Vetinformatics: An Insight for Decoding Livestock Systems Through In Silico Biology

Editorial

30 October 2023

Editorial: Vetinformatics: an insight for decoding livestock systems through in silico biology

Jun-Mo Kim

and

Rajesh Kumar Pathak

1,567 views

7 citations

Editors

Impact

Original Research

21 June 2023

Translating conventional wisdom on chicken comb color into automated monitoring of disease-infected chicken using chromaticity-based machine learning models

Mohd Anif A. A. Bakar

, 4 more and

Abdul Rahman Omar

3,262 views

3 citations

Original Research

12 May 2023

Comparative expression analysis of water buffalo (Bubalus bubalis) to identify genes associated with economically important traits

Dwijesh Chandra Mishra

, 8 more and

Krishna Kumar Chaturvedi

2,299 views

0 citations

Comparison of assembly statistics for selection of effective indicators for genome quality evaluation of various species relatively. (A) Investigation of correlation between various assembly statistics and repeat elements that are presumed to be related to genome quality evaluation. Pearson's correlation coefficients were used to pairwise investigation. Four major types of indicators showed strong correlations. (B) The number of spanned gaps remaining in the genomes of 109 species. (C) Comparison of adjusted N50 in scaffold level by genome size. (D) Comparison of adjusted N50 in contig level by genome size. (E) Strong correlation between genome size and total length of repeat elements in each species. R2 and r2 represents coefficient of determination and correlation coefficient, respectively. (F) Correlation between the assembly statistics and the amount of various types of repeat elements found in the genome of 108 species. (B–E) The colors in the figure share group information separated by class taxonomic level, except for human-mouse and eight livestock animals.

Original Research

21 February 2023

Benchmark study for evaluating the quality of reference genomes and gene annotations in 114 species

Sinwoo Park

, 5 more and

Minseok Seo

3,364 views

5 citations

Original Research

26 January 2023

A pilot study for a non-invasive system for detection of malignancy in canine subcutaneous and cutaneous masses using machine learning

Gillian Dank

, 5 more and

Michael S. Kent

Classification of cytology and histopathology results.

Introduction: Early diagnosis of cancer enhances treatment planning and improves prognosis. Many masses presenting to veterinary clinics are difficult to diagnose without using invasive, time-consuming, and costly tests. Our objective was to perform a preliminary proof-of-concept for the HT Vista device, a novel artificial intelligence-based thermal imaging system, developed and designed to differentiate benign from malignant, cutaneous and subcutaneous masses in dogs.

Methods: Forty-five dogs with a total of 69 masses were recruited. Each mass was clipped and heated by the HT Vista device. The heat emitted by the mass and its adjacent healthy tissue was automatically recorded using a built-in thermal camera. The thermal data from both areas were subsequently analyzed using an Artificial Intelligence algorithm. Cytology and/or biopsy results were later compared to the results obtained from the HT Vista system and used to train the algorithm. Validation was done using a “Leave One Out” cross-validation to determine the algorithm's performance.

Results: The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the system were 90%, 93%, 88%, 83%, and 95%, respectively for all masses.

Conclusion: We propose that this novel system, with further development, could be used to provide a decision-support tool enabling clinicians to differentiate between benign lesions and those requiring additional diagnostics. Our study also provides a proof-of-concept for ongoing prospective trials for cancer diagnosis using advanced thermodynamics and machine learning procedures in companion dogs.

6,045 views

6 citations

Amino acid composition of avUCP in different avian species.

Original Research

19 January 2023

In silico investigation of uncoupling protein function in avian genomes

Peymaneh Davoodi

, 5 more and

Jacqueline Smith

2,379 views

5 citations

Structural analysis and validation of designed vaccine. (A) Schematic design of the final vaccine construct. AAY Linkers join the CTL epitopes, HTL epitopes are joined by GPGPG linkers and B-cell epitopes by KK linkers. The Cholera Toxin B (CTB) adjuvant is added to the N-terminus of the sequence by an EAAK linker. An additional EAAK linker C-Terminal and HEYGAEALERAG linkers between CTL and HTL epitopes were incorporated. (B) The refined three-dimensional structure of vaccine construct; (C) ProSA-web assessment of the vaccine tertiary structure. The evaluation revealed a Z-score of −4.49, indicating good quality. (D) Ramachandran plot analysis of the refined structure. The evaluation revealed that 96.0% of the residues of the vaccine are present in the favored region.

Original Research

13 January 2023

A multiepitope vaccine candidate against infectious bursal disease virus using immunoinformatics-based reverse vaccinology approach

Irfan Gul

, 8 more and

Nadeem Shabir

Infectious bursal disease virus is the causative agent of infectious bursal disease (Gumboro disease), a highly contagious immunosuppressive disease of chicken with a substantial economic impact on small- and large-scale poultry industries worldwide. Currently, live attenuated vaccines are widely used to control the disease in chickens despite their issues with safety (immunosuppression and bursal atrophy) and efficiency (breaking through the maternally-derived antibody titer). To overcome the drawbacks, the current study has, for the first time, attempted to construct a computational model of a multiepitope based vaccine candidate against infectious bursal disease virus, which has the potential to overcome the safety and protection issues found in the existing live-attenuated vaccines. The current study used a reverse vaccinology based immunoinformatics approach to construct the vaccine candidate using major and minor capsid proteins of the virus, VP2 and VP3, respectively. The vaccine construct was composed of four CD8⁺ epitopes, seven CD4⁺ T-cell epitopes, 11 B-cell epitopes and a Cholera Toxin B adjuvant, connected using appropriate flexible peptide linkers. The vaccine construct was evaluated as antigenic with VaxiJen Score of 0.6781, immunogenic with IEDB score of 2.89887 and non-allergenic. The 55.64 kDa construct was further evaluated for its physicochemical characteristics, which revealed that it was stable with an instability index of 16.24, basic with theoretical pI of 9.24, thermostable with aliphatic index of 86.72 and hydrophilic with GRAVY score of −0.256. The docking and molecular dynamics simulation studies of the vaccine construct with Toll-like receptor-3 revealed fair structural interaction (binding affinity of −295.94 kcal/mol) and complex stability. Further, the predicted induction of antibodies and cytokines by the vaccine construct indicated the possible elicitation of the host's immune response against the virus. The work is a significant attempt to develop next-generation vaccines against the infectious bursal disease virus though further experimental studies are required to assess the efficacy and protectivity of the proposed vaccine candidate in vivo.

4,211 views

10 citations

Review

11 November 2022

Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science

Rajesh Kumar Pathak

and

Jun-Mo Kim

Having played important roles in human growth and development, livestock animals are regarded as integral parts of society. However, industrialization has depleted natural resources and exacerbated climate change worldwide, spurring the emergence of various diseases that reduce livestock productivity. Meanwhile, a growing human population demands sufficient food to meet their needs, necessitating innovations in veterinary sciences that increase productivity both quantitatively and qualitatively. We have been able to address various challenges facing veterinary and farm systems with new scientific and technological advances, which might open new opportunities for research. Recent breakthroughs in multi-omics platforms have produced a wealth of genetic and genomic data for livestock that must be converted into knowledge for breeding, disease prevention and management, productivity, and sustainability. Vetinformatics is regarded as a new bioinformatics research concept or approach that is revolutionizing the field of veterinary science. It employs an interdisciplinary approach to understand the complex molecular mechanisms of animal systems in order to expedite veterinary research, ensuring food and nutritional security. This review article highlights the background, recent advances, challenges, opportunities, and application of vetinformatics for quality veterinary services.

4,205 views

19 citations

Original Research

26 September 2022

Impact of preweaning vaccination on host gene expression and antibody titers in healthy beef calves

Matthew A. Scott

, 3 more and

Sarah F. Capik

The impact of preweaning vaccination for bovine respiratory viruses on cattle health and subsequent bovine respiratory disease morbidity has been widely studied yet questions remain regarding the impact of these vaccines on host response and gene expression. Six randomly selected calves were vaccinated twice preweaning (T1 and T3) with a modified live vaccine for respiratory pathogens and 6 randomly selected calves were left unvaccinated. Whole blood samples were taken at first vaccination (T1), seven days later (T2), at revaccination and castration (T3), and at weaning (T4), and utilized for RNA isolation and sequencing. Serum from T3 and T4 was analyzed for antibodies to BRSV, BVDV1a, and BHV1. Sequenced RNA for all 48 samples was bioinformatically processed with a HISAT2/StringTie pipeline, utilizing reference guided assembly with the ARS-UCD1.2 bovine genome. Differentially expressed genes were identified through analyzing the impact of time across all calves, influence of vaccination across treatment groups at each timepoint, and the interaction of time and vaccination. Calves, regardless of vaccine administration, demonstrated an increase in gene expression over time related to specialized proresolving mediator production, lipid metabolism, and stimulation of immunoregulatory T-cells. Vaccination was associated with gene expression related to natural killer cell activity and helper T-cell differentiation, enriching for an upregulation in Th17-related gene expression, and downregulated genes involved in complement system activity and coagulation mechanisms. Type-1 interferon production was unaffected by the influence of vaccination nor time. To our knowledge, this is the first study to evaluate mechanisms of vaccination and development in healthy calves through RNA sequencing analysis.

4,921 views

8 citations