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Prediction of Structural and Functional Effects of Single Nucleotide Polymorphisms in NAT2gene, a Computational Analysis
Amna Elsadig Elsafi Abodlaa,
Dalia Mursi,
Mona Abdelrahman Mohamed Khaier,
Mai Abdul RahmanMasri,
Nazik Elmalaika Obaid Seid Ahmed Husain,
Hind Abdelaziz Elnasri
Issue:
Volume 7, Issue 4, December 2019
Pages:
88-97
Received:
3 August 2019
Accepted:
4 October 2019
Published:
15 October 2019
Abstract: N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xenobiotics and drugs components. It is a critical enzyme in clinical pharmacology. It has remarkable genetic polymorphisms, which is associated with the risk of developing cancer due to the change of normally fast acetylation of substrates to slow acetylation. This study assessed single nucleotide polymorphisms (SNPs) in the coding region and (3ʹUTR) of NAT2. Computational approaches were used in this study for functional and structural effects of NAT2 gene. SNPs. Were retrieved from NCBI SNPsdatabase. TheNAT2 protein sequence and amino acid change were used as an input to the SIFT, PolyPhen-2, PhD-SNP, SNPs& GO, SNPAnalyzer, I-Mutant 3.0 and PMut to determine the deleterious and SNPs conditions. Other software for predication of the structural change were Mutation3D, Chimera and Project HOPE. GeneMANIA software was used to show gene –gene interaction. PolymiRTs was used to investigate the disruption or creation of SNPs of miRNA region. In Homosapiens182 were nonsynonymous SNPs (nsSNPs), 60 synonymous SNPs, 48 3ʹUTRSNPs and 19 5ʹUTR SNPs. A total, 65 of thosensSNPs were predicted to be highly damaging with 3-6 score rates when analyzed with six software. Re-computation of results with I-Mutant 3.0 showed adecrease in the effective stability of the protein due to 55 nsSNPs. Consequent structural changes were shown using Project HOPE and Chimera. NAT2 is a highly polymorphic gene; the majority of deleterious NAT2SNPs are nsSNPs that alter the physiochemical and structural properties of the protein, possibly leading to the loss or distortion of the protein's ability to detoxify and metabolize xenobiotic and aromatic amine compounds. There were three SNPs at the 3ʹUTR that changed the miRNA binding sites, which might affect the gene regulation.
Abstract: N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xenobiotics and drugs components. It is a critical enzyme in clinical pharmacology. It has remarkable genetic polymorphisms, which is associated with the risk of developing cancer due to the change of normally fast acetylation of substrates to slow acetylat...
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Incidence of Groundnut Rosette Disease (GRD) and Genetic Diversity of Groundnut Rosette Assistor Virus (GRAV) in Western Kenya
Benard Mukoye,
Millicent Florence Owuor Ndonga,
Hassan Karakacha Were
Issue:
Volume 7, Issue 4, December 2019
Pages:
98-102
Received:
11 September 2019
Accepted:
4 October 2019
Published:
16 October 2019
Abstract: This study determined the incidence of groundnut rosette disease (GRD) and genetic diversity of groundnut rosette assistor virus (GRAV, genus Luteovirus) in western Kenya. The diseases is a major constraint of groundnuts in Sub-Saharan Africa (SSA) causing up to 100% yield losses in severe cases. Among the GRD associated viruses, GRAV plays a crucial role in vector transmission of the other viruses. Therefore understanding the genetics of GRAV across SSA could enhance development of resistance to the disease. In Kenya, groundnuts are mainly grown in western region, however, the yields are poor mainly due to GRD. Information on occurrence and distribution of GRD in western Kenya was not documented and little was known about the characteristics of associated viruses. Two diagnostic surveys were conducted in six counties; Bungoma, Busia, Homabay, Kakamega, Siaya and Vihiga. Symptomatic and asymptomatic groundnut were collected in RNAlater® solution for laboratory analysis. Total RNA was extracted from the leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol and used for double stranded cDNA synthesis using the SuperScript II kit. The cDNA was column-purified with the DNA Clean & ConcentratorTM-5 – DNA kit. The samples were then processed with the transposon-based chemistry library preparation kit (Nextera XT, Illumina) following manufacturer’s instructions. The fragment sizes structure of the DNA libraries was assessed using the Agilent 2100 Bioanalyzer. The indexed denatured DNA libraries were sequenced (200-bp paired-end sequencing) on the Illumina MiSeq platform (Illumina). Reads quality check was done using FastQC. Trimmed reads were used for de novo assembly and contigs aligned to the viral genomes database using CLC Genomics Workbench 10.1.2. The assembled contigs were subjected to a BLASTn search against the GenBank database. Phylogenetic analyses and comparisons were performed using the MEGA X. Average incidence was 53% and 41% in the short and long rain seasons, respectively. Chlorotic rosette was the dominant symptom followed by Green rosette and Mosaic. The GRAV coat protein (GRAV-CP) gene sequences revealed 97-100% identity with GeneBank isolates showing very slight variations across SSA. The study concludes that GRD incidence is high in western Kenya and that GRAV is highly conserved across SSA. The study recommends an urgent need to curb GRD, possibly through the exploitation of pathogen derived resistance (PDR) with GRAV as the suitable candidate.
Abstract: This study determined the incidence of groundnut rosette disease (GRD) and genetic diversity of groundnut rosette assistor virus (GRAV, genus Luteovirus) in western Kenya. The diseases is a major constraint of groundnuts in Sub-Saharan Africa (SSA) causing up to 100% yield losses in severe cases. Among the GRD associated viruses, GRAV plays a cruci...
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Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep
Antonios Kominakis,
Aggeliki Saridaki,
George Antonakos
Issue:
Volume 7, Issue 4, December 2019
Pages:
103-109
Received:
18 July 2019
Accepted:
11 September 2019
Published:
21 October 2019
Abstract: Aim of the present study was to identify genomic regions and candidate genes impacting on somatic cell count in the Frizarta dairy sheep. A total number of 482 Frizarta ewes genotyped with the medium density SNP array with available records on milk somatic cell count were used. Associations between genomic markers and the trait under study were detected by application of a multi-locus mixed model treating markers as fixed additive effects. Positional candidate genes identified within 1Mb flanking distances from significant markers were in silico prioritized based on their functional similarity to a training gene list including 1,120 genes associated with the term ‘immunity’. Association analysis pinpointed 4 chromosome-wide significant SNPs dispersed on four autosomes (OAR2, OAR18, OAR19 and OAR22). A total number of 37 positional candidate genes were identified within the searched genomic distances while 13 candidate genes were highly prioritized. Seven highly prioritized genes (NFIB, GFRA1, PSIP1, ARHGAP5, HECTD1, EMX2, STRN3) along with genes FREM1 and GPR33 had evidenced involvement in immune-related processes. Current results extent previous findings by providing novel candidate genes for the somatic cell count phenotype in dairy sheep.
Abstract: Aim of the present study was to identify genomic regions and candidate genes impacting on somatic cell count in the Frizarta dairy sheep. A total number of 482 Frizarta ewes genotyped with the medium density SNP array with available records on milk somatic cell count were used. Associations between genomic markers and the trait under study were det...
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Nanoparticles Induce Oxidative Stress in HT-29 Colon Adenocarcinoma Cell Line After 24 and 48 Hour Exposure
Issue:
Volume 7, Issue 4, December 2019
Pages:
110-114
Received:
31 August 2019
Accepted:
18 October 2019
Published:
26 October 2019
Abstract: Nanoparticle research is currently an area of intense scientific research, due to a wide variety of potential applications in biomedical, optical, and electronic fields. Nanoparticles are of great scientific interest as they are effectively a bridge between bulk materials and atomic or molecular structures. Superoxide dismutase (SOD), Glutamine synthetase (GS), Catalase (CAT) are some of the defense mechanisms against cellular oxidative stress, especially against free oxygen radicals. In this study, we aimed to investigate that Ag, SiO2 and ZnO nanoparticles affect cancer cell lines (HT-29) and relationship between SOD, GS and CAT. We investigated that alterations in gene expressions of SOD, GS and CAT caused by exposure to nanoparticles in HT-29 cells. The difference between the Ct values (ΔCt) of the gene of interest was calculated for each experimental sample. As a result of Ag, SiO2 and ZnO nanoparticle application, there was a 2-fold increase in SOD and CAT expression in the first 24 hours compared to control. As a result of 48 hours of application, it was observed that Ag nanoparticles caused 4-fold increase in SOD and 6-fold statistically significant increase in CAT and GS expression of SiO2 nanoparticles. Consequently, after 48 hours of nanoparticle application, SiO2, CAT and GS expression were more effective than 24-hour application. Our results suggest that nanoparticles may cause increased oxidative stress in colon cells and may have therapeutic properties by affecting cancer cells in these aspects.
Abstract: Nanoparticle research is currently an area of intense scientific research, due to a wide variety of potential applications in biomedical, optical, and electronic fields. Nanoparticles are of great scientific interest as they are effectively a bridge between bulk materials and atomic or molecular structures. Superoxide dismutase (SOD), Glutamine syn...
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Evaluation of Common Bean Cultivars Resistance to the Bean Common Mosaic Necrosis Virus in Western Kenya
Mangeni Bonphace Collins,
Ndong’a Millicent,
Mukoye Benard,
Were Hassan Karakacha
Issue:
Volume 7, Issue 4, December 2019
Pages:
115-118
Received:
1 October 2019
Accepted:
14 October 2019
Published:
15 November 2019
Abstract: The common bean (Phaseolus vulgaris), is a high protein crop and the main legume in the cropping system of western Kenya. Despite its importance, common bean yields are low (<1.0 t/ha) and declining. Bean Common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are the most common and most destructive and can cause a yield loss as high as 100%. In Kenya, limited cultivars and exotic genotypes with resistance to BCMV and BCMNV strains have been reported. Reports indicate BCMNV being a widespread virus compared to BCMV in western Kenya. This study therefore, sought to screen popular cultivars for resistance to the virus. Sixteen popularly grown bean cultivars together with cowpea (Vigna unguiculata), soybean (Glycine max) and groundnut (Arachis hypogaea) were planted in a green house in a completely randomized block design with three replicates. The plants were inoculated with BCMNV Enzyme Linked Immunosorbent Assay (ELISA) positive isolate at 3-leaf stage. Data was taken weekly for 3 weeks on type of symptoms expressed and number of plants infected. Ten bean cultivars were susceptible, 4 tolerant and 2 resistant. For improved yields of common bean, farmers should be advised to plant certified seeds for all legumes in the cropping system.
Abstract: The common bean (Phaseolus vulgaris), is a high protein crop and the main legume in the cropping system of western Kenya. Despite its importance, common bean yields are low (<1.0 t/ha) and declining. Bean Common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are the most common and most destructive and can cause a yield loss as high as 100%. In Kenya, limited cultivars and exotic genotypes with resistance to BCMV and BCMNV strains have been reported. Reports indicate BCMNV being a widespread virus compared to BCMV in western Kenya. This study therefore, sought to screen popular cultivars for resistance to the virus. Sixteen popularly grown bean cultivars together with cowpea (Vigna unguiculata), soybean (Glycine max) and groundnut (Arachis hypogaea) were planted in a green house in a completely randomized block design with three replicates. The plan...
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First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya
Orakha Odhiambo Patrick,
Hassan Were,
Millicent Ndonga,
Mukoye Benard
Issue:
Volume 7, Issue 4, December 2019
Pages:
119-123
Received:
14 September 2019
Accepted:
4 November 2019
Published:
19 November 2019
Abstract: Cowpea is an important legume crop for nutritional security, livestock feed and source of income in Kenya. Cowpea yield in Kenya is very low and declining further due to high incidences of pests and diseases among other factors. Like other pathogens, viruses have continued to cause yield losses of up to 100% depending on the prevailing epidemiological factors. This study had sought to determine the distribution, prevalence and genetic diversity of Cowpea Mild Mottle Virus (CPMMV) in western Kenya. Two surveys were conducted in the main legume growing areas of western Kenya. A total of 139 legume leafy samples were collected from 5 Counties; Bungoma, Nandi, Vihiga, Kakamega and Busia in June and October 2016. Collected samples were analyzed by Double Antibody Sandwich Enzyme Linked Immunosorbent Assay (DAS–ELISA) for detection CPMMV. ELISA was not carried out to test for CPPV1. Total RNA was extracted from the symptomatic leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol. Next Generation Sequencing (NGS) protocol proceeded. Assembled contigs were then subjected to a BLASTn search against the Genbank database. Phylogenetic analyses and comparisons were performed using MEGA X. Symptoms observed on legumes in the fields were mosaic, severe yellowing, chlorotic blotches and downward leaf curling. Some of the groundnut, cowpea and common bean samples collected in June and October tested CPMMV positive by DAS-ELISA. Legume samples of soybean, lablab, green grams, bambara nuts and legume weed collected tested negative for CPMMV. Results from Next Generation Sequencing technique revealed the presence of Cowpea Polero Virus 1 (CPPV1), the first full-length CPPV1 report and sequence to be reported in Eastern Africa. Phylogenetic analysis of VCP1 Kenyan isolate sequence revealed 98.27% similarity with that of Burkina faso isolate BE 167 (KY364846.1) (Palanga et al., 2017) and they clustered together. Kenyan isolate VCP1 and the Burkina faso BE 167 isolate are closely related. It is not clear if the spread of CPPV1 is through international trade from either country. Revelation of CPPV1 show that there could be more viruses affecting legume crops in the region whose identities are still unknown. There is need to conduct more diagnosis using NGS technique to detect more unknown but occurring viruses in the region. CPPV1 has been found infecting cowpea in Burkina faso, to the best of our knowledge this is the first report of CPPV1 in Kenya.
Abstract: Cowpea is an important legume crop for nutritional security, livestock feed and source of income in Kenya. Cowpea yield in Kenya is very low and declining further due to high incidences of pests and diseases among other factors. Like other pathogens, viruses have continued to cause yield losses of up to 100% depending on the prevailing epidemiologi...
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In Silico Analysis of Single Nucleotide Polymorphisms (SNPs) in Human MPL Gene
Mohamed Mubarak Babeker,
Afra Mohamed Suliman Albakry,
Mohammed Nagm Eldin Elsamani,
Gihan Mossalami,
Hind Abdelaziz Elnasri,
Mona Abdelrahman Mohamed Khaier
Issue:
Volume 7, Issue 4, December 2019
Pages:
124-131
Received:
30 September 2019
Accepted:
23 October 2019
Published:
22 November 2019
Abstract: Thrombopoietin was shown to be the major regulator of megakaryocytopoiesis and platelet formation. The protein encoded by the c-mpl gene, CD110, is a 635 amino acid transmembrane domain, with two extracellular cytokine receptor domains and two intracellular cytokine receptor box motifs. Mutations to this gene are associated with myelofibrosis and essential Thrombocythemia. In essential Thrombocythemia, these mutations lead to the production of Thrombopoietin receptors that are constitutively activated, or constantly turned on, which results in the overproduction of abnormal megakaryocytes. MPL gene was investigated in NCBI database (http://www.ncbi.nlm.nih.gov/) and computational software’s analyzed SNPs. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNP) were analyzed by (sift, polyphen, Imutant and PHD-snp) softwares, and then SNPs at un-traslated region at 5’ ends (5UTR) were analyzed too by SNPs Function prediction software. In this study, Bioinformatics’ analysis of MPL gene initiated by SIFTand Polyphen-2server issued to review 197 SNPs and among this SNPs 23 pathological polymorphisms. Among these 23, 20 pathological polymorphisms were found to be very damaging, with higher Polyphen-2score, of the Polyphen-2 server (=1) and SIFT tolerance index of 0.000-0.005. Protein structural analysis was done by modeling of amino acid substitutions using Project Hope. AlsoI-Mutant software used to check their stability and the effect of the native and mutant residues protein and structure for all these pathological polymorphisms. We hope our results will provide useful information that is needed to help researchers to do further studies.
Abstract: Thrombopoietin was shown to be the major regulator of megakaryocytopoiesis and platelet formation. The protein encoded by the c-mpl gene, CD110, is a 635 amino acid transmembrane domain, with two extracellular cytokine receptor domains and two intracellular cytokine receptor box motifs. Mutations to this gene are associated with myelofibrosis and e...
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First Full Length Genome Sequence of Bean Common Mosaic Necrosis Virus (BCMNV) Isolated from Common Bean in Western Kenya
Mangeni Bonphace Collins,
Were Hassan Karakacha,
Mukoye Benard,
Ndong’a Milicent
Issue:
Volume 7, Issue 4, December 2019
Pages:
132-135
Received:
23 October 2019
Accepted:
22 November 2019
Published:
2 December 2019
Abstract: Bean common mosaic necrosis virus (BCMNV) is one of the most common and most destructive viruses of common bean and can cause a yield loss as high as 100%. The common bean (Phaseolus vulgaris L) is an important legume crop for food and cash in Kenya. In Kenya, there is inadequate documentation on the strains of the virus infecting common bean. This information is crucial in devising control measures. This study therefore, sought to characterize BCMNV isolates from western Kenya. Leafy samples showing virus-like symptoms were collected and analysed by Enzyme linked immunosorbent Assay (ELISA) and or next generation sequencing (NGS). Extraction of total RNA from ELISA positive samples was done using RNeasy Plant Mini Kit and NGS carried out following Illumina protocol to determine diversity of the virus. NGS data was trimmed and the sequence reads assembled into contigs, which were analyzed against virus sequence database. Phylogenetic analyses and comparisons were performed using MEGA7 program. The first complete genome sequence of Bean common mosaic virus (BCMNV) is reported from a Kenyan isolate. NGS technology revealed full-length sequence of BCMNV from an isolate BG 12 from Bungoma County with a genome of 9584 nt in length. Phylogenetic analysis of full-length sequences available through the Genbank clustered the isolate with the Tanzanian isolate strain TN-1 and two USA isolates, TN1a and NL-3K.
Abstract: Bean common mosaic necrosis virus (BCMNV) is one of the most common and most destructive viruses of common bean and can cause a yield loss as high as 100%. The common bean (Phaseolus vulgaris L) is an important legume crop for food and cash in Kenya. In Kenya, there is inadequate documentation on the strains of the virus infecting common bean. This...
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Ameliorative Effect of Peach Seed Extract on Cyclophosphamide- Induced Cytogenetic and Histological Effects in Mice
Heba Mohamed Salah,
Ezzat Ibrahim Aboul-Ela,
Hamdy Hamed Swelim
Issue:
Volume 7, Issue 4, December 2019
Pages:
136-147
Received:
2 November 2019
Accepted:
22 November 2019
Published:
4 December 2019
Abstract: Cyclophosphamide (CP) is a frequently used drug for its anticancer and immunosuppressive potential. However metabolism of CP in the body results into toxic chemical compounds (to the liver itself and other non-target vital organs) via oxidative stress, apoptosis induction and finally necrosis. Since there is no escaping of using such medications in spite of their harms this study was designed to access the ability to alleviate the side-effects of CP by using peach seed methanolic extract, due to its nutritional value and therapeutic properties. The peach seed extract has bioactive constituents such as phenols and carotenoids. Methanoloic extract is the most widely used since it offers a high recovery of antioxidant compounds. Mice were divided into five major groups: negative control (untreated group), positive control, was injected (IP) with CP in dose 75mg/kg b. wt., Third group received peach seed extract only in a dose of 500 mg/kg b.w., and the fourth and fifth groups received two doses of Peach seeds extract 500 and 250 mg/kg b.wt. after receiving a single dose of CP intraperitoneally. Assessment of the extract was performed using micronucleus test, mitotic chromosomal aberration assay using bone marrow cells, and liver samples were collected for histopathology. Our results demonstrated that CP induced highly significant e genotoxicity, which recorded 9.49% PE's with micronuclei, comparing to 1.03% as control, while the induction of chromosomal aberrations was recorded as 67.6% against 4.4% as negative control. The histological study on the liver cells recorded noticeable damage with liver cells treated with CP. After peach treatment a significant reduction in CP- induced damage was observed and those groups treated with both extract and CP became nearly similar to the untreated group in all tested parameters. peach methanolic seed extract has the potential to ameliorate the damaging effect of cyclophosphamide at both the genetic and histological levels.
Abstract: Cyclophosphamide (CP) is a frequently used drug for its anticancer and immunosuppressive potential. However metabolism of CP in the body results into toxic chemical compounds (to the liver itself and other non-target vital organs) via oxidative stress, apoptosis induction and finally necrosis. Since there is no escaping of using such medications in...
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