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Home > Formal Modelling and Analysis of the Role of Hexosamine Biosynthetic Pathway in Cancer: Exploiting Parallelism in Qualitative Biological Regulatory Networks

Formal Modelling and Analysis of the Role of Hexosamine Biosynthetic Pathway in Cancer: Exploiting Parallelism in Qualitative Biological Regulatory Networks

Thesis Info

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Author

Saeed, Muhammad Tariq

Program

PhD

Institute

National University of Sciences & Technology

City

Islamabad

Province

Islamabad

Country

Pakistan

Thesis Completing Year

2018

Thesis Completion Status

Completed

Subject

Computational Science & Engineering

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/10083/1/Muhammad%20Tariq%20Saeed_Computational%20Sci%20%26%20Engg_2018_NUST_PRR.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726225743

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Background: Cancer is one of the leading causes of death worldwide. With advancements in high throughput technologies and availability of data on gene regulations, knowledge about progression of cancer has improved and it is now viewed as a complex multifaceted systems level disease. Despite heterogeneity of the malignancies, key functions in development of cancer are common. The alteration of glucose metabolism is considered as important hallmark of cancer and an essential factor towards cell growth and invasion. Increased flux of glucose through the Hexosamine Biosynthetic Pathway (HBP) drives increased cellular O-GlcNacylation and contributes to cancer progression. However, the role of HBP in activation of key oncogenes and progression of cancer is poorly characterized. In this study, a systems-biology approach based on qualitative modelling framework (proposed by René Thomas) is used to investigate the role of HBP in activation of oncogenes that lead to cancer progression. In qualitative modelling approach, dynamic behavior of the system under investigation is determined by model parameters which are not known in advance. The parameter estimation required for qualitative modelling is computationally intensive task and takes lot of processing time. By using parallel computing, we address computationally challenging aspects of qualitative modelling which involve parameters estimation and identification of important trajectories in the model. Methodology: The methodology used to investigate the role of HBP in progression of cancer is based on qualitative modelling, model-checking, network 1 Abstract analysis using betweenness centrality and petri net modelling approach. First, in order to construct a qualitative model, key regulatory entities from the literature are incorporated in the model. Second, model parameters are computed from observations using the model-checking technology. The total number of model parameters increases exponentially with increase in number of entities. In order to cope with the complexity of parameters estimation for qualitative modelling, we use a Java based software MPJ-Express for parallelization of sequential implementation of SMBioNet software. The parallel approach divides the parameter space into different regions and each region is explored concurrently on multicore and cluster platforms. Third, from the computed set of model parameters, a dynamic qualitative model is constructed by using GinSim software. The dynamic model cannot be analyzed manually because of large number of trajectories. Hence, centrality based network analysis is carried out by using Cytoscape software for identification of important trajectories. These trajectories are further analyzed by investigating step-by-step alterations in gene expressions that lead to activation of key oncogenes and development of cancer. Fourth, hybrid modelling is carried out to compute delay constraints using HyTech model-checker. These delay constraints highlight logical relationships between synthesis and degradation rates of important genes in the model. Finally, a stochastic petri net model is developed using Snoopy software for validation of delay constraints. Results: The experimental results indicate O-linked N-acetylglucosamine transferase (OGT) as a key regulator that promotes oncogenesis in a feedback mechanism through the stabilization of C-Myc. The absence of p53-Mdm2 oscillation 2 Abstract is identified as another important contributor towards progression of cancer. Silencing of OGT and C-Myc loop reduces the glycolytic flux, while restoration of P53-Mdm2 oscillations leads to recovery and restoration of homeostasis. Together, our findings suggest potential targets that may provide a mechanismbased therapeutic approach for regulation of hyper-O-GlcNacylation in human cancer. The parallel approach presented in the study reduces processing time for parameter estimation for our qualitative model of the Hexosamine Biosynthetic Pathway and achieves almost linear speed-up on multicore and cluster platforms . The Parallel-SMBioNet implementation for logical parameters estimation is provided at http://systemsbiology.tools. Conclusion: We use a formal modelling approach to study the function of the Hexosamine Biosynthetic Pathway, which triggers hyper O-GlcNAcylation. Within the p53-Mdm2 circuit, we compute important delay constraints involving synthesis rates in order to restore homeostasis. We analyze different simulation trajectories, which showed that enhanced expression of O-GlcNAc-transferase (OGT) consistently upregulates NF-κB, PI3K and FoxM1. Moreover, persistent activation of OGT through c-Myc drives the system to a deadlock state from where recovery is not possible. These findings suggest that OGT is acting as a critical mediator of various oncogenic and tumor suppressor proteins implicated in tumor growth and development. We acknowledge that our findings are derived from a qualitative approach and could be dependent on cellular dynamics and environment. However, these discoveries form the foundation and direction of future translational research studies to design a quantitative model with additional 3 Abstract tools and experimental verification for the development of molecular therapeutics. Taken together, mechanism-based therapies that are designed to target hyper O-GlcNAcylation and OGT may hold clinical benefits in the treatment of cancer.
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۲۹۔ ہم کیسے جی رہے ہیں ؟

ہم کیسے جی رہے ہیں؟

ہم زندگی سے بھاگے ہوئے

نجانے کدھر جا رہے ہیں

ہمیں کچھ خبر نہیںہے

اپنی محرومیوں میں رنگ بھر نے کی خاطر

سفید لمحوں میں جی رہے ہیں

موت بھی ہم پر ترس کھاتی ہے

ہم بھی کیا جی رہے ہیں ؟

 آنکھوں کو بند کیے

تشنہ ہونٹوں کو سیے ہوئے

مگر کیا کیجیے

صحیح بخاری کی کتاب التفسیر کے فنی مباحث کا اختصاصی مطالعہ

The book of tafseer of Sahi Bukhari is most comprehensive book among the books of Hadith and on the basis of many features, it is considered superior to many other books of Hadith. Imam Bukhari annotates each surah one by one in his book of tafseer and constructs 114 chapters equal to the number of surah and these chapters carry 548 hadith of Zikr in which 465 are Mosool and remaining are mualaq and 100 hadith are not described before and remaining are repetitive. Imam Bukhari implements both style of description that is tafseer bil masaur and tafseer bil rai which proves the fact that Imam Bukhari supports the style of tafseer bil rai mehmood. Many Quranic information can be collected from book of tafseer for example: sabub nazool, makki & madni, ilmul qirat, ghareebul quran etc. The derivation of these features the book of tafseer of Sahi Bukhari is not the end but it is a starting point for new study.

Nutrient Management for Sunflower Production

Fertilizer management is an important part for sunflower production and one must know how input affects the crop and soil traits. Determination of optimum fertilizer rates is important because of increasing economic and environmental concerns. This study was therefore conducted to determine optimum fertilizer and manure requirement for sunflower production. In this regard, three field experiments were conducted at Students Farm, Sindh Agriculture University, Tandojam, Pakistan, located at 25o25’60’N 68o31’ 60E, altitude 19.5 m asl. In all the experiments sunflower variety HO-1 was sown in rows (75 cm spacing). The experiment-1, was meant to evaluate NPK, Zn and B requirements for sunflower production. The treatments consisted: Factor-A=Seasons (Spring and Autumn), Factor-B NPK Levels (0-0-0 NPK kg ha-1, 60-30-30 NPK kg ha-1 (N as broadcast), 90-45-45 NPK kg ha-1 (N as broadcast), 120-60-60 NPK kg ha-1 kg ha-1 (N as broadcast), 60-30-30 NPK kg ha-1 (N as fertigation), 90-45-45 NPK kg ha-1 (N as fertigation) and 120-60-60 NPK kg ha-1 (N as fertigation) and Factor-C (zinc and boron levels (0-0, 10.0-1.5, 10.0-2.0, 15.0-1.5, 15.0.2.0, 20.0-1.5 and 20.0-2.0 Zn+B kg ha-1). The results recorded taller plants (207.2 cm), maximum stem girth (12.2 cm), better head diameter (23.0 cm), more seeds head-1 (696.4), heavier seeds weight head-1 (49.0 g), bolder seed index (71.2 g), maximum seed yield (2743.0 kg ha-1) and higher dry matter (11666.7 kg ha-1), higher N-uptake (70.2 kg ha-1), P-uptake (19.1 kg ha-1), K-uptake (93.9 kg ha-1), Zn-uptake (335.8 g ha-1) and B-uptake (199.2 g ha-1) under application of 90-45- 45 NPK x 15-1.5 Zn-B kg ha-1 (N applied as fertigation). Similarly, higher values of physiological traits at flowering phase i.e dry matter (1353.0 g m-2), leaf area index (5.7), leaf area duration (55.6 days), crop growth rate (8.7 g m-2 day-1) and net assimilation rate (24.3 g m-2 day-1) were also noted for the same treatement. However, oil content in this Interactive effect showed non-significant differences. The regression coefficient (b) revealed that a unit increase in various traits resulted in corresponding increase of sunflower seed yield by head diameter (101.2 kg ha-1) seeds head-1 (6.2 kg ha-1), seed weight head-1 (55.2 kg ha-1), seed index (58.2 kg ha-1), dry matter (0.3 kg ha-1), leaf area index (1108.3 kg ha-1), leaf area duration (113.4 kg ha-1), crop growth rate (378.4 kg ha- 1 ), net assimilation rate (213.7 kg ha-1), nitrogen uptake (27.4 kg ha-1), phosphorus uptake (131.8 kg ha-1), potassium uptake (32.4 kg ha-1), zinc uptake (6.5 kg ha-1) and boron uptake (10.9 kg ha-1). However, a unit increase in seed oil content resulted corresponding decrease in seed yield by 1339.2 kg ha-1. The experiment-2, involved “Integrated use of organic manures and inorganic fertilizers nutrients for sunflower production” The treatments consisted: no manure, cattle manure (5, 10 and 15 tons ha-1) and poultry manure (5, 10 and 15 tons ha-1) with 90-45- 45 NPK + 15 Zn + 1.5 B (kg ha-1). The results of the study showed that the incorporation of fertilizers and manures significantly enhanced all the crop parameters. The taller plants (232.3, 231.2 cm), more stem girth (13.9, 13.9 cm), maximum head diameter (27.1 and 26.5 cm), higher number of seeds head-1 (801.9 and 797.9), heavier seed weight head-1 (66.6 and 65.9 g) bolder seed index (83.2 and 83.0), superior seed yield (3681.8 and 3643.2 kg ha-1) and higher dry matter at harvest (12859.3 and 12845.0 kg ha-1), higher N- uptake (80.7 and 82.2 kg ha-1), P-uptake (24.2 and 24.5 kg ha-1), K-uptake (114.2 and 114.0 kg ha-1), Zn-uptake (531.9 and 530.4 g ha-1) and B-uptake (320.4 and 314.9 g ha-1), higher dry matter (2075.0 and 2066.7 g m-2), maximum leaf area index (7.2 and 7.2), greater leaf area duration (67.4 and 67.3 days), more crop growth rate (10.3 and 10.2 g m- 2 day-1) and superior net assimilation rate (30.7 and 30.7 g m-2day-1) were recorded under cattle manure 10 t ha-1 + 90-45-45 NPK + 15-1.5 Zn-B kg ha-1 and poultry manure 5 t ha-1 + 90-45-45 NPK + 15-1.5 Zn-B kg ha-1, respectively, where N was applied as fertigation. Whereas, seed oil content showed inverse relationship under higher applications of in- organic fertilizers and manures. It was observed that application of poultry manure at 5 t ha-1 or cattle manure at 10 t ha-1 with 90-45-45 NPK + 15-1.5 Zn-B kg ha-1 significantly enhanced all these traits and beyond these treatments no significant differences were exhibited even at higher levels of manures and were economically optimum levels for achieving satisfactory crop parameters. The regression coefficient indicates that a unit increase in various traits resulted in corresponding increase of sunflower seed yield by head diameter (150.0 kg ha-1) seeds head-1 (6.5 kg ha-1), seed weight head-1 (53.1 kg ha-1), seed index (62.8 kg ha-1), dry matter (0.4 kg ha-1), leaf area index (1027.5 kg ha-1), leaf area duration (116.0 kg ha-1), crop growth rate (469.9 kg ha-1), net assimilation rate (218.3 kg ha-1), nitrogen uptake (36.1 kg ha-1), phosphorus uptake (172.1 kg ha-1), potassium uptake (40.4 kg ha-1), zinc uptake (5.9 kg ha-1) and boron (9.5 kg ha-1). However, a unit increase in oil content resulted corresponding decrease in seed yield by (1546.3 kg ha-1). The experiment-3 entitled “residual effect of organic manures and supplemental inorganic fertilizers on sunflower production” revealed prolonged maturity (99.3 and 99.33 days), taller plants (258.1 and 256.9 cm), more stem girth (16.2 and 16.2 cm), maximum head diameter (31.1 and 31.0 cm), higher number of seeds head-1 (888.1 and 884.2), heavier seed weight head-1 (80.1 and 79.7 g) bolder seed index (90.9 and 92.0 g), superior seed yield (4420.2 and 4450.4 kg ha-1) and higher dry matter (14395.9 and 14381.2 kg ha-1), higher N-uptake (100.9 and 100.3 kg ha-1), P-uptake (33.9 and 33.7 kg ha-1), K-uptake (159.1 and 158.8, kg ha-1), Zn-uptake (603.0 and 605.1g ha-1), B-uptake (361.0 and 364.7 g ha-1), maximum leaf area index (7.9 and 7.9), greater leaf area duration (76.0 and 75.8, days), higher dry matter (2808.7 and 2740.4 g m-2), more crop growth rate (12.1 and 12.0 g m-2 day-1) and superior net assimilation rate (36.9 and 36.0 g m-2day-1) were recorded under residual cattle manure 10 t ha-1 + 90-45-45 NPK + 15-1.5 Zn-B kg ha-1 and residual poultry manure 5 t ha-1 + 90-45-45 NPK + 15-1.5 Zn-B kg ha-1 respectively where N applied as fertigation and beyond these treatments no significant increase in all the crop traits was noted. The regression coefficients indicate a unit increase in various traits resulted in corresponding increase of sunflower seed yield by head diameter (157.2 kg ha-1) seeds head-1 (7.3 kg ha-1), seed weight head-1 (53.7 kg ha-1), seed index (67.9 kg ha-1), dry matter (0.4 kg ha-1), leaf area index (1064.0 kg ha-1), leaf area duration (111.2 kg ha-1), crop growth rate (456.8 kg ha-1), net assimilation rate (195.3 kg ha-1), nitrogen uptake (36.0 kg ha-1), phosphorus uptake (143.0 kg ha-1), potassium uptake (33.3 kg ha-1), zinc uptake (6.5 kg ha-1) and boron (10.3 kg ha-1), however, a unit increase in oil content resulted in corresponding decrease in seed yield by 2037.6 kg ha-1. It is concluded that the fertilizers and manures enhanced all the crop traits, nutrient uptake and improved soil fertility. The application of NPK (90-45-45 kg ha-1, N applied as fertigation) + Zn+B (15+1.5 kg ha-1) with 10 t ha-1 of cattle or 5 t ha-1 poultry manure for their residual effect in the subsequent crop were superior and optimum fertilizer and manure doses for sunflower production without degrading fertility of soil. It is suggested that any source of well decomposed organic manures could be incorporated in the field to enrich the soil fertility on long term basis and higher sunflower production. Thus, it is recommended that sunflower crop should be fertilized with incorporation of NPK (90-45-45 kg ha-1, N as fertigation) + Zn+B (15+1.5 kg ha-1) with 10 t ha-1 cattle or 5 t ha-1 poultry manures for satisfactory yield and maintenance of soil fertility.