Current Bioinformatics resources in combating infectious diseases

Leptospirosis in India: insights on circulating serovars, research lacunae and proposed strategies to control through one health approach

Leptospirosis is one of the most neglected zoonotic infections of public health concern worldwide and a remerging infection in tropical countries such as India. The infection least explored disease and the epidemiological and other critical data are scarce for the disease rate reported and to control the infection. Leptospirosis as sapronosis is as underrated as the infection itself, and this article aims to explore the significance of this aspect of the disease. The research review aimed at the epidemiological understanding of the infection to control the negative impact of the disease. A mixed review and analysis were carried out to understand the knowledge published on the critical and understudied areas like epidemiology, transmission, diagnosis, treatment, and control of infection. A systematic analysis was carried out to extract information about the reported circulating strains, and research lacunae in India with the published data available in PubMed. The article elaborately discusses crucial inference areas of infection transmission and addresses lacunae in critically unacclaimed areas of infection to control the spread of infection using one health approach (OHA), and strategies to control leptospiral infection are proposed. The article also reviewed how and why Leptospirosis can be best studied and controlled by "One health approach" in India.

In Silico Comparison of Bioactive Compounds Characterized from Azadirachta indica with an FDA-Approved Drug against Schistosomal Agents: New Insight into Schistosomiasis Treatment

The burden of human schistosomiasis, a known but neglected tropical disease in Sub-Saharan Africa, has been worrisome in recent years. It is becoming increasingly difficult to tackle schistosomiasis with praziquantel, a drug known to be effective against all Schistosoma species, due to reports of reduced efficacy and resistance. Therefore, this study seeks to investigate the antischistosomal potential of phytochemicals from Azadirachta indica against proteins that have been implicated as druggable targets for the treatment of schistosomiasis using computational techniques. In this study, sixty-three (63) previously isolated and characterized phytochemicals from A. indica were identified from the literature and retrieved from the PubChem database. In silico screening was conducted to assess the inhibitory potential of these phytochemicals against three receptors (Schistosoma mansoni Thioredoxin glutathione reductase, dihydroorotate dehydrogenase, and Arginase) that may serve as therapeutic targets for schistosomiasis treatment. Molecular docking, ADMET prediction, ligand interaction, MMGBSA, and molecular dynamics simulation of the hit compounds were conducted using the Schrodinger molecular drug discovery suite. The results show that Andrographolide possesses a satisfactory pharmacokinetic profile, does not violate the Lipinski rule of five, binds with favourable affinity with the receptors, and interacts with key amino acids at the active site. Importantly, its interaction with dihydroorotate dehydrogenase, an enzyme responsible for the catalysis of the de novo pyrimidine nucleotide biosynthetic pathway rate-limiting step, shows a glide score and MMGBSA of -10.19 and -45.75 Kcal/mol, respectively. In addition, the MD simulation shows its stability at the active site of the receptor. Overall, this study revealed that Andrographolide from Azadirachta indica could serve as a potential lead compound for the development of an anti-schistosomal drug.

PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling

Background

Computational methods based on initial screening and prediction of peptides for desired functions have proven to be effective alternatives to lengthy and expensive biochemical experimental methods traditionally utilized in peptide research, thus saving time and effort. However, for many researchers, the lack of expertise in utilizing programming libraries, access to computational resources, and flexible pipelines are big hurdles to adopting these advanced methods.

Results

To address the above mentioned barriers, we have implemented the peptide design and analysis under Galaxy (PDAUG) package, a Galaxy-based Python powered collection of tools, workflows, and datasets for rapid in-silico peptide library analysis. In contrast to existing methods like standard programming libraries or rigid single-function web-based tools, PDAUG offers an integrated GUI-based toolset, providing flexibility to build and distribute reproducible pipelines and workflows without programming expertise. Finally, we demonstrate the usability of PDAUG in predicting anticancer properties of peptides using four different feature sets and assess the suitability of various ML algorithms.

Conclusion

PDAUG offers tools for peptide library generation, data visualization, built-in and public database peptide sequence retrieval, peptide feature calculation, and machine learning (ML) modeling. Additionally, this toolset facilitates researchers to combine PDAUG with hundreds of compatible existing Galaxy tools for limitless analytic strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04727-6.

Teaching next-generation sequencing to medical students with a portable sequencing device

BACKGROUND

There continues to be a disjoint between the emergence of new diagnostic technologies and venues to train new physicians on how to apply them. Next-generation sequencing (NGS) has become a very important tool for a wide range of clinical applications. Technical complexity and cost have been the major obstacles in incorporating these technologies into the classroom.

GOAL FOR INNOVATION

We opted to use the MinION, which is a new portable DNA sequencer that can produce data in real-time at a relatively low cost, for a NGS hands-on workshop with medical students.

STEPS TAKEN

We conducted a pilot NGS hands-on practical module in order to expose an interested group of medical students to this new portable sequencer device. A pre- and post-survey, using a Likert-type scale survey items and open-ended questions, evaluated participant resistance to new diagnostic tools, familiarity with NGS, and likelihood to use a portable sequencer in clinical practice.

OUTCOMES

Prior to participating in our learning workshop, students did not understand how to incorporate NGS into clinical practice, and expressed that cost and prior training/knowledge were among the limiting factors in their likelihood to use NGS as a diagnostic tool. After participating in the module, students' responses demonstrated a shift in their understanding of the scientific principles and applications of NGS (pre- and post-survey scores p < 0.05).

REFLECTION

The hands-on experience not only helped students become closer to and more comfortable with NGS, but also served as a venue to discuss the science and application of this technology in medicine. Such discussion helped to provide participants with current "genetic literacy" that is often incompletely covered in the typical undergraduate medical education curriculum.

Landscape of ROD9 Island: Functional annotations and biological network of hypothetical proteins in Salmonella enterica

Salmonella, an Enterobacteria is a therapeutically important pathogen for the host. The advancement of genome sequencing of S. enterica serovar Enteritidis have identified a distinct ROD9 pathogenic island, imparting virulence. The occurrence of 17 ROD9 hypothetical proteins, necessitates subsequent bioinformatics approach for structural and functional aspects of protein-protein relations or networks in different pathogenic phenotypes express. A collective analysis using predictive bioinformatics tools that includes NCBI-BLASTp and BLAST2GO annotated the motif patterns and functional significance. The VFDB identified 10 virulence proteins at both genomic and metagenomic level. Phylogenetic analysis revealed a divergent and convergent relationship between 17 ROD9 and 41 SP-1 proteins. Here, combining a comprehensive approach from sequence based, motif recognitions, domain identification, virulence ability to structural modelling provides a precise function to ROD9 proteins biological network, for which no experimental information is available.

Viral Detection: Past, Present, and Future

Viruses are essentially composed of a nucleic acid (segmented or not, DNA, or RNA) and a protein coat. Despite their simplicity, these small pathogens are responsible for significant economic and humanitarian losses that have had dramatic consequences in the course of human history. Since their discovery, scientists have developed different strategies to efficiently detect viruses, using all possible viral features. Viruses shape, proteins, and nucleic acid are used in viral detection. In this review, the development of these techniques, especially for plant and mammalian viruses, their strengths and weaknesses as well as the latest cutting-edge technologies that may be playing important roles in the years to come are described.

Bioinformatics-based tools in drug discovery: the cartography from single gene to integrative biological networks

Originally developed for the analysis of biological sequences, bioinformatics has advanced into one of the most widely recognized domains in the scientific community. Despite this technological evolution, there is still an urgent need for nontoxic and efficient drugs. The onus now falls on the 'omics domain to meet this need by implementing bioinformatics techniques that will allow for the introduction of pioneering approaches in the rational drug design process. Here, we categorize an updated list of informatics tools and explore the capabilities of integrative bioinformatics in disease control. We believe that our review will serve as a comprehensive guide toward bioinformatics-oriented disease and drug discovery research.