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Home > Molecular Characterization of Familial Ataxic, Paraplegic and Related Movement Disorders

Molecular Characterization of Familial Ataxic, Paraplegic and Related Movement Disorders

Thesis Info

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Author

Tariq, Huma

Program

PhD

Institute

University of the Punjab

City

Lahore

Province

Punjab

Country

Pakistan

Thesis Completing Year

2019

Thesis Completion Status

Completed

Subject

Biology

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/11005/1/Huma%20Tariq_Bio%20Sci_2019_UoPunjab.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726683411

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Movement disorders are heterogeneous neurological syndromes affecting voluntary movement, coordination, causing ataxia or some involuntary movements. Many of these disorders have a genetic cause and can have any mode of inheritance. The rate of consanguineous marriages is very high in Pakistan and therefore there is a high probability of recessively inherited rare genetic disorders, including movement disorders. The genetics of movement disorders is not very well studied in Pakistan. Next generation sequencing technology can facilitate diagnosis and identification of novel genes from affected individuals in families practicing consanguineous marriages. In this study, sixteen families with multiple affected individuals were recruited from Punjab province of Pakistan. The patients exhibited either all, or combination of symptoms including movement disability, abnormality in voluntary movements, abnormal postures, frequent falls, unusual gait with or without abnormal speech. A standard protocol was adopted for videotaping of participants. Diagnosis was made by neurologists either in Pakistan or UK. The required medical investigations and neuroimaging were performed for the probands in the families. The genetic causes of the disorder in eight families out of sixteen were identified. Most of these were in those genes which play vital roles in genome integrity, DNA repair and membrane trafficking. Novel homozygous and compound heterozygous missense variants in SETX were identified in families RDHT01, RDHT02 and RDHT10. These families were reverse phenotyped and found to suffer from ataxia with oculomotor apraxia type 2. Whole exome sequencing was performed for one or two members of all the sixteen families. Exome data was analyzed in a sequential way using appropriate filters. Variants having high frequency in public databases (>0.01) were excluded and others were prioritized based on their effect on the encoded proteins. Only homozygous and compound heterozygous variants were considered. Segregation of candidate variants was analyzed by Sanger Sequencing in all family participants. Functional assays and computational analysis were performed for selected missense variants to check their effect on protein function. ii Affected individuals in family RDHT04 were homozygous for an identified pathogenic variant in TFG and significantly extended the phenotypic spectrum of TFG related disorders. Sleep disturbances, poor intellect, undeveloped speech, obesity, and severity of the disability to bed ridden status are the important phenotypic extensions in RDHT04 patients. This report also reinforces the differential impact of same variant to cause the disease. Another family RDHT05 had a novel pathogenic homozygous variant in ALS2 in affected members. They were found to suffer from infantile onset of spastic paraplegia. The pathomechanism due to this variant is hypothesized to be a truncated protein with loss of important functional domains. This was hypothesized as mRNA was found to be expressed in blood samples of both unaffected and affected members of the family. Patients of family RDHT06 had a known pathogenic nonsense mutation in ATM which was identified for the first time in homozygous condition. The patients suffered from ataxia telangiectasia with onset at five years of age. One of their sibling was still asymptomatic at the age of six years although he also carried the variant in a homozygous form. Perhaps, he will manifest the disorder later in life or may be a modifier gene will prevent disease progression. In family RDHT08 a nonsense homozygous variant in C19orf12 was segregating with mitochondrial protein associated neurodegeneration (MPAN). The disease mechanism of this variant is hypothesized to be reduced mRNA as a result of nonsense mediated mRNA decay. The carriers for the variant exhibited no disease, which together with more than 70 unaffected C19orf12 heterozygous individuals from other reports supports the biallelic nature of neurological disorders due to C19orf12 variants. It further negates the monoallelic nature of disorder as suggested recently. In family RDHT03 a novel homozygous missense variant in DRD4 was segregating with dystonia phenotype. The variant was not conserved in zebrafish, chicken and pig, but none of the organisms had Arg>Cys substitution at this position. The segregation with dystonia in patients, absence in ethnically control chromosomes and absence of any other potential homozygous variant in affected individuals,supports the potential association of this variant with dystonia. Observation of the crystalline DRD4 at the position of the variant also supports the importance of this residue in DRD4-ligand interactions. A second homozygous novel variant in GENEA was fully conserved and segregated with iii phenotype of delayed milestones in this family. Absence of this variant in normal population and high pathogenicity scores support its disease association. Previous association of heterozygous variants in this gene with ataxia has been reported but recessive inheritance is presented for the first time, though with different phenotype. In family RDHT16, three variants were found to segregate with dopa responsive dystonia like phenotype.However, missense variant p.(Lys231Glu) in GENEB was the most likely candidate. Replication of the study is required in additional patients to establish it as bona fide gene implicated pathomechanism of neurological movement disorders if mutated. Fibroblasts of a South Asian patient who had a novel compound heterozygous variants in FGD4, associated with Charcot-Marie-Tooth disease, type 4H were collected at Institute of Neurology, University College London, UK. The fibroblasts were grown and their proliferation rates were observed to be normal. The stability and localization of the encoded protein was not affected by these pathogenic mutations which suggests that further exploration of pathomechanism of these variant is required. In a collaborative project at UCL, a novel bilallelic repeat expansion in RFC1was identified after analysis of whole genome sequencing in cerebellar atrophy, neuropathy and vestibular areflexia syndrome (CANVAS) (OMIM 614575) patients. A cohort of 304 normal individuals was screened by flanking PCR and reverse-prime PCR (RPPCR) for this newly identified expansion.The frequency of this mutant allele expansion was 0.7% in normal population with no homozygous individual for the variant. This work served as a verification that the variant is indeed rare and causes the disorder only in the homozygous condition. For five families, exome sequencing failed to identify a pathogenic variant. The genetic disorder characterization may be completed in future through whole genome sequencing.This will reveal the underlying genetic cause for the disorder and perhaps will identify some new gene involvement in these disorders. This study has benefited many families by providing the diagnosis and genetic counselling. At the same time it has revealed clinical and genetic information regarding movement disorders in Pakistani families. The results suggest that clinical and genetic diagnosis should be undertaken together to properly diagnose the disorders. Misdiagnosis undermines the possible treatment options and also negatively impacts the family in search of the right diagnosis. In future, once all genes have been identified, candidate panels could be developed for rapid identification of the involved genes and their variants.
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مولانا مناظر احسن گیلانی

آہ حبر امت!
الی اﷲ اشکولاالی الناس اننی
اری الارض تبقی والا خلاء تذھب
وادریغا!جو خامۂ گوہر فشاں چالیس برس تک اسلامی علوم وفنون کے انمول موتی صفحۂ قرطاس پربکھیرتا اورلٹاتارہا۔گذشتہ ماہ جون کی ایک صبح کو یک بیک خاموش ہوگیا۔وہ مسیحا نفس جواپنے انفاس قدس سے اسلامی احساس وفکر کے تن بے جان کی عروقِ مردہ میں زندگی کانیا اور تازہ خون دوڑاتا رہا۔دین قیم کاوہ پیکر خجستہ گوہر جو اپنے لب ِاعجازنما سے قال اﷲ اورقال الرسول کاپیام حق التیام ایک عرصہ تک جھوم جھوم کے سناتارہا۔علم وفضل،عمل وکردار اوراخلاق وشمائل کاوہ پیکر حسین جو اس عہد میں اسلام کی چہاردہ صد سالہ تاریخ کی آبروتھا اورجس کانفس نفس گلبن دین محمدی کی عطر آفرینیوں کاامین و رازداں تھا۔اچانک خاکِ لحدکی امانت بن گیا۔ملت بیضا کی ایک متاع گراں مایہ لٹ گئی۔بزم انس وقدس کا چراغ فروزاں بجھ گیا۔یعنی حبر امت مولانا سید مناظر احسن گیلانی نے اس عالم آب وگل کوخیرآباد کہہ کر عالم آخرت کی راہ لی۔اناﷲ وانا الیہ راجعون
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Study of Pragmatic Losses in the English Translation of Surah Al Ikhlas: A Comparative Pragma-Linguistic Analysis

The comprehension of the message of the Holy Qur’ān is obligatory for the whole of humanity which is revealed in the Arabic language. Scholars all over the world, Muslims as well as non-Muslims have devoted their best efforts to translate the word of Allah Almighty in different languages of the world, although absolute translation is not possible. These translations from Arabic to other languages of the world result into pragmatic losses. Small wonder, these pragmatic losses cause problems in the process of understanding the actual message of the Holy Qur’ān enshrined in the source text. This study was conducted to analyze the pragmatic losses in the English translations of Sūrah Ikhlāṣ (chapter 112) through a comparative pragma-linguistic analysis. Three different translations have been selected for the study. A comparative and critical study of these translations has established the presence of certain pragmatic losses which are likely to bear upon the comprehension of the reader in more than one way. To the researchers, the presence of these losses calls for the greater sensitivity towards and understanding of the pragmatic aspects of interlingual translation, specifically for a text which in its primordial form was intended to be a Speech (Kalām). To retain the pragmatic value and meaning of the source text become all the more paramount when the text translated is sacred one with its own canonical conventions and discursive norms.

Wavelets and Radial Basis Functions in Scienti C Computing

The present work is an application of wavelets and radial basis functions to numerical computing. More specifically, we have used Haar and Legendre wavelet for applications of wavelets and multiquadric for applications of radial basis functions. The application areas considered in this thesis are the numerical solution of Integral Equations (IEs), various order Integrodifferential Equations (IDEs), systems of IEs, Elliptic Partial Differential Equations (EPDEs), Parabolic Partial Differential Equations (PPDEs) and highly oscillatory integrals. A few theoretical results are proved for efficient evaluation of some particular systems that arise when we apply one- or two-dimensional Haar wavelet in the wavelet collocation method. Based on these theoretical results new numerical methods based on Haar wavelet are developed for solution of IEs, IDEs and systems of IEs. EPDEs are solved numerically using collocation methods with Haar and Legendre wavelet. Legendre wavelet is also applied for the numerical solution of PPDEs. A new method based on multiquadric radial basis functions is introduced for numerical solution of highly oscillatory integrals. While applying Haar wavelet to numerical solution of IEs we have considered both nonlinear Fredholm and nonlinear Volterra IEs of the second kind. Similarly in case of IDEs a Haar wavelet based method is applied to find numerical solution of first and higher orders nonlinear Fredholm and nonlinear Volterra IDEs. The main advantage of this method is that it is generic as it can be applied to IEs, IDEs and systems of IEs. More specifically the new approach aims at the numerical solution of Fredholm, Volterra and Volterra-Fredholm types of IEs, IDEs and IDEs of higher orders including initial- as well as boundary-value problems. With a slight modification the method can also be applied to find numerical solution of two-dimensional IEs, system of IDEs and partial IDEs. Another distinguishing feature of themethod is that unlike many other existing methods in the literature it does not use any intermediate technique for numerical integration of the kernel function in IEs or IDEs. We have developed two new types of collocation methods based on Haar wavelet and Legendre wavelet for numerical solution of EPDEs. A modification of the collocation method based on Haar wavelet for elliptic differential equations is also introduced that improves the efficiency of the method. The collocation method based on Legendre wavelet is extended to find numerical solution of PPDEs. An advantage of the proposed methods is that it can be applied to different types of boundary conditions (BCs) with slight modifications. For highly oscillatory multidimensional integrals a new Levin’s type method based on multiquadric radial basis functions is developed. Levin method converts the numerical integration problem of highly oscillatory multidimensional integral to a PDE which is subsequently solved using meshless method. The proposed methods are validated on a variety of problems as well as numerical results of the proposed methods are compared with several existing methods from the literature. The numerical results show better performance of the proposed methods for several benchmark problems.