Soja Soman

Soja Soman

orcid

Research Focus & Metrics

Academic Career Length

18Years (2009-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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1 June 2009 in Molecular Immunology
Verified
Journal Article
Closed access
SSSoja Soman
Soja Soman
DAD.S. Arathy
D.S. Arathy
ESE. Sreekumar
E. Sreekumar

Verified
Journal Article
Open access
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SSSoja Soman
Soja Soman
Vijayavenkataraman SanjairajVijayavenkataraman Sanjairaj
Vijayavenkataraman Sanjairaj
The peripheral nervous system controls the functions of sensation, movement and motor coordination of the body. Peripheral nerves can get damaged easily by trauma or neurodegenerative diseases. The injury can cause a devastating effect on the affected individual and his aides. Treatment modalities include anti-inflammatory medications, physiotherapy, surgery, nerve grafting and rehabilitation. 3D bioprinted peripheral nerve conduits serve as nerve grafts to fill the gaps of severed nerve bodies. The application of induced pluripotent stem cells, its derivatives and bioprinting are important techniques that come in handy while making living peripheral nerve conduits. The design of nerve conduits and bioprinting require comprehensive information on neural architecture, type of injury, neural supporting cells, scaffold materials to use, neural growth factors to add and to streamline the mechanical properties of the conduit. This paper gives a perspective on the factors to consider while bioprinting the peripheral nerve conduits.

18 January 2010 in BMC Bioinformatics
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Journal Article
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SSSoja Soman
Soja Soman
SKSivakumar KC
Sivakumar KC
ESEaswaran Sreekumar
Easwaran Sreekumar
Background: Defensins comprise a group of antimicrobial peptides, widely recognized as important elements of the innate immune system in both animals and plants. Cationicity, rather than the secondary structure, is believed to be the major factor defining the antimicrobial activity of defensins. To test this hypothesis and to improve the activity of the newly identified avian β-defensin Apl_AvBD2 by enhancing the cationicity, we performed in silico site directed mutagenesis, keeping the predicted secondary structure intact. Molecular dynamics (MD) simulation studies were done to predict the activity. Mutant proteins were made by in vitro site directed mutagenesis and recombinant protein expression, and tested for antimicrobial activity to confirm the results obtained in MD simulation analysis. Results: MD simulation revealed subtle, but critical, structural variations between the wild type Apl_AvBD2 and the more cationic in silico mutants, which were not detected in the initial structural prediction by homology modelling. The C-terminal cationic 'claw' region, important in antimicrobial activity, which was intact in the wild type, showed changes in shape and orientation in all the mutant peptides. Mutant peptides also showed increased solvent accessible surface area and more number of hydrogen bonds with the surrounding water molecules. In functional studies, the Escherichia coli expressed, purified recombinant mutant proteins showed total loss of antimicrobial activity compared to the wild type protein. Conclusion: The study revealed that cationicity alone is not the determining factor in the microbicidal activity of antimicrobial peptides. Factors affecting the molecular dynamics such as hydrophobicity, electrostatic interactions and the potential for oligomerization may also play fundamental roles. It points to the usefulness of MD simulation studies in successful engineering of antimicrobial peptides for improved activity and other desirable functions.

8 July 2022 in Lab on a Chip
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Journal Article
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NKNityanand Kumawat
Nityanand Kumawat
SSSoja Soman
Soja Soman
Vijayavenkataraman SanjairajVijayavenkataraman Sanjairaj
Vijayavenkataraman Sanjairaj
SKSunil Kumar
Sunil Kumar
Cut and heat microfluidic paper-based analytical devices (CH-microPADs) are simple-to-use, low-cost point-of-care testing platforms.

14 October 2019 in Scientific Reports
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Journal Article
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AAAmanat Ali
Amanat Ali
BBBincy Baby
Bincy Baby
SSSoja Soman
Soja Soman
RVRanjit Vijayan
Ranjit Vijayan
Hemorphins are atypical endogenous opioid peptides produced by the cleavage of hemoglobin beta chain. Several studies have reported the therapeutic potential of hemorphin in memory enhancement, blood regulation, and analgesia. However, the mode of interaction of hemorphin with its target remains largely elusive. The decapeptide LVV-hemorphin-7 is the most stable form of hemorphin. It binds with high affinity to mu-opioid receptors (MOR), angiotensin-converting enzyme (ACE) and insulin-regulated aminopeptidase (IRAP). In this study, computational methods were used extensively to elucidate the most likely binding pose of mammalian LVV-hemorphin-7 with the aforementioned proteins and to calculate the binding affinity. Additionally, alignment of mammalian hemorphin sequences showed that the hemorphin sequence of the camel harbors a variation – a Q > R substitution at position 8. This study also investigated the binding affinity and the interaction mechanism of camel LVV-hemorphin-7 with these proteins. To gain a better understanding of the dynamics of the molecular interactions between the selected targets and hemorphin peptides, 100 ns molecular dynamics simulations of the best-ranked poses were performed. Simulations highlighted major interactions between the peptides and key residues in the binding site of the proteins. Interestingly, camel hemorphin had a higher binding affinity and showed more interactions with all three proteins when compared to the canonical mammalian LVV-hemorphin-7. Thus, camel LVV-hemorphin-7 could be explored as a potent therapeutic agent for memory loss, hypertension, and analgesia.

1 May 2024 in Biomicrofluidics
Verified
Journal Article
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SSSoja Soman
Soja Soman
SSShafeek Abdul Samad
Shafeek Abdul Samad
PVPriyamvada Venugopalan
Priyamvada Venugopalan
NKNityanand Kumawat
Nityanand Kumawat
SKSunil Kumar
Sunil Kumar
Foodborne pathogens, food adulterants, allergens, and toxic chemicals in food can cause major health hazards to humans and animals. Stringent quality control measures at all stages of food processing are required to ensure food safety. There is, therefore, a global need for affordable, reliable, and rapid tests that can be conducted at different process steps and processing sites, spanning the range from the sourcing of food to the end-product acquired by the consumer. Current laboratory-based food quality control tests are well established, but many are not suitable for rapid on-site investigations and are costly. Microfluidic paper analytical devices (μPADs) are a fast-growing field in medical diagnostics that can fill these gaps. In this review, we describe the latest developments in the applications of microfluidic paper analytic device (μPAD) technology in the food safety sector. State-of-the-art μPAD designs and fabrication methods, microfluidic assay principles, and various types of μPAD devices with food-specific applications are discussed. We have identified the prominent research and development trends and future directions for maximizing the value of microfluidic technology in the food sector and have highlighted key areas for improvement. We conclude that the μPAD technology is promising in food safety applications by using novel materials and improved methods to enhance the sensitivity and specificity of the assays, with low cost.