Abstract: SARS-CoV-2 virus is currently one of the most
infectious pathogens for humans. It started in China at the end of
2019 and now it is spread in all over the world. The origin and
diffusion of the SARS-CoV-2 epidemic, is analysed based on the
discussion of viral phylogeny theory. With the aim of understanding
the spread of infection in the affected countries, it is crucial to
modelize the spread of the virus and simulate its activity. In this
paper, the prediction of coronavirus outbreak is done by using SIR
model without vital dynamics, applying different numerical technique
solving ordinary differential equations (ODEs). We find out that ABM
and MRT methods perform better than other techniques and that the
activity of the virus will decrease in April but it never cease (for
some time the activity will remain low) and the next cycle will start
in the middle July 2020 for Norway and Denmark, and October 2020
for Sweden, and September for Finland.
Abstract: Water lily (Nymphaea L.) is the largest genus of Nymphaeaceae. This family is composed of six genera (Nuphar, Ondinea, Euryale, Victoria, Barclaya, Nymphaea). Its members are nearly worldwide in tropical and temperate regions. The classification of some species in Nymphaea is ambiguous due to high variation in leaf and flower parts such as leaf margin, stamen appendage. Therefore, the phylogenetic relationships based on 18S rDNA were constructed to delimit this genus. DNAs of 52 specimens belonging to water lily family were extracted using modified conventional method containing cetyltrimethyl ammonium bromide (CTAB). The results showed that the amplified fragment is about 1600 base pairs in size. After analysis, the aligned sequences presented 9.36% for variable characters comprising 2.66% of parsimonious informative sites and 6.70% of singleton sites. Moreover, there are 6 regions of 1-2 base(s) for insertion/deletion. The phylogenetic trees based on maximum parsimony and maximum likelihood with high bootstrap support indicated that genus Nymphaea was a paraphyletic group because of Ondinea, Victoria and Euryale disruption. Within genus Nymphaea, subgenus Nymphaea is a basal lineage group which cooperated with Euryale and Victoria. The other four subgenera, namely Lotos, Hydrocallis, Brachyceras and Anecphya were included the same large clade which Ondinea was placed within Anecphya clade due to geographical sharing.
Abstract: Some Metapenaeus monoceros cox1 gene fragments were isolated, purified, sequenced, and comparatively analyzed with some other Crustacean Cox1 gene sequences (obtained from National Center for Biotechnology Information). This work was designed for testing the efficiency of this system in reconstruction of phylogenetic relations among some Crustacean species belonging to four genera (Metapenaeus, Artemia, Daphnia and Calanus). The single nucleotide polymorphism and haplotype diversity were calculated for all estimated mt-DNA fragments. The genetic distance values were 0.292, 0.015, 0.151, and 0.09 within Metapenaeus species, Calanus species, Artemia species, and Daphnia species, respectively. The reconstructed phylogenetic tree is clustered into some unique clades. Cytochrome oxidase subunit 1 gene (cox1) was a powerful system in reconstruction of phylogenetic relations among evaluated crustacean species.
Abstract: This study solves a phylogeny problem by using modified wild dog pack optimization. The least squares error is considered as a cost function that needs to be minimized. Therefore, in each iteration, new distance matrices based on the constructed trees are calculated and used to select the alpha dog. To test the suggested algorithm, ten homologous genes are selected and collected from National Center for Biotechnology Information (NCBI) databanks (i.e., 16S, 18S, 28S, Cox 1, ITS1, ITS2, ETS, ATPB, Hsp90, and STN). The data are divided into three categories: 50 taxa, 100 taxa and 500 taxa. The empirical results show that the proposed algorithm is more reliable and accurate than other implemented methods.
Abstract: Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.
Abstract: In April 2009, a new variant of Influenza A virus
subtype H1N1 emerged in Mexico and spread all over the world. The
influenza has three subtypes in human (H1N1, H1N2 and H3N2)
Types B and C influenza tend to be associated with local or regional
epidemics. Preliminary genetic characterization of the influenza
viruses has identified them as swine influenza A (H1N1) viruses.
Nucleotide sequence analysis of the Haemagglutinin (HA) and
Neuraminidase (NA) are similar to each other and the majority of
their genes of swine influenza viruses, two genes coding for the
neuraminidase (NA) and matrix (M) proteins are similar to
corresponding genes of swine influenza. Sequence similarity between
the 2009 A (H1N1) virus and its nearest relatives indicates that its
gene segments have been circulating undetected for an extended
period. Nucleic acid sequence Maximum Likelihood (MCL) and
DNA Empirical base frequencies, Phylogenetic relationship amongst
the HA genes of H1N1 virus isolated in Genbank having high
nucleotide sequence homology.
In this paper we used 16 HA nucleotide sequences from NCBI for
computing sequence relationships similarity of swine influenza A
virus using the following method MCL the result is 28%, 36.64% for
Optimal tree with the sum of branch length, 35.62% for Interior
branch phylogeny Neighber – Join Tree, 1.85% for the overall
transition/transversion, and 8.28% for Overall mean distance.