DataSheet_1_Identification of potential candidate vaccines against Mycobacterium ulcerans based on the major facilitator superfamily transporter protein.docx

Buruli ulcer is a neglected tropical disease that is characterized by non-fatal lesion development. The causative agent is Mycobacterium ulcerans (M. ulcerans). There are no known vectors or transmission methods, preventing the development of control methods. There are effective diagnostic techniques and treatment routines; however, several socioeconomic factors may limit patients’ abilities to receive these treatments. The Bacillus Calmette–Guérin vaccine developed against tuberculosis has shown limited efficacy, and no conventionally designed vaccines have passed clinical trials. This study aimed to generate a multi-epitope vaccine against M. ulcerans from the major facilitator superfamily transporter protein using an immunoinformatics approach. Twelve M. ulcerans genome assemblies were analyzed, resulting in the identification of 11 CD8+ and 7 CD4+ T-cell epitopes and 2 B-cell epitopes. These conserved epitopes were computationally predicted to be antigenic, immunogenic, non-allergenic, and non-toxic. The CD4+ T-cell epitopes were capable of inducing interferon-gamma and interleukin-4. They successfully bound to their respective human leukocyte antigens alleles in in silico docking studies. The expected global population coverage of the T-cell epitopes and their restricted human leukocyte antigens alleles was 99.90%. The population coverage of endemic regions ranged from 99.99% (Papua New Guinea) to 21.81% (Liberia). Two vaccine constructs were generated using the Toll-like receptors 2 and 4 agonists, LprG and RpfE, respectively. Both constructs were antigenic, non-allergenic, non-toxic, thermostable, basic, and hydrophilic. The DNA sequences of the vaccine constructs underwent optimization and were successfully in-silico cloned with the pET-28a(+) plasmid. The vaccine constructs were successfully docked to their respective toll-like receptors. Molecular dynamics simulations were carried out to analyze the binding interactions within the complex. The generated binding energies indicate the stability of both complexes. The constructs generated in this study display severable favorable properties, with construct one displaying a greater range of favorable properties. However, further analysis and laboratory validation are required.</p

Genetic Variation of Goat Interferon Regulatory Factor 3 Gene and Its Implication in Goat Evolution

<div><p>The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (<i>IRF</i>) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, <i>IRF3</i> is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the <i>IRF3</i> gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (<i>Capra aegagrus</i>). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats’ populations. Fu and Li tests were significantly positive but Tajima’s D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of <i>IRF3</i> gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model d_N/d_S ratio for all goats was greater than one. <a href="http://www.baidu.com/link?url=kkqzjLCQ_0ML92i5pxFn22m8yH-Ee0kuL6OdTRr1Ko76Iu8UyUCCRDpL8jgIpt2B4NUepOc7MJC9vWhiozorAK" target="_blank">Phylogenetic Analysis by Maximum Likelihood (PAML)</a> gave a ω₀ (d_N/d_S) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in <i>IRF3</i> gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat <i>IRF3</i> led us to conclude that the gene evolution may have been influenced by domestication processes in goats.</p></div

Neighbor joining phylogenetic trees for goat <i>IRF3</i> gene sequences constructed by Neighbor-joining (NJ) method in MEGA 6.0 with bootstrap value set to 1000 and <i>Ovis aries IRF3</i> gene sequence as outgroup.

<p>MOCH = Moroccan goats; IRCH = Iranian goats; WAD = West African Dwarf.</p

Accession Identification for goat <i>IRF3</i> Sequences downloaded from NCBI and NextGen Capra Project for Moroccan and Iranian goats.

<p>Accession Identification for goat <i>IRF3</i> Sequences downloaded from NCBI and NextGen Capra Project for Moroccan and Iranian goats.</p

Population statistics and neutrality test in <i>IRF3</i> gene in goats alone and goats with Sheep.

<p>Population statistics and neutrality test in <i>IRF3</i> gene in goats alone and goats with Sheep.</p

The phylogeny of goat <i>IRF3</i> gene was inferred by the maximum likelihood (ML) method using the PhyML program in MEGA software to analyze aligned sequences and this tree was rooted using the <i>Ovis aries IRF3</i> gene sequence.

<p>MOCH = Moroccan goats; IRCH = Iranian goats; WAD = West African Dwarf.</p

Chromosome identity, number of exons and mutations in codons under positive selection pressure in <i>IRF3</i> gene.

<p>Chromosome identity, number of exons and mutations in codons under positive selection pressure in <i>IRF3</i> gene.</p

Inference of positive selection in <i>IRF3</i> genes using two pairs of models in Phylogenetic Analysis by Maximum Likelihood (PAML).

<p>Inference of positive selection in <i>IRF3</i> genes using two pairs of models in <a href="http://www.baidu.com/link?url=kkqzjLCQ_0ML92i5pxFn22m8yH-Ee0kuL6OdTRr1Ko76Iu8UyUCCRDpL8jgIpt2B4NUepOc7MJC9vWhiozorAK" target="_blank">Phylogenetic Analysis by Maximum Likelihood (PAML)</a>.</p

Selection pressures among goat <i>IRF3</i> gene sequences using mechanistic empirical combination (MEC) model of selecton online tool.

<p>Yellow and brown highlights represent positive selection, grey and white highlights represent neutral selection and purple highlight represent negative selection on codons.</p

Haplotypes found in different goat types.

<p>Haplotypes found in different goat types.</p