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: Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.
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: The median problem is significantly applied to derive
the most reasonable rearrangement phylogenetic tree for many
species. More specifically, the problem is concerned with finding
a permutation that minimizes the sum of distances between itself
and a set of three signed permutations. Genomes with equal number
of genes but different order can be represented as permutations.
In this paper, an algorithm, namely BeamGA median, is proposed
that combines a heuristic search approach (local beam) as an
initialization step to generate a number of solutions, and then a
Genetic Algorithm (GA) is applied in order to refine the solutions,
aiming to achieve a better median with the smallest possible reversal
distance from the three original permutations. In this approach,
any genome rearrangement distance can be applied. In this paper,
we use the reversal distance. To the best of our knowledge, the
proposed approach was not applied before for solving the median
problem. Our approach considers true biological evolution scenario
by applying the concept of common intervals during the GA
optimization process. This allows us to imitate a true biological
behavior and enhance genetic approach time convergence. We were
able to handle permutations with a large number of genes, within
an acceptable time performance and with same or better accuracy as
compared to existing algorithms.
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: Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.
Abstract: To understand life as biological system, evolutionary
understanding is indispensable. Protein interactions data are rapidly
accumulating and are suitable for system-level evolutionary analysis.
We have analyzed yeast protein interaction network by both
mathematical and biological approaches. In this poster presentation,
we inferred the evolutionary birth periods of yeast proteins by
reconstructing phylogenetic profile. It has been thought that hub
proteins that have high connection degree are evolutionary old. But
our analysis showed that hub proteins are entirely evolutionary new.
We also examined evolutionary processes of protein complexes. It
showed that member proteins of complexes were tend to have
appeared in the same evolutionary period. Our results suggested that
protein interaction network evolved by modules that form the
functional unit. We also reconstructed standardized phylogenetic trees
and calculated evolutionary rates of yeast proteins. It showed that
there is no obvious correlation between evolutionary rates and
connection degrees of yeast proteins.
Abstract: Phylogenetic tree is a graphical representation of the
evolutionary relationship among three or more genes or organisms.
These trees show relatedness of data sets, species or genes
divergence time and nature of their common ancestors. Quality of a
phylogenetic tree requires parsimony criterion. Various approaches
have been proposed for constructing most parsimonious trees. This
paper is concerned about calculating and optimizing the changes of
state that are needed called Small Parsimony Algorithms. This paper
has proposed enhanced small parsimony algorithm to give better
score based on number of evolutionary changes needed to produce
the observed sequence changes tree and also give the ancestor of the
given input.
Abstract: Multiple sequence alignment is a fundamental part in
many bioinformatics applications such as phylogenetic analysis.
Many alignment methods have been proposed. Each method gives a
different result for the same data set, and consequently generates a
different phylogenetic tree. Hence, the chosen alignment method
affects the resulting tree. However in the literature, there is no
evaluation of multiple alignment methods based on the comparison of
their phylogenetic trees. This work evaluates the following eight
aligners: ClustalX, T-Coffee, SAGA, MUSCLE, MAFFT, DIALIGN,
ProbCons and Align-m, based on their phylogenetic trees (test trees)
produced on a given data set. The Neighbor-Joining method is used
to estimate trees. Three criteria, namely, the dNNI, the dRF and the
Id_Tree are established to test the ability of different alignment
methods to produce closer test tree compared to the reference one
(true tree). Results show that the method which produces the most
accurate alignment gives the nearest test tree to the reference tree.
MUSCLE outperforms all aligners with respect to the three criteria
and for all datasets, performing particularly better when sequence
identities are within 10-20%. It is followed by T-Coffee at lower
sequence identity (30%), trees scores of all methods
become similar.
Abstract: MMR vaccine failure had been reported globally and
here we report that it occurs now in India. Samples were collected from clinically suspected mumps cases were subjected for anti
mumps antibodies, virus isolation, RT-PCR, sequencing and
phylogenetic tree analysis. 56 samples collected from men and women belonging to various age groups. 30 had been vaccinated and
the status of 26 patients was unknown. 28 out of 30 samples were
found to be symptomatic and positive for Mumps IgM, indicating
active mumps infection in 93.4% of the vaccinated population. A
phylogenetic tree comparison of the clinical isolate is shown to be genotype C which is distinct from vaccine strain. Our study clearly sending warning signs that MMR vaccine is a failure and it needs to be revamped for the human use by increasing its efficacy and efficiency.