide in evaluating the health status of turtle populations relative to the level of regional pollution. The compilation of data obtained here will be useful for future toxicological studies and insure proper investigation of the effects of environmental pollution on marine species over a long period of time to promote biodiversity conservation and sustainable development.

Project Title: Proteomic Screening for Salt and Drought Tolerance Factors In Grey Mangrove
Project Code: IG/SCI/BIOL/11/4
Investigators: Mahmoud Yaish and Ahlam Said Al-Azkawi
Duration: 2011-2012
Budget: 5335
Year: 2011
Summary:
Soil salinity is a serious problem in the Sultanate of Oman. Recently, this problem led to desertification of large agricultural areas especially in AL-Batina region where it is causing a significant economical loss for the local farmers. Biotechnology may provide a solution to this problem by generating genetically modified plants with an enhanced salt tolerance property. This can be achieved by transforming the salt susceptible plants with specific genes isolated from the salt tolerant plants. As a preliminary study, in this project we aim to identify some proteins from the Grey mangrove  (Avicennia marina) which  are differentially accumulate due to salt conditions.
The outcome of this project is supposed to facilitate the production of transgenic plants with novel salt tolerance traits.

Project Title: Development of a Bacterial Insecticide Against The Pomegranate Butterfly.
Project code: IG/SCI/2011-23
Investigators: Derek Roberts, Mahmoud Yaish & Michael Barry
Duration: 3 years
Budget: RO 5,335
Summary:
Pomegranate is an important fruit plant in the Sultanate of Oman. This plant is affected by some agricultural pests including the butterfly (Virachola isocrate). The larva of this insect causes a significant loss in the yield and recently it has become a major problem for the pomegranate growers. Chemical treatment using conventional pesticides cause environmental pollution. In addition, their effect on the pomegranate butterfly is limited by the development of insecticide resistance and because the larval stage of the butterfly is an internal parasite of the plant and so can only be reached by systemic insecticides. Biological insecticides are proteins secreted by some bacteria that are poisonous to the insects, and so are toxins. Several forms of Bacillus thuringiensis toxin (Bt) have been previously used to control some insect species in corn and cotton. These proteins are harmless to vertebrates. In this project we aim to look for an insecticidal Bt protein suitable to control the pomegranate butterfly. This includes cloning and genetically transformation of a Bt gene into punica plant. Identifying that protein will be the first step toward cloning the coding gene in the pomegranate plant and produce a plant resistant to the butterfly.

Project Title: Optimization of recovery, culture and cryopreservation of camel donor cells for cloning
Project Code: IG/SCI/BIOL/11/02
Investigators: N/A
Duration:  2 Years
Budget: 7850
Year: 2011
Summary:
Cloning of domestic animals is a reality. This reality is manifested by the latest announcement of cloning the dromedary camel in the UAE. Given the fact that the camel species is of paramount importance in the GCC from a cultural and economical aspect, the race to optimize and standardize the nuclear transfer/cloning procedure has just began.  Although the first cloned animal was produced from a cumulus cell, no other cell type has been tested to date. Our objective is to characterize other donor cell types namely those of a somatic or embryonic background and to test their potential for cryopreservation and genomic stability. Characterization and improvement in the cryo-survivability of donor cells would enhance the reprogramability and compatibility of donor with the recipient oocyte. Thereby improving the success rate of camel cloning. Those state of the art biotechnologies would provide the means to preserve the genetics of the most valuable milk producing and high merit racing camels in Oman and the entire GCC countries.