A quantitative analysis of the similarities and differences of the HIV/FIV gag genome

Among viruses, human immunodeficiency virus (HIV) presents the greatest challenge to humans. Here, we retrieved genome sequences from NCBI and were then run through LALIGN bioinformatics software to compute the E value, bit score, Waterman eggert score, and percent identity, which are four important indicators of how similar the sequences are. The E value was 3.1 x 10^-9, the percent identity was 54.4 percent, and the bit score was 51.9. It was also sensed that bases 1600 to 1990 in HIV and bases 800 to 910 in FIV have a higher than normal similarity. This reflects that while the DNA sequences of the gag region of both the HIV and FIV genomes are rather similar, it is unlikely that this similarity is due to random chance; therefore, there are a noticeable number of differences. A better understanding of the level of similarity and differences in the gag region of the genome sequence would facilitate our understanding of structural and cellular behavioral differences between FIV and HIV, and in the long term, it will provide new insights into the differences observed in previous studies or even facilitate the development of an effective HIV treatment.

A quantitative analysis of the FIV and HIV genome using bioinformatics software

Among viruses, the human immunodeficiency virus (HIV) presented the greatest challenge to human kinds. the HIV and FIV gag genome was sequenced using the Illumina MiSeq Benchtop next-generation sequencer.The DNA sequences obtained were then run through the LALIGN bioinformatics software to compute the E value, bit score, waterman eggert score, percent identity,which are four important indicators of how similar the sequences are. The E value was 3.1 x 10 ^-9, the percent identity was 54.4 percent and the bit score was 51.9. It was also sensed that base 1600 to 1990 in HIV and base 800 to 910 in FIV have a higher than normal similarity. This reflects that while the DNA sequences of the gag region of both the HIV and FIV genome are rather similar and it is unlikely that this similarity is due to random chance, there are a noticeable amount of differences. A better understanding of the level of similarity and differences in the gag region of the genome sequence would facilitate our understanding of structural and cellular behavioral differences between FIV and HIV, and in the long term it prevides new explanations to differences observed in previous studies, or even facilitate the development of an effective HIV treatment.

New Short RNA Motifs Potentially Relevant in the Severe Acute Respiratory Syndrome Coronavirus 2 Genome

As time passes, identifying new pharmacological targets is becoming more difficult. Shortly, it will be necessary to devise new strategies to tackle the problem. The coronavirus disease outbreak caused by the severe acute respiratory syndrome coronavirus 2 , represents a threat to human health serving as example from what we just said. The present study was aimed to collect a set of short RNA motifs with potential biological impact, most of which have not been observed heretofore. Categorizing RNA triplets by their gross-composition, the study collected 88 short RNA motifs, shared by most coronavirus genera independent on the percent identity between genomes. Selected motifs contain all nearest-neighbours of the triplets A, T, G and A, C, G. The high percent identity between severe acute respiratory syndrome coronavirus genomes makes it difficult these peptides to be found by current methods. The results provide 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf and 6 in the nucleocapsid-encoding orf. They also provide insights about the validity of the procedure, confirming some motifs interspersed or attached to known relevant functional fragments of the genome, although most of them have not yet been associated to any known function. The high level of preservation of these motifs in most coronavirus genera suggest they might have potential to be used for diagnostic, in vaccines, or as substrate for protease inhibitors.

Evolutionary and Expression Analysis of CAMTA Gene Family in Three Species (Arabidopsis, Maize and Tomato), and Gene Expression in Response to Developmental Stages

The calmodulin-binding transcriptional activator (CAMTA) family has been known to be one of the fast responsive stress proteins. In this study, 17 CAMTA genes were selected in Arabidopsis, tomato and maize. The chromosomal distributions, gene structures, duplication patterns, phylogenetic tree, and developmental stage of the 17 CAMTA genes in the three species were analyzed to further investigate their functions. According to the synteny analysis, CAMTA genes of maize and tomato revealed higher similarity with each other as compared with Arabidopsis. A higher than 90 percent identity was observed between maize CAMTA genes (ZmCAMTA2 and ZmCAMTA3) and tomato CAMTA genes (SlCAMTA4, SlCAMTA4.1). To detect expression levels in different plant tissues, mRNA analysis of CAMTA genes were performed using publicly available expression data in the genvestigator. The aim of study was to identify and characterize CAMTA genes in three species, for the first time, via insilico genome-wide analysis approach. AtCAMTA1 and AtCAMTA2 and SlCAMTA2 and ZmCAMTA1 and ZmCAMTA2 genes were up-regulated during all developmental stages. The conserved motifs and gene structure in most proteins in each group were similar, validating the CAMTA phylogenetic classification. This study could be considered as a useful source for future CAMTA comparative studies in different plant species.

Design of the env-su Gene Coding for Surface Unit Protein as a Vaccine Candidate for Jembrana Disease Virus in In Silico

Bali cattle are superior meat producers, but they are susceptible to Jembrana disease. The injection of the crude vaccine was considered ineffective, so the env-su gene was selected to express the Jembrana Surface Unit (JSU) protein as a candidate for the Jembrana vaccine. This study aimed to analyze the potential of the JSU protein as a candidate for the Jembrana vaccine and analyze the increase in the env-su gene expression which codon has been optimized in silico. Vaccine design was carried out through in silico including the selection of the SU protein sequences of the genus Lentivirus and sequence alignment of UniProt. The construction phylogeny tree of SU protein using MEGA-X program, optimization of env-su gene codon with preference codon Esherichia coli str. K-12 substr. MG1655 using Optimizer. The optimized env-su gene was inserted into the plasmid pET-21a (+) using GenScript. The result of sequence alignment showed that there is no SU protein that has a percent identity value of more than 30% with JSU protein. The SU JDV and BIV proteins are monophyletic groups and have a percent identity of 20.57%. Codon optimization showed an increase in CAI by 1,000 and GC 54.5%, and a decrease in ENc to 22 and AT 45.5%. EcoR1 and HindIII can recognize the gene target and MCS cut regions on the plasmid so that the env-su gene can be inserted into the pET-21a (+) plasmid. The JSU protein has the potential to be a candidate for the Jembrana vaccine, but it needs further research in vitro and in vivo.

CO1 Metabarcoding of Marine Water Samples from the 2nd Turkish Antarctic Expedition (TAE2) Highlights the Deficiencies in the Reference Barcoding Databases for the Continent

Based on climate projections, the Antarctic Peninsula is one of the regions on the earth expected to be most drastically affected by climate change in the 2nd half of the 21st century. In order to establish baseline levels of marine biodiversity using the environmental DNA approach, we undertook metabarcoding based on the CO1 gene. Samples were collected using 0.22 mM pore-sized Sterivex filters during TAE2 undertaken in 2018, from one site at Deception Island (2 filters), one site at Nansen Island (2 filters), and three sites (one offshore) at Robert Island. A total of 20 taxa were identified (unique hits with BLAST percent identity ≥ 97%) belonging to three kingdoms (Chromista, Plantae, Animalia), nine phyla, 11 classes, 17 orders, 19 families, and 20 genera. Of these, 18 were identified to the species level, one to the genus level, and the other one to the family level. Genetically identified taxa included seven planktonic algae, nine seaweeds, a stalked jellyfish, a nematode, a planktonic copepod, and a demersal fish. In addition, 129 unique OTUs were detected (unique hits with BLAST percent identity < 97%) as unidentified. These results indicate the high levels of undocumented genetic diversity (without CO1 barcode sequences in GenBank) in the Antarctic Peninsula region and adjacent waters, and the need for more work to complete the reference barcode databases for the continent. A dendrogram resulting from cluster analysis (Bray-Curtis similarity measure, group-average linkage) based on the presence/absence data of 20 identified species revealed three well-defined sample (i.e. filter containing DNA fragments of multiple taxa) groups, which almost coincided with their geographical locations. First group included samples (filters) collected from the coast of Deception Island and the second one from the coast of Robert Island, both in the South Shetland Islands, off the northern tip of the Antarctic Peninsula. The third group included samples from Nansen Island coast (off the west coast of Graham Land, Antarctic Peninsula) together with the only sample collected offshore, off Robert Island. The significance of this clustering, thus the difference among sampling sites with regard to species composition, was confirmed by Analysis of Similarity (ANOSIM) results (Global R = 0.982, p = 0.001). The highest number of identified taxa (per filter) and unidentified OTUs (per filter) were observed offshore off Robert Island. Considering that all of the other sampling sites were by the coasts of islands, this observation indicates i) the offshore waters might contain more DNA-bearing material than coastal sites, and/or ii) a methodological issue where the high phytoplankton and suspended matter concentrations by the coasts created a bottleneck in terms of capturing actual species diversity at the coasts, due to clogging of filters by phytoplankton and fine suspended particles.

Bioinformatic analyses of kappa casein gene in mammalian livestock species

Kappa casein (CSN3) gene is a variant of the milk protein highly conserved in mammalian species. Genetic variations in CSN3 gene of six mammalian livestock species were investigated using bioinformatics approach. A total of twenty-seven CSN3 gene sequences with corresponding amino acids belonging to the six species studied were retrieved from GenBank. Using a comparative genomic approach, we obtained 1797 bp of the CSN3 sequences from cattle, goat, horse, pig, rabbit and sheep. Alignment of twenty-seven sequences within the region of 1713 bp and containing gaps was carried out using Clustal W. The sequence alignment revealed high polymorphisms of CSN3 sequences among the six species. The percent identity and similarity between species were determined by conducting pair-wise comparisons of the sequences. Results revealed high level of identity and similarity among the ruminant animals (84-97% and 86-99%) which implied the gene is conserved in all the ruminants. However, percent identity and similarity between pig and rabbit were relatively low (45%, 61%). This revealed that CSN3 protein from them might be functionally different and divergence between them is more ancient. Higher polymorphism of amino acids was observed among the species than within species. Four non-synonymous mutations occurred in cattle, six in goat, four in horse, three in rabbit and seven in sheep. The results of DnaSP analysis indicated that the selected region (1-1797 bp) of the twenty-seven sequences from all the species had 1298 nucleotide sites excluding sites with gaps (499). There are invariable and variable sites that include 185 singleton variable sites and 56 parsimony informative sites. The nucleotide diversity (ð= 0.212) and average number of nucleotide diversity (k = 94.84) for all sequences which were lower than the highest values in rabbit (ð = 0.557, k = 229) were estimated. Divergence of the species could be inferred from high genetic diversity of the CSN3 gene. The haplotype diversity was 1.00 in goat, horse and sheep indicating abundant genetic diversity in those species. Close relationship between goat and sheep was observed in phylogenetic tree of CSN3 gene which showed that the comparability of CSN3 gene sequences was highest between the goat and sheep and they evolved from a most recent common ancestor. A more detailed study involving more divergent taxa and complete amino acid sequence will help to delineate how the mutations affect the functions of the gene.

Identification and Characterization of 33 Bacillus cereus sensu lato Isolates from Agricultural Fields from Eleven Widely Distributed Countries by Whole Genome Sequencing

The phylogeny, identification, and characterization of 33 B. cereus sensu lato isolates originating from 17 agricultural soils from 11 countries were analyzed on the basis of whole genome sequencing. Phylogenetic analyses revealed all isolates are divided into six groups, which follows the generally accepted phylogenetic division of B. cereus sensu lato isolates. Four different identification methods resulted in a variation in the identity of the isolates, as none of the isolates were identified as the same species by all four methods—only the recent identification method proposed directly reflected the phylogeny of the isolates. This points to the importance of describing the basis and method used for the identification. The presence and percent identity of the protein product of 19 genes potentially involved in pathogenicity divided the 33 isolates into groups corresponding to phylogenetic division of the isolates. This suggests that different pathotypes exist and that it is possible to differentiate between them by comparing the percent identity of proteins potentially involved in pathogenicity. This also reveals that a basic link between phylogeny and pathogenicity is likely to exist. The geographical distribution of the isolates is not random: they are distributed in relation to their division into the six phylogenetic groups, which again relates to different ecotypes with different temperature growth ranges. This means that we find it easier to analyze and understand the results obtained from the 33 B. cereus sensu lato isolates in a phylogenetic, patho-type and ecotype-oriented context, than in a context based on uncertain identification at the species level.

Sequence and evolutionary analysis of bacterial ribosomal S1 proteins

The multi-domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a “bead-on-string” organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla; we demonstrate how such phyla can independently/dependently form during evolution. To our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data suggested that the evolutionary development of bacterial ribosomal proteins S1 evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.

VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses

Nucleotide-based intergenomic similarities are useful to understand how viruses are related with each other and to classify them. Here we have developed VIRIDIC, which implements the traditional algorithm used by the International Committee on Taxonomy of Viruses (ICTV), Bacterial and Archaeal Viruses Subcommittee, to calculate virus intergenomic similarities. When compared with other software, VIRIDIC gave the best agreement with the traditional algorithm, which is based on the percent identity between two genomes determined by BLASTN. Furthermore, VIRIDIC proved best at estimating the relatedness between more distantly-related phages, relatedness that other tools can significantly overestimate. In addition to the intergenomic similarities, VIRIDIC also calculates three indicators of the alignment ability to capture the relatedness between viruses: the aligned fractions for each genome in a pair and the length ratio between the two genomes. The main output of VIRIDIC is a heatmap integrating the intergenomic similarity values with information regarding the genome lengths and the aligned genome fraction. Additionally, VIRIDIC can group viruses into clusters, based on user-defined intergenomic similarity thresholds. The sensitivity of VIRIDIC is given by the BLASTN. Thus, it is able to capture relationships between viruses having in common even short genomic regions, with as low as 65% similarity. Below this similarity level, protein-based analyses should be used, as they are the best suited to capture distant relationships. VIRIDIC is available at viridic.icbm.de, both as a web-service and a stand-alone tool. It allows fast analysis of large phage genome datasets, especially in the stand-alone version, which can be run on the user’s own servers and can be integrated in bioinformatics pipelines. VIRIDIC was developed having viruses of Bacteria and Archaea in mind; however, it could potentially be used for eukaryotic viruses as well, as long as they are monopartite.