Genetic Detection and Phylogenetic Tree Study for SARS COV-2 (N Gene) In Iraq

2021 ◽  
Vol 12 (3) ◽  
pp. 131
Author(s):  
NOOR ABADY ◽  
ZAYTOON ALKHAFAJI ◽  
ALI BAAY
Keyword(s):  
Phylogenetic Tree ◽  
N Gene ◽  
Genetic Detection

scholarly journals Greek measles epidemic strain, 2005–2006

2006 ◽  
Vol 135 (4) ◽  
pp. 570-573 ◽  
Author(s):  
G. GIOULA ◽  
A. PAPA ◽  
M. EXINDARI ◽  
A. MELIDOU ◽  
D. CHATZIDIMITRIOU ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Vaccine Strain ◽  
Virus Strain ◽  
Measles Virus ◽  
Molecular Study ◽  
N Gene ◽  
Epidemic Strain ◽  
Rt Pcr ◽  
Measles Outbreak ◽  
Genotype A

SUMMARYThe purpose of this work was the molecular study of the virus strain that caused the last measles outbreak in Greece. Twenty-four saliva specimens were obtained from selected patients serologically confirmed as measles cases between December 2005 and March 2006. Measles virus (MV) detection was performed by a nested RT–PCR. The 447-bp segment of the N gene of these MV strains was used for genotyping. The N gene sequences of the Greek MV strains were identical to each other, therefore a phylogenetic tree was constructed using one representative MV (ThesGRE/06). Our data show that the MV strain which caused the 2005–2006 outbreak in Greece belongs to genotype D6, and differs by 0·68% from the New Jersey D6 strain and by 5·5% from the MV vaccine strain Edmonston B (U03656) belonging to genotype A.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

THREE-DIMENSIONAL VISUALIZATION FOR PHYLOGENETIC TREE

2017 ◽  
Vol 9 (4) ◽  
pp. 59-66
Author(s):  
M. Forghani ◽  
P. Vasev ◽  
V. Averbukh
Keyword(s):  
Phylogenetic Tree ◽  
Three Dimensional

Method of constructing phylogenetic tree based on fuzzy clustering

2009 ◽  
Vol 29 (3) ◽  
pp. 836-838
Author(s):  
Gang-cheng LI ◽  
Zan-bo LIU ◽  
Qing-guang ZENG
Keyword(s):  
Phylogenetic Tree ◽  
Fuzzy Clustering

Phylogeny of 2019-nCoVs and SARS-like CoVs of Human, Bat and Pangolin Origin

2020 ◽  
Keyword(s):  
N Gene ◽  
Whole Genome ◽  
Human Origin ◽  
Gene Sequences ◽  
M Gene ◽  
S Gene ◽  
Shared Identity ◽  
Novel Coronavirus ◽  
S Genes

A novel coronavirus first broke out in Wuhan, China in December, 2019 has been declared a pandemic by WHO on March, 2020. This work aimed to search for probable ancestor of the virus, phylogeny of 2019-nCoVs and similar SL-CoVs based on the whole genome, M, N, ORF1ab, orf3a, and S gene sequences (n=84) obtained from GenBank using BLASTn software in the NCBI was done. Nucleotides of ORF3a and S-genes among 2019-nCoVs are identical, whereas its similar on the whole genome (99.9-100%), M-gene (99.7-100%), N-gene (99.9-100%) and ORF1ab-gene (99.7-100%). nCoVs are similar to bat CoV/RaTG13 on the whole genome (96.2%), M-gene (95.0%), N-gene (97%), ORF1ab-gene (95.3%), ORF3a-gene (99.1%) and S-gene (90.7%). Likewise, nCoVs exhibited homology to bat-CoVZXC21 on M-gene (93.2%), N-gene (91.5%), ORF1ab-gene (93.1%) and ORF3a-gene (94.4%). The emergent viruses shared identity to bat-CoVZC45 on N-gene (91.3%), ORF1ab-gene (92.8%) and ORF3a-gene (94.0%). In addition, pangolin-CoV/MP789 exhibited common sequences on M-gene (91.0%), N-gene (96.3%) and ORF3a-gene (93.3%) to nCoV. Furthermore, pangolin-CoV/MP789 is analogous to bat CoV/RaTG13 (91.3%) and bat-SL-CoVZXC21 (92.2%) on M-gene and to bat CoV/RaTG13 (94.8%) on N-gene. Nevertheless, nCoVs are distinct from the previously identified SL-CoVs of human origin. The present analysis indicates that nCoVs may have transmitted from bats, pangolin and/or unidentified hosts.

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

Systematics and evolution of Lentibulariaceae: II. Genlisea

2018 ◽  
Author(s):  
Andreas Fleischmann
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
Karyotype Evolution ◽  
Distribution Map ◽  
Genome And Karyotype Evolution

Systematics and evolution of Genlisea (corkscrew plants) (Lentibulariaceae) are treated. Vegetative and generative morphology of the plants, and anatomy of their rhizophylls (‘root-leaves’) that function as sophisticated eel traps are explained and illustrated. A simplified phylogenetic tree and a detailed distribution map are provided, and the evolutionary history, including genome and karyotype evolution, and phylobiogeography of the 30 currently known species of Genlisea are discussed.

Systematics and evolution of Lentibulariaceae: I. Pinguicula

2018 ◽  
Author(s):  
Andreas Fleischmann ◽  
Aymeric Roccia
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
Infrageneric Classification ◽  
Distribution Maps

Systematics and evolution of Pinguicula (butterworts) (Lentibulariaceae) are treated. Vegetative and generative morphology of the genus are illustrated and interpreted in the light of available phylogenetic evidence. A new infrageneric classification is proposed for Pinguicula; a simplified phylogenetic tree and detailed distribution maps are provided. Evolutionary history and phylobiogeography are briefly discussed together with the habitats, ecology, and conservation of the genus.

scholarly journals Effects of Inbreeding on Genetic Characteristic, Growth, Survival Rates, and Immune Responses of a New Inbred Line of Exopalaemon carinicauda

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jiajia Wang ◽  
Jitao Li ◽  
Qianqian Ge ◽  
Zhao Chen ◽  
Jian Li
Keyword(s):  
Immune Responses ◽  
Inbred Line ◽  
Survival Rates ◽  
The Body ◽  
Exopalaemon Carinicauda ◽  
Economic Traits ◽  
Gene Frequencies ◽  
Research Fields ◽  
Ssr Loci ◽  
Genetic Detection

The Exopalaemon carinicauda could be a useful crustacean laboratory animal in many research fields. We newly established an inbred line of Exopalaemon carinicauda named EC4 inbred line by brother×sister mating and keeping to F11 generation. Trends in heterozygosity in the process of producing EC4 inbred line were examined through the characterization of polymorphisms based on gene frequencies of SNP and EST-SSR loci. The results demonstrated that the number of alleles (N), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) gradually decreased with the increase of inbreeding generations. The genetic detection results indicated that 9 (29.03%, 9/31) of the SNP loci and 15 (32.61%, 15/46) of the EST-SSR loci were homozygous in F11 generation of EC4 inbred line. The variation of the growth-related traits, the immune responses, and antioxidant status were described in experimental full-sibling inbred populations of E. carinicauda at five levels of inbreeding coefficient (F=0.785, F=0.816, F=0.859, F=0.886, F=0.908) under controlled laboratory conditions. The body weight, body length, and survival rate in EC4 inbred line of all generations were less than the control population. Inbreeding affected the antibacterial activity, phenoloxidase (PO) activity, and superoxide dismutase (SOD) which decreased at the eleventh generation of EC4 inbred line. This study demonstrated that inbreeding had a negative effect on the economic traits and immune response, but our inbred line was established successfully until F11 and confirmed by genetic detection using SNP and EST-SSR loci.

DNA Barcoding and Phylogenetic Analysis Sugarcane (Saccharum officinarum L.) Based on matK ( maturase K) Gene

2020 ◽  
Vol 840 ◽  
pp. 162-170
Author(s):  
Ganies Riza Aristya ◽  
Fauzana Putri ◽  
Rina Sri Kasiamdari ◽  
Arni Musthofa
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Level ◽  
Economic Value ◽  
Saccharum Officinarum ◽  
Saccharum Spontaneum ◽  
Dna Barcodes ◽  
Pcr Method ◽  
Hybrid Cultivar ◽  
I Gene ◽  
Sequencing Process

Sugarcane (Saccharum officinarum L.) is an agricultural commodities with a great extent of diversity and high economic value. In Indonesia, the great extent of diversity of sugarcane is evidenced by a large number of cultivars cultivated. Sugarcane diversities at the molecular level can be seen using DNA barcodes, one of which is the matK. The purpose of the study was to identify and characterize matK and reconstruct the phylogenetic tree to determine the phylogeny of 24 sugarcane cultivars Indonesia. matK was amplified using the PCR method with matK F-5’ATGATTAATTAAGAGTAAGAGGAT-3’ and matK R-5’AATGCAAAAATTCGAAGGGT-3. Results showed that the matK gene was successfully amplified as many as 1531 bp. The sequencing process was done to determine the nucleotide sequence and compared with those of the GenBank database. It showed that the samples used had a similarity of 98.87%-99.44% to that of matK in Saccharum officinarum, Saccharum hybrid cultivar and Saccharum spontaneum. Reconstruction of the phylogenetic tree showed that the samples used were located in the same clade with a zero genetic distance, while all the references from NCBI were also located in the same clade. The analysis of genetic variation indicated that it had no haplotype value.

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