Biological Networks: Modeling and Structural Analysis

Biological networks are receiving increased attention due to their importance in understanding life at the cellular level. There exist many different kinds of biological networks, and different models have been proposed for them. In this dissertation we focus on suitable network models for representing experimental data on protein interaction networks and protein complex networks (protein complexes are groups of proteins that associate to accomplish some function in the cell), and to design algorithms for exploring such networks. Our goal is to enable biologists to identify the general principles that govern the organization of protein-protein interaction networks and protein complex networks. For protein complex networks, we propose a hypergraph model which more accurately represents the data than earlier models. We define the concept of k-cores in hypergraphs, which are highly connected subhypergraphs, and design an algorithm for computing k -cores in hypergraphs. A major challenge in computational systems biology is to understand the modular structure of biological networks. We construct computational models for predicting functional modules through the use of graph clustering techniques. The application of earlier graph clustering techniques to proteomic networks does not yield good results due to the high error rates present, and the small-world and power-law properties of these networks. We discuss the various requirements that clusterings of biological networks are required to satisfy, design an algorithm for computing a clustering, and show that our clustering approach is robust and scalable. Moreover, we design a new algorithm to compute overlapping clustering rather than exclusive clustering. Our approach identifies a set of clusters and a set of bridge proteins that form the overlap among the clusters. Finally we assess the quality of our proposed clusterings using different reference sets

Modeling Oscillatory Flow in a Cone-and-Plate Device Using Computational Fluid Dynamics

Calcific aortic heart valve disease has been investigated in literature over the past three decades. Researches have been trying to understand the mechanism by which the calcification occurs on the aortic valve leaflets. Mechanical forces due to the flow of blood have been shown to have a significant contribution to the calcification of the leaflets, however, no one was able to study the native mechanical environment in the heart valve due to the complexity of the geometry. There is a soluble factor that is a known precursor for the disease called Transforming Growth Factor-β1. TGF-β1 is a protein which exists in large amounts in platelets that are flowing in the blood. The mechanism by whichTGF-β1 activates and contributes to the disease is not known, but its known that calcification is seen in areas were disturbed flow exists. This disturbed flow is defined as low and oscillatory shear environment, therefore, researchers studied the activation of TGF-β1 under oscillatory shear versus steady shear using a cone and plate device. There is, however, a lot of ambiguity in the way one produces oscillatory shear in a cone and plate. In this thesis we first study a simple geometry of a parallel plate. We see that abruptly stopping the plate to change directions of translation yields two spikes in the volume averaged shear rate that are 1.6 and 1.2 times higher than the average when stopping and restarting the movement of the plate, respectively. Areas of the fluid which experience elevated shear rates compared to the average constitute 65 percent of the volume of the fluid in the parallel plate. A different shear rate profile was seen when the plate was linearly decelerated to zero then re-accelerated to translate in the opposite direction. We only saw one peak which was 1.3 times higher than the average value with 20 percent by volume of the fluid experiencing shear rate value higher than the average value of 380s−1. Moreover, a sinusoidal oscillation of the plate did not show any spike in the shear rate and 98 percent of the fluid, at the end of the stopping period, experienced shear rate values between 107s−1and 120s−1where the minimum and maximum shear rate values were 106.2s−1and 120.2s−1. We then studied the more complicated geometry of the cone and plate and saw similar behaviors in the volume averaged shear rate profiles compared to those computed in the parallel plate case. Abruptly stopping the cone showed two spikes upon stopping and starting that were both 1.6 times higher than the average. At the end of the sinusoidal rotation we computed a volume averaged value of 175s−1with a minimum shear rate value of 0.001s−1and 963s−1. We further computed that5 percent of the fluid is experiencing shear rate values that are 2x the average value or higher. In the case of the linear deceleration/acceleration, we saw apeak that is 1.7 times higher than the average. We computed that at the end of the stopping period the volume averaged shear rate value is 380s−1with a minimum shear rate value of 0.6s−1and a maximum value of 3973s−1. We further computed that 13 percent of the fluid experiences values of shear rate that are 2x the average value or higher. In the case of the sinusoidal rotation, no spikes in shear rate were seen. At the end of the sinusoidal oscillation, we computed a minimum shear rate value of 0.6s−1, a maximum shear rate value of 1690s−1, and a volume averaged shear rate value of 350s−1. We further computed that 5 percent of the fluid experiences shear rate values that are 2x the average or higher

The Architecture of a Proteomic Network in the Yeast

We describe an approach to clustering the yeast protein-protein inter-action network in order to identify functional modules, groups of proteins forming multi-protein complexes accomplishing various functions in the cell. We have developed a clustering method that accounts for the small-world nature of the network. The algorithm makes use of the concept of k-cores in a graph, and employs recursive spectral clustering to compute the functional modules. The computed clusters are annotated using their protein memberships into known multi-protein complexes in the yeast. We also dissect the protein interaction network into a global subnetwork of hub proteins (connected to several clusters), and a local network consisting of cluster proteins

Replantation of Nine Fingers in a Patient: A case report

Amputation of multiple fingers of both hands is a rare and serious injury. We report a case of a 41-year-old male patient who presented to Khoula Hospital, Muscat, Oman, in 2015 with the amputation of nine fingers due to a workplace injury. With two teams working in tandem, all the amputated fingers were re-attached. A total of seven fingers survived and the patient regained reasonable functionality of his hands. To the best of the authors’ knowledge, this is the first case of several finger amputations in Oman.Keywords: Fingers; Traumatic Amputation; Crush Injuries; Replantation; Case Report; Oman

The potentiality of hydrocarbon generation of the Jurassic source rocks in Salam-3x well, North Western Desert, Egypt

AbstractThe present work deals with the identification of the potential and generating capability of oil generation in the Jurassic source rocks in the Salam-3x well. This depending on the organo-geochemical analyses of cutting samples representative of Masajid, Khatatba and Ras Qattara formations, as well as, representative extract samples of the Khatatba and Ras Qattara formations. The geochemical analysis suggested the potential source intervals within the encountered rock units as follows: Masajid Formation bears mature source rocks and have poor to fair generating capability for generating gas (type III kerogen). Khatatba Formation bears mature source rock, and has poor to good generating capability for both oil and gas. Ras Qattara Formation constituting mature source rock has good to very good generating capability for both oil and gas. The burial history modeling shows that the Masajid Formation lies within oil and gas windows; Khatatba and Ras Qattara formations lie within the gas window. From the biomarker characteristics of source rocks it appears that the extract is genetically related as the majority of them were derived from marine organic matters sources (mainly algae) deposited under reducing environment and take the direction of increasing maturity and far away from the direction of biodegradation. Therefore, Masajid Formation is considered as effective source rocks for generating hydrocarbons, while Khatatba and Ras Qattara formations are the main source rocks for hydrocarbon accumulations in the Salam-3x well

Long-Term Aerosol Trends and Variability over Central Saudi Arabia Using Optical Characteristics from Solar Village AERONET Measurements

Natural and anthropogenic aerosols over the Kingdom of Saudi Arabia (KSA) play a major role in affecting the regional radiation budget. The long-term variability of these aerosols’ physical and optical parameters, including aerosol optical depth (AOD) and Ångström exponent (α), were measured at a location near central KSA using the Solar Village (SV) AERONET (Aerosol Robotic Network) station during the period December 1999–January 2013. The AERONET measurements show an overall increase in AOD on an annual basis. This upward trend is mainly attributed to a prolonged increase in the monthly/seasonal mean AOD during March–June and during August– September. In contrast, lower AOD values were observed during November–December. This can be attributed to a low frequency of dust outbreaks and higher precipitation rates. An overall, weak declining trend in α was observed, except during the summer. The spring and summer seasons experienced a pronounced increase in the number of coarse particles (~2 µm) during April 2006– January 2013 as compared to December 1999–March 2006, suggesting an increase in natural aerosol loadings. Using the HYSPLIT model, it was found that the March 2009 dust storm contributed to the mixing of long-transported dust with anthropogenic local emissions near the SV. The results suggest that extensive industrial activity contributed to the increase of anthropogenic emissions over KSA during the period April 2006–January 2013

Solar potential in Saudi Arabia for flat-plate surfaces of varying tilt tracking the sun

The objective of the present work is to investigate the performance of flat-plate solar panels in Saudi Arabia that continuously follow the daily motion of the sun. To that end, the annual energy sums are estimated for such surfaces at 82 locations covering all Saudi Arabia. All calculations use a surface albedo of 0.2 and another one with a near-real value. The variation of the solar energy sums on annual, seasonal, and monthly basis is given for near-real ground albedos; the analysis provides regression equations for the energy sums as function of time. A map of the annual inclined solar energy for Saudi Arabia is derived and presented. The annual energy sums are found to vary between 2159 and 4078 kWhm −2 year −1. Finally, a correction factor, introduced in a recent publication, is used; it is confirmed that the linear relationship between the correction factor and the ground-albedo ratio is general enough to be graphically representable as a nomogram. A discussion regarding the differences among solar systems on horizontal, fixed-tilt, 1-axis, and 2-axis systems is presented

Phytochemical studies on Diplotaxis harra growing in Sinai

Five main flavonoid glycosides were isolated from the ethanolic extract of Diplotaxis harra (Cruciferae), and were identified as quercetin, isorhamnetin 3-rhamnoside, isorhamnetin 3-o-rutinoside, isorhamnetin 3-glucosyl-4`-rhamnoside and isorhamnetin 3-o-β-glucoside. These compounds were identified according to their Rf values, partial and complete acid hydrolysis, UV, 1H-NMR, 13C-NMR and 2D NMR (HSQC, HMBC) spectroscopy. The alcoholic extract of plant was evaluated against some bacterial strains which showed moderate antibacterial activity, while petroleum ether extract doesn't show any activity

Physical and in silico approaches identify DNA-PK in a Tax DNA-damage response interactome

<p>Abstract</p> <p>Background</p> <p>We have initiated an effort to exhaustively map interactions between HTLV-1 Tax and host cellular proteins. The resulting Tax interactome will have significant utility toward defining new and understanding known activities of this important viral protein. In addition, the completion of a full Tax interactome will also help shed light upon the functional consequences of these myriad Tax activities. The physical mapping process involved the affinity isolation of Tax complexes followed by sequence identification using tandem mass spectrometry. To date we have mapped 250 cellular components within this interactome. Here we present our approach to prioritizing these interactions via an <it>in silico </it>culling process.</p> <p>Results</p> <p>We first constructed an <it>in silico </it>Tax interactome comprised of 46 literature-confirmed protein-protein interactions. This number was then reduced to four Tax-interactions suspected to play a role in DNA damage response (Rad51, TOP1, Chk2, 53BP1). The first-neighbor and second-neighbor interactions of these four proteins were assembled from available human protein interaction databases. Through an analysis of betweenness and closeness centrality measures, and numbers of interactions, we ranked proteins in the first neighborhood. When this rank list was compared to the list of physical Tax-binding proteins, DNA-PK was the highest ranked protein common to both lists. An overlapping clustering of the Tax-specific second-neighborhood protein network showed DNA-PK to be one of three bridge proteins that link multiple clusters in the DNA damage response network.</p> <p>Conclusion</p> <p>The interaction of Tax with DNA-PK represents an important biological paradigm as suggested via consensus findings <it>in vivo </it>and <it>in silico</it>. We present this methodology as an approach to discovery and as a means of validating components of a consensus Tax interactome.</p