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Home > Gene Identification in Mendelian Disorders Using Whole Exome Sequencing

Gene Identification in Mendelian Disorders Using Whole Exome Sequencing

Thesis Info

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Author

Jameel, Muhammad

Program

PhD

Institute

Pakistan Institute of Engineering and Applied Sciences

City

Islamabad

Province

Islamabad

Country

Pakistan

Thesis Completing Year

2016

Thesis Completion Status

Completed

Subject

Applied Sciences

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/7255/1/Muhammad_Jameel_Biotechnology_2016_HEC_Scholar_HSR_PIEAS_13.05.2016.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726254775

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Genetic disorders are a major cause of disabling conditions in regions of the world with high rates of consanguinity. Pakistan has a tradition of consanguineous marriages and therefore a high prevalence of Mendelian disorders. Charcot-Marie-Tooth syndrome and autosomal recessive spastic ataxia of Charlevoix-Saguenay affect peripheral nerves leading to severe foot deformity. Cerebral palsy, ataxia telangiectasia and hereditary multiple exostoses are some examples of the disorders that renders a person incapable of spending a normal life style. Such abnormalities may incapacitate the socioeconomic development of a country by putting forth major burden with respect to providing health care facilities. Importantly, ensuring the normality of a fetus will likely decrease the number of pregnancies a couple may have thereby decreasing the burden on society and family. Recent advancements in genomics enable genetic screening of large cohorts. Next generation sequencing technologies are used to identify genes, gene variants and variable expression associated with specific phenotypes. Exonic regions are known to contain most of the variants responsible for Mendelian disorders. Traditional approaches like linkage analysis and Sanger sequencing of candidate genes are costly or time consuming and a large samples size is required for this purpose. In this study ten inbred families from Pakistan were investigated using whole exome sequencing as a diagnostic and mutation identifying tool. Variants form whole exome sequencing were prioritized based on their functional relevance, disease association, pedigree information, inheritance pattern and pathogenicity scores using bioinformatics software. All the variants were validated through Sanger sequencing to rule out errors. Five novel mutations and two previously reported mutations were identified in this study. These variants were also evaluated for their functional impact using various bioinformatics tools. The findings in this study will help in understanding the disease mechanism and related pathways as well as annotating various entities of genome. The incidence of these disorders in Pakistan can be reduced through efficient carrier screening, genetic counseling, prenatal diagnosis and improved therapeutic approaches.
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علم کے فائدے

علم کے فائدے
علم نور ہے جہالت تاریکی ہے۔ علم کی شعائیں جہاں پہنچتی ہیں جہالت کے گھٹا ٹوپ اندھیرے اپنا وجود ختم کر بیٹھتے ہیں۔ قصر جہالت و لاعلمی کے در و دیوارلرزنے لگتے ہیں، خزاں رسیدہ دل و دماغ بہار آشنا ہوتے ہیں۔ علم کے زیور سے مرصعّ ومزیّن انسان عزّت وعظمت کے قصر رفیع میں مکین ہوتا ہے، معرفت وآگہی کا تاج سر پر سجائے فرائض منصبی کی ادائیگی کے لیے کمر بستہ رہتا ہے ،علم و آگہی کے نشتر سے معاشرے میں موجو ظلم و بربریّت کے ناسور کے متعفن مادے کے اخراج میں اہم کردار ادا کرتا ہے وہ کشور علم و دانش کا شہنشاہ اور اقلیم روحانیت کا تاجدار ہوتا ہے۔
علم انسان کوانسانیّت کی معراج پر فائز کرتا ہے، تاریخ شاہد ہے کہ اس عالم رنگ و بو میں جو مقام و مرتبہ اہل علم کو نصیب ہوا ہے وہ کسی اور کونہیں ملا ،علم ہی کی بدوت ہم نے فضاؤں کومسخر کیا ہے ،علم ہی کے ذریعے ہم نے ہواؤں میں پرواز یں کی ہیں، علم ہی کے سبب ہم نے جبال شامخہ کی سینہ شگافی کی ہے، علم ہی کی وجہ سے ہم نے اپنے کھیتوں اور کھلیانوں کو کشت ِزعفران بنایا ہے، علم کی تیغ سے غفلت و لاپرواہی کی جڑ کاٹی ہے ،علم کی شمع سے اندھیروں کوا جالا بخشا ۔علم نے ہمیں سچ اور جھوٹ میں فرق کرنے کا سلیقہ عطا کیا، اسی علم ہی کی بدولت اللہ اور اس کے رسول صلی اللہ علیہ و آلہٖ وسلمکی شناخت نصیب ہوئی۔
علم ہے میراث مومن کی ، اسے حاصل تو کر
علم ہے درمان راشدؔ اور جہالت اک مرض
اللہ تعالیٰ خالق ہے اور اس کے علاوہ دنیا کی ہر شے مخلوق ہے، انسان کو اللہ تعالیٰ نے اشرف المخلوقات بنایا ہے، اور اس جملہ...

البعد الأخلاقي في سياسة الرسول صلى الله عليه وسلم

The Arab’s tribes were diverse and were scattered all over Arabia. They were alien to any system, were unfamiliar of any rules and regulations. When the prophet PBUH came to them, He gently handled them, made them lenient, gathered them at the one true platform and eventually he was succeeded in uplifting them into the bondage of brotherhood. He guided them towards the political structure so that they can live under its shadow and follow its rules and regulations. He trained amongst them Preachers, judges, leaders and politicians. He sent his messengers to all the rulers of the worlds. These messengers were able to shake the Persians and Roman thrones which were considered the greatest empires of that time. They all got united against this newly arising force which later brought the greatest revolution in the history of humankind. The solutions presented by the Prophet PBUH while confronting the challenges in spreading his message,  enjoy the political wit, which is considered far better than the wit of political scholars and political tycoons. His ability of prior reading of the incidents, uncovers his huge potential in his prior dealing of the matters and suggesting its solutions and substitutes. His policies played a vital role in establishing the prior relations with Njashi, and later to facilitate the Muslims during their first immigration towards Abyssinia from the cruelty of the idolaters. Moreover, He chose the best time for the Treaty of Hudaybiyyah and Conquest of Mecca. He chose among his companions the one who knew the International languages and sent them as his Ambassadors to the rulers and tribal chiefs along with his written or verbal messages. He addressed the each with the method appropriate to him and suited him the best. He made best use of alliance, as he alienated the Arab tribes, from Jews and the others. In this way he was able to take a huge time to concentrate on those nations and was able to make a lot of allies. In his internal policy matters, he always tried to solve his problems, developing the society and to sabotage the malicious intentions which were planned by hypocrites, who were considered as his most dangerous enemies. His policy towards them was to admit apparently and leaving their unrevealed intentions to ALLAH. He treated them well, because he was anxious on preserving the freedom of all and the unity among his companions. When their malicious intentions started turning to become a threat to the security of Islam and started harming the interests of the society, He had not reply them strongly and dissuasively. He demolished the Mosque through which they were planning to harm the Muslim community. Moreover, he drew a line to their plans of aggression without harming anyone. He was very witty in his policies through which he was able to defeat them in the end. In this way he was able to change the course of the whole history on mankind. In this research we will try to deal with his moral wit which is considered the main characteristic of his policy.

Documenting the Therapeutic Potential of Encapsulated Cardamom Essential Oil

Proposed study was an effort to investigate the antimicrobial and nutraceutical worth of black and green cardamom extracts. For the purpose, cardamom powders were analyzed followed by the supercritical fluid extraction, GC-MS quantification, estimation of antimicrobial and antioxidant potential of the extracts. Afterwards, encapsulation of cardamom essential oils in guar gum and whey protein isolates blends and finally bio-evaluation trial was carried out for the management of hypercholesterolemia, liver and renal malfunctioning. In present study, supercritical fluid extraction technique was used to obtain high extraction efficiency. In terms of antioxidant potential, black cardamom showed higher amount of polyphenols than green cardamom as 1325.03±7.69 and 934.72±6.94 mg GAE/100g for TPC, 208.63±10.36 and 192.45±9.62 μmol Fe2+/g for FRAP, 172.58±6.14 and 143.96±7.38 μM Trolox/g for ABTS, 63.57±3.48 and 56.81±2.01 % for DPPH assays. However, total flavonoids contents were present in greater amount in green cardamom compared to black cardamom investigated as 215.74±6.32 and 168.25±5.26 mg CE/g. GC-MS quantification indicated that 1,8-cineole (44.24% and 28.71%) and α-terpinyl acetate (12.25% and 38.4%) were the principle components in black and green cardamom essential oils which were responsible for pungency and pleasant aroma, respectively. Moreover, antimicrobial evaluation revealed that green cardamom extract exhibited more inhibitory effects than black cardamom extract on the growth of microorganisms, quorum sensing inhibition of C. violaceum and biofilm formation inhibition of S. typhimurium and E. coli. The results related to encapsulation of black and green cardamom supercritical fluid extracts showed that encapsulation efficiency, entrapment capacity and moisture content ranged between 63.54% to 84.72%, 5.77% to 7.08% and 5.81% to 6.33% in freeze dried capsules. On the basis of encapsulation efficiency, one from black and one from green cardamom encapsulates were used for cupcakes development and in the preparation of nurtaceutical diets. Cupcakes containing green cardamom (Elettaria cardamomum) extract produced good aroma while taste was good with the cupcakes prepared from black cardamom (Amomum subulatum) extract. The diets contained green cardamom (D1) and black cardamom (D2) encapsulated essential oils were prepared alongside control (Do) for comparison purpose. Bio-evaluation study conducted on male Sprague Dawley rats, accordingly two different studies were designed on the basis of diets i.e. study I (rats fed on normal diet) and study II (rats were given high cholesterol diet). The body weights of experimental rats were significantly effected with diets in both studies. Black cardamom encapsulated extract (D2) instigated highest reduction in weight gain during the study period. Likewise, D2 imparted maximum decrease in total cholesterol levels in study I and II, by 4.42% and 12.53% whereas LDL by 6.75% and 14.08% respectively. However, levels of HDL and triglycerides were effected non-significantly by diets in study I but effects were significant in study II. Likewise, D2 instigated maximum reduction in urea and creatinine levels in study I and II i.e. 8.63% and 19.25% and 9.2% and 20.46%. Furthermore, diets resulted improved antioxidant status by increasing glutathione levels and decreasing thiobarbituric acid reactive substances (TBARS). Amongst diets, black cardamom encapsulated extract (D2) was proved more effective for glutathione contents enhancement during the investigation in study II. The restoration/stabilization of liver function tests towards normal ranges proved the safety of resultant therapeutic diets. From the current explorations, results concluded that diets supplemented with encapsulated black and green cardamom essential oils were efficient tool to mitigate lifestyle related disorders.