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Genetic Diversity and Phylogenetic Relationship Among Eight Species of Order: Rodentia in Egypt Based on Random Amplified Polymorphic DNA (RAPD) Marker
Fawzeya Abdelhadi Zayed,
Sobhy Hasab El-Naby,
Fatma Ahmady Al-Zahaby,
Sabha Elsayed Elballat
Issue:
Volume 8, Issue 2, June 2020
Pages:
54-62
Received:
31 December 2019
Accepted:
20 January 2020
Published:
10 March 2020
Abstract: Of all mammals the rodents have an importance and great diversity. The phylogenetic relationships between the different species of the order Rodentia has an interest and investigations for many researchers. The current study suggests the ability of Random Amplified Polymorphic DNA (RAPD)-PCR to estimate the genetic distance and reflect the genetic relations and variability among eight rodent species of order Rodentia in Egypt. After the use of five arbitrary short primers (OPA-4, OPT-7, OPG-2, OPN-4 and OPM-1) to generate polymorphic, reproducible and score able bands. The results explained that, the highest genetic distance 1 was pronounced between Rattus norvegicus and Mus musculus praetextus similarly between Mus musculus domesticus and Rattus norvegicus. This is followed by the genetic distance between Mesocricetus auratus and Mus musculus domesticus as well as between Cavia porcellus and Rattus norvegicus. Nonetheless, the lowest genetic distance 0.31 was noticeable between Mus musculus praetextus and Mus musculus musculus.
Abstract: Of all mammals the rodents have an importance and great diversity. The phylogenetic relationships between the different species of the order Rodentia has an interest and investigations for many researchers. The current study suggests the ability of Random Amplified Polymorphic DNA (RAPD)-PCR to estimate the genetic distance and reflect the genetic ...
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DNA Identification of Human Remains in Disaster Victim Identification (DVI): An Identification of Burned Girls Students in Tanzania
Fidelis Charles Bugoye,
Elias Zakaria Mulima,
David Luhende Elias,
Fidelis Saimon Segumba,
Leticia Nchagwa Waitara
Issue:
Volume 8, Issue 2, June 2020
Pages:
63-65
Received:
14 September 2019
Accepted:
4 March 2020
Published:
17 March 2020
Abstract: The Government Chemist Laboratory Authority (GCLA) in Tanzania is the only institution offering DNA testing in solving various human identification challenges using Human DNA technology. Globally, forensic DNA typing has undeniably been a useful tool employed in cases such as criminal investigation,, missing persons and parentage testing. In Tanzania, the indispensable need for Human DNA technology in human identification was greatly emphasized in August 2009 following the inferno at Idodi secondary school in Iringa region whereby the fire burnt and razed a girl’s dormitory to the ground killing twelve girls student while leaving twenty students severely wounded. The cause of the fire was later determined to have been due to a lit candle by a student aiming to study late into the night even after the power generator had been switched off. DNA typing of 15 autosomal Short Tandem Repeat markers using ABI 3100 Genetic Analyser was performed on samples collected from the recovered deceased bodies and their relatives. Successful human identification was achieved for all twelve recovered bodies and their reunification with their respective families. Therefore, the Idodi gruesome incident marked both an icon in scientific approach towards the utilization of DNA technology for disaster victim identification and usefulness of experts’ collaborations from different disciplines in mass fatalities and human identification in Tanzania.
Abstract: The Government Chemist Laboratory Authority (GCLA) in Tanzania is the only institution offering DNA testing in solving various human identification challenges using Human DNA technology. Globally, forensic DNA typing has undeniably been a useful tool employed in cases such as criminal investigation,, missing persons and parentage testing. In Tanzan...
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Prevalence of Mutations of the MED12 and CYP17A1 Genes in Mammary Fibroadenomas in Senegalese Women
Gueye Rokhaya,
Tendeng Jacques Noël,
Kénémé Bineta,
Sembene Pape Mbacké
Issue:
Volume 8, Issue 2, June 2020
Pages:
66-77
Received:
25 February 2020
Accepted:
10 March 2020
Published:
23 March 2020
Abstract: Fibroadenoma is the most common benign breast tumor in women under 30 years. This study aimed to contribute to the knowledge of the genetic factors involved in the occurrence and progression of mammary fibroadenomas. MED12 and CYP17A1 were sequenced in fibroadenomas and blood in 43 Senegalese women. The Alamut-visual software, which includes the pathogenicity prediction software SIFT, Polyphen2 and MutationTaster, was used to search for mutations. DnaSP version 5.10.01, MEGA version 7.0.14 and Arlequin version 3.5.1.3 were used to determine phylogenetic parameters including indices of genetic variability and diversity and genetic differentiation parameters. A deletion in the poly-A tail of MED12 was identified in our study population. An alteration of Methionine (M1) was observed on exon 1 of CYP17A1. Our results also show that most of the variants found on exon 2 of MED12 and exon 1 of CYP17A1 have the probability of causing the appearance of breast fibroadenomas according by the three pathogenicity prediction software. We found 23 new variants on the MED12 gene and 109 new variants on the CYP17A1 gene. The amino acid frequency distribution between blood and fibroadenomas shows a statistically significant difference in Glycine, Arginine and Valine for MED12 and Cysteine, Phenylalanine, Histidine, Asparagine, Arginine, Tryptophan and Tyrosine for CYP17A1. In addition the selection test shows that codon 20 of exon 1 of CYP17A1 which codes for Arginine (p.20Arg) is under positive selection in mammary fibroadenomas. Genetic differentiation parameters show a clear difference between blood and breast fibroadenomas. These results show for the first time the involvement of the CYP17A1 gene in breast fibroadenomas and confirm the involvement of MED12. Codon 20 of exon 1 of CYP17A1 being under positive selection could be used as a biomarker in breast fibroadenomas.
Abstract: Fibroadenoma is the most common benign breast tumor in women under 30 years. This study aimed to contribute to the knowledge of the genetic factors involved in the occurrence and progression of mammary fibroadenomas. MED12 and CYP17A1 were sequenced in fibroadenomas and blood in 43 Senegalese women. The Alamut-visual software, which includes the pa...
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Data Analysis of Single Nucleotide Polymorphism in Human AGT Gene Using Computational Approach
Mohammed Youssif Mohammed,
Afra Mohamed Al Bkrye,
Hind Abdelaziz Elnasri,
Mona Abdelrahman Mohamed Khaier
Issue:
Volume 8, Issue 2, June 2020
Pages:
78-84
Received:
10 January 2020
Accepted:
27 January 2020
Published:
7 April 2020
Abstract: Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen which regulates blood pressure and balances fluids in the body. Hypertension happens due to many causes one of this is the defect in AGT gene. Hypertension usually has no symptoms. However, it is a major risk factor for heart diseases, stroke, kidney failure, and eye problems. Objectives: in this study we use software to analyze the gene using different software and represented statistically and to detect the SNPs that can cause the disease. Material and Method: In this analysis using many software tools that can analyze the nsSNPs retrieved from NCBI website. These software include SIFT, I-mutant, Polyphen-2, PHD SNP and SNP& Go, Projecthop and GeneMANIA. Results: The study showed that from 172 nsSNPs only 46 nsSNPs were deleterious while 126 were tolerated using SIFT. Two were benign, 11 were possibly damaging and 33 were probably damaging by Polyphen-2. Using Provean, 19 nsSNPs were neutral and 27 were deleterious. For PHD-SNP software 20 nsSNPs were disease related and 18 were neutral. Also SNPs were checked using SNP & Go software that showed 32 neutral nsSNPs and 14 nsSNPs were disease associated variants. Using I-Mutant software 13 nsSNPs increase the stability of the protein and 33 decrease the protein stability. Conclusions: In conclusion, extensive functional and structural analyses are carried out to predict potentially damaging and deleterious nsSNPs of AGT gene using bioinformatics and computational methods. In the study, 14 high confidence damaging nsSNPs are identified from 172 nsSNPs. Although bioinformatics tools have their limitations, the results from the present study may be convenient in future for further population based research activities and towards development of accuracy medicines.
Abstract: Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen which regulates blood pressure and balances fluids in the body. Hypertension happens due to many causes one of this is the defect in AGT gene. Hypertension usually has no symptoms. However, it is a major risk factor for heart diseases, stroke, kidney failu...
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Effects of Copper (Cu) on Yield Components and Associated Traits in Segregating Populations of Lowland Rice (O. sativa L.)
Efisue Andrew,
Ogunwole Dorcas,
Olaoye Olawale
Issue:
Volume 8, Issue 2, June 2020
Pages:
85-93
Received:
17 April 2020
Accepted:
9 May 2020
Published:
18 May 2020
Abstract: Trace elements are very critical for rice growth of which Cu is one of the essential trace elements for rice and excess of cupper becomes toxic to rice growth. The aim of this study was to determine the productivity increase in rice crop and genotype reactions to application of Copper under the tropical rainforest condition. Three experiments were established concurrently in randomized complete block design in three replications in pots. Treatment comprised of 6 breeding lines each from two rice populations of F2 and F3 generations and two popular checks. Experiment one is the control without CuSO4 treatment, while experiment two and three is the F2 and F3 populations, respectively treated with CuSO4 solution. Three concentration levels of CuSO4 solution (15mg Cu /kg of soil, 30mg Cu /kg of soil and 60mg Cu /kg of soil) were applied into each pots a week before transplanting in the treated experiments. This study observed that at 30mg of Cu/kg of soil is the optimum level for rice performance based on these experiments beyond, reduction in rice performance. Reduction of 24.92% and 22.12% of total grain yield of F2 and F3 populations at 60mg of Cu/kg of soil as compared to the control were recorded, stable and high yielding genotypes across the copper concentration levels were identified for copper breeding programme.
Abstract: Trace elements are very critical for rice growth of which Cu is one of the essential trace elements for rice and excess of cupper becomes toxic to rice growth. The aim of this study was to determine the productivity increase in rice crop and genotype reactions to application of Copper under the tropical rainforest condition. Three experiments were ...
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