Identification of Novel Mutations in Amniotic Fluid Derived Stem Cells Collected from the Mothers Having Case of Neural Tube Defects
Ajit Kumar Saxena,
Madhu Jain,
Meenakshi Tiwari,
Ramanuj Kumar Gupta
Issue:
Volume 4, Issue 3, June 2016
Pages:
16-19
Received:
15 March 2016
Accepted:
11 April 2016
Published:
27 May 2016
Abstract: Neural tube defects (NTDs) are severe congenital malformations of central nervous system that have high prevalence with severe consequences. The etiology of NTDs involves interactions of both genetic and epigenetic factors and their complex interactions with stems cells during organogenesis. Despite of recent advances, there has been limited progress in delineating the molecular basis of NTDs that can pave way for prevention, diagnostics and therapeutics. We have previously identified a role for stem cell markers Oct 4, Sox 2 and Nanog 3 in neural tube defect affected pregnancies. In the present report we identified mutations in stem cell pluripotency markers from amniotic fluid derived stem cells isolated from women with NTD affected pregnancy. Oct 4 and Nanog 3 were studied to find a correlation with the disease and its severity. Interestingly, sequence based DNA analysis revealed two different forms of nucleotide changes that were observed in different clinical conditions of NTDs. The mutation in Oct 4 at position 183 G →T and in the sequence of Nanog 3 at 63CAAAAA ACA72 to 38ACAGTCTCT47 appears in the cases of anencephaly and meningomyelocele respectively in comparison to control. These findings suggest that these mutational spectra might be responsible for the alterations in the developmental process during embryogenesis leading to NTDs.
Abstract: Neural tube defects (NTDs) are severe congenital malformations of central nervous system that have high prevalence with severe consequences. The etiology of NTDs involves interactions of both genetic and epigenetic factors and their complex interactions with stems cells during organogenesis. Despite of recent advances, there has been limited progre...
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Characterization of Phenotypic Variability of Sudanese Gum Arabic Tree Acacia Senegal var. senegal Using Multiprimer Random Amplificatıon of Polymorphic DNA (RAPD)
Saad Samah Mahgoub Hassan Mohammed,
Mukhtar Moawia Mohammed,
Warag Essam Eelldin,
Elamin Hassan Basher,
Aycan Murat,
Yıldız Mustafa
Issue:
Volume 4, Issue 3, June 2016
Pages:
20-23
Received:
21 May 2016
Accepted:
8 June 2016
Published:
20 June 2016
Abstract: Acacia Senegal var. senegal (Gum Arabic) as it is known world-wide, is one of the most important trees in Sudan with valuable contribution to the national income export commodity. Gum Arabic is an important ingridunt in several medicinal and food products. Little is known on the genetic markers and diversity of Acacia senegal. To our knowledge, this is the first study represents attempt to characterize genotypic variability of Acacia senegal var. senegal. The aim of this study was the molecular characterization of Acacia senegal var senegal using RAPD technique as molecular marker and to correlate the results obtained from genetic marker with the production and the geographical distribution of the trees. Acacia seeds were collected from different geographical areas of Sudan. Seeds of trees Acacia senegal var. senegal were cultivated in small pots. The seeds were germinated for 4 to 6 weeks then the new leaves were collected for DNA extraction using CTAB protocol. DNA was also extracted from the roots. Two octamer RAPD primers were evaluated for amplification of Acacia DNA. Phylogenetic tree was constructed based on RAPD-PCR which clustered the trees from each geographic area as separate group that were genetically related. The data showed a common ancestor of the three clusters suggesting.
Abstract: Acacia Senegal var. senegal (Gum Arabic) as it is known world-wide, is one of the most important trees in Sudan with valuable contribution to the national income export commodity. Gum Arabic is an important ingridunt in several medicinal and food products. Little is known on the genetic markers and diversity of Acacia senegal. To our knowledge, th...
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The Method of a Gene Sequence Alignment BWT Index Based on Hadoop
Nan Li,
Jing Gao,
Bailong Feng
Issue:
Volume 4, Issue 3, June 2016
Pages:
24-30
Received:
1 July 2016
Published:
12 July 2016
Abstract: Gene sequence alignment, used to recognize the homology and variability in different species, is an important part of Bioinformatics. Creating indexes is a crucial step of gene sequence alignment algorithm. Usual algorithms of creating indexes are divided into two types. The first is algorithm based on hash table, while another is based on suffix tree or suffix array, among which BWT (Burrows-Wheeler Transform) index is a significant index structure. Currently, BWT index needs several hours’ serial computing in building a large genome sequence (such as human genome sequence). A parallel computing method based on Hadoop is presented is this paper to build suffix array and BWT index. Map Reduce is adopted as a type of data processing function, cutting suffix array into block, which will be handled separately. Ultimately, totally ordered suffix array and BWT index are output, reducing the time in building index. Meanwhile, verifying the effectiveness of the algorithm by experiments.
Abstract: Gene sequence alignment, used to recognize the homology and variability in different species, is an important part of Bioinformatics. Creating indexes is a crucial step of gene sequence alignment algorithm. Usual algorithms of creating indexes are divided into two types. The first is algorithm based on hash table, while another is based on suffix t...
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