Department of Biological Sciences
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Item Genomic dynamics of clinical Plasmodium vivax: comparative genomic hybridization in severe malaria cases(Frontiers Media, 2025-11) Das, AshisCopy number variations (CNVs) in the Plasmodium vivax genome can influence key parasite traits such as erythrocyte invasion, immune evasion, drug resistance, and survival in the human host. Their potential role in severe manifestations of P. vivax malaria, such as cerebral malaria (CM) remains underexplored. In regions like India, where P. vivax is endemic, understanding genomic factors that contribute to disease severity is crucial. Given the limited understanding of genomic factors contributing to disease severity in P. vivax, this study aims to investigate genome-wide CNVs in clinical isolates from patients with cerebral and uncomplicated malaria.Item Integrative transcriptomic and machine learning approaches to decipher mitochondrial gene regulation in severe Plasmodium vivax malaria(Springer, 2025-12) Das, AshisMitochondria in Plasmodium vivax are functionally vital despite possessing a highly reduced genome and differing substantially from the human organelle. Beyond their classical role in energy production, they dynamically coordinate processes like pyrimidine biosynthesis and heme metabolism, adapting their functions across the intra-erythrocytic development cycle (IDC). Their unique architecture and stage-specific roles enable the parasite to fine-tune mitochondrial gene expression, involving both protein-coding sense transcripts and long non-coding natural antisense transcripts (NATs). This study unveils an unprecedented regulatory complexity by integrating transcriptomic profiling with advanced machine learning to decode the role of mitochondrial sense and natural antisense transcripts (NATs) in severe P. vivax malaria. We reveal distinct, clinically relevant expression signatures, where NATs emerge not as transcriptional by-products but as potent regulators tightly linked to mitochondrial pathways and translational machinery. This dual-layered transcriptomic landscape reflects an intricate molecular strategy by which the parasite fine-tunes mitochondrial function to survive under severe disease conditions. Importantly, while these findings illuminate novel regulatory mechanisms and position mitochondrial NATs as promising targets for antimalarial drug development, they represent preliminary insights derived from a limited clinical cohort and should not be interpreted as definitive clinical indicators. Validation in larger and diverse patient populations is essential to confirm their broader biological and clinical relevance. However, these results serve as indicators for potential innovative therapeutic interventions aimed at disrupting parasite bioenergetics and regulatory networks.Item Plasmodium falciparum: genetic diversity of C-terminal region of MSP-1 in isolates from Indian sub-continent(Elsiever, 2005-08) Saxena, Vishal; Das, AshisMalaria parasites exhibit sequence diversity for a number of stage specific antigens. Several studies have proved that merozoite surface protein-1 (MSP-1) is an effective target eliciting a protective immune response. The MSP-142 region comprising two EGF-like domains is involved in generating protective immune response in humans and other experimental animals. Searching for point mutations in this region is essential in view of vaccine development. We have investigated the sequence variations in Plasmodium falciparum MSP-1 carboxy terminal region in field isolates from different regions in India. Our study reveals the presence of eight variant types of MSP-119 in the Indian sub-continent, which comprise of E-TSR-L, Q-TSR-L, E-TSG-L, Q-KNG-L, Q-KNG-F, E-KNG-L, E-KNG-F, and E-KYG-F. The last named allele is a novel variant being reported for the first time.Item Dataset of natural antisense transcripts in P. vivax clinical isolates derived using custom designed strand-specific microarray(Elsiever, 2014-12) Garg, Shilpi; Saxena, Vishal; Das, AshisNatural antisense transcripts (NATs) have been detected in many organisms and shown to regulate gene expression. Similarly, NATs have also been observed in malaria parasites with most studies focused on Plasmodium falciparum. There were no reports on the presence of NATs in Plasmodium vivax, which has also been shown to cause severe malaria like P. falciparum, until a recent study published by us. To identify in vivo prevalence of antisense transcripts in P. vivax clinical isolates, we performed whole genome expression profiling using a custom designed strand-specific microarray that contains probes for both sense and antisense strands. Here we describe the experimental methods and analysis of the microarray data available in Gene Expression Omnibus (GEO) under GSE45165. Our data provides a resource for exploring the presence of antisense transcripts in P. vivax isolated from patients showing varying clinical symptoms. Related information about the description and interpretation of the data can be found in a recent publication by Boopathi and colleagues in Infection, Genetics and Evolution 2013.Item A prospective study on adult patients of severe malaria caused by Plasmodium falciparum, Plasmodium vivax and mixed infection from Bikaner, northwest India(JVBD, 2014-10) Garg, Shilpi; Das, AshisDescription of severe vivax malaria and mixed species infection requires good clinical study. The present study was undertaken to evalute the characteristics of severe malaria patients in Bikaner, northwest India.Item Analysis of elongation factor Tu (tuf A) of apicoplast from Indian Plasmodium vivax isolates(Elsiever, 2007-09) Garg, Shilpi; Saxena, Vishal; Das, AshisThe Apicomplexan parasite Plasmodium vivax is responsible for causing greater than 50% of human malaria cases in Central and South America, Southeastern Asia and the Indian subcontinent. The rising severity of the disease and the resistance shown by the parasite towards usual therapeutic regimen has put forth a demand for a novel drug target to combat this disease. Apicoplast, an organelle of prokaryotic origin, and its circular genome are being looked upon as a potential drug target. The Apicoplast genome is known to carry various genes of functional importance, including the gene encoding for the protein Elongation factor Tu (tuf A) that participates in the translational process in prokaryotes. The tuf A gene is translationally active within the organelle and is believed to be one of the best functionally conserved protein throughout the species. Till date there are no reports of this gene from another major human malaria parasite P. vivax. This is the first report detailing any complete gene analysis from the Apicoplast genome of the Indian P. vivax isolates. The study predicts and evaluates the complete Apicoplast Elongation factor tuf A gene and EF–Tu protein at primary, secondary and tertiary structure level. In addition, a comparative phylogenetic analysis using this gene is done to understand the evolutionary status of Indian P. vivax isolates. Our study shows that although the Indian P. vivax EF–Tu is not showing any major difference at the structural and predicted functional level, it is diverging way ahead from the P. vivax clade.Item Novel point mutations in sulfadoxine resistance genes of Plasmodium falciparum from India(Elsiever, 2009-04) Garg, Shilpi; Saxena, Vishal; Das, AshisPoint mutations in the dhfr and dhps genes of Plasmodium falciparum are associated with pyrimethamine and sulfadoxine resistance respectively. In this study we have analyzed these genes from Bikaner (situated in North-West region of India), where both uncomplicated and severe manifestations of P. falciparum malaria are seen. A majority of isolates showed double mutant allele for DHFR. In contrast, the only reported mutation present in DHPS was A437G in few isolates. In addition, three novel non-synonymous mutations were observed in the PfDHPS from this region viz., S587F, N666K and C668W. The mutations at the 666 and 668 codon seem to form a bend in the big loop region of the DHPS enzyme and may affect the binding of the drug to the enzyme. Molecular docking of sulfadoxine to this mutated structure indicates reduction in its binding affinity to this enzymeItem Thrombocytopenia in Plasmodium falciparum, Plasmodium vivax and mixed infection malaria: A study from Bikaner (Northwestern India)(Taylor & Francis, 2010) Garg, Shilpi; Saxena, Vishal; Das, AshisThe occurrence, relation and magnitude of thrombocytopenia in different species of malaria are not clearly defined. This study included 1,064 patients admitted with malaria to study thrombocytopenia (platelet count <150,000 /cumm) in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) mono infection and mixed infection (Pf + Pv). The species diagnosis was done by peripheral blood film (PBF) and rapid diagnostic test (RDT). Validation by polymerase chain reaction (PCR) was done only in patients with severe thrombocytopenia (platelet count <20,000 /cumm). The breakup of patients was 525 (49.34%) Pf, 460 (43.23%) Pv and 79 (7.42%) mixed malaria (Pf + Pv). Thrombocytopenia was observed in 24.6% (262/1064) patients. The risk was greatest in the mixed infections in comparison to monoinfection individually (43.04% [34/79]; mixed vs Pv monoinfection: Odds Ratio [OR] = 1.675 [95% Confidence Interval (CI) 1.029–2.726], p < 0.0366; mixed vs Pf monoinfection: OR=3.911 [95% CI 2.367–6.463], p < 0.0001). Pv monoinfection (31.09% [143/460]) had greater risk compared to Pf monoinfection (16.19% [85/525]; OR = 2.335 [95% CI 1.722–3.167], p < 0.0001). The occurrence of severe thrombocytopenia was also higher in Pv monoinfection (18.18% [26/143]) in comparison to either Pf monoinfection (10.59% [9/85], OR = 1.877 (95% CI 0.834–4.223)) or mixed infection (11.76% [4/34]; OR = 1.667 (95% CI 0.540–5.142) but this association was statistically not significant. Six patients (3 Pv, 2 Pf and 1 mixed) developed severe epistaxis requiring platelet transfusion. There was no relation between parasite density and platelet count as many patients with severe thrombocytopenia had parasite density similar to patients without thrombocytopenia. We found that the association of thrombocytopenia was statistically more significant with P. vivax monoinfection as compared to P. falciparum.Item Clinical Features of Children Hospitalized with Malaria—A Study from Bikaner, Northwest India(ASTMH, 2010) Garg, Shilpi; Saxena, Vishal; Das, AshisSevere Plasmodium vivax malaria in adults has been reported from Bikaner (northwestern India) but the reports on children are scanty. This prospective study was done on 303 admitted children of malaria. The diagnosis was done by peripheral blood smear and rapid diagnostic test. Further confirmation of severe P. vivax monoinfection was done by polymerase chain reaction (PCR). The proportion of P. falciparum, P. vivax, and mixed (P. falciparum and P. vivax) infection was 61.01%, 33.99%, and 4.95%, respectively. Severe disease was present in 49.5% (150/303) children with malaria, with the risk greatest among P. vivax monoinfection (63.1% [65/103]) compared with P. falciparum, either alone (42.7% [79/185]; odds ratio [OR] = 2.3 [95% confidence interval (CI) = 1.40–3.76], P = 0.001) or mixed infections (40% [6/15]; OR = 2.57 [95% CI = 0.88–7.48]). In children < 5 years of age, the proportion of severe malaria attributable to P. vivax rose to 67.4% (31/46) compared with 30.4% (14/46) of P. falciparum (OR = 4.7 [95% CI = 2.6–8.6], P < 0.0001) and 2.2% (1/46) of mixed infection (OR = 92 [95% CI = 24.6–339.9], P < 0.0001). The proportion of patients having severe manifestations, which included severe anemia, thrombocytopenia, cerebral malaria, acute respiratory distress syndrome, hepatic dysfunction, renal dysfunction, abnormal bleeding was significantly high in association with P. vivax monoinfection in 0–5 year age group, while the same was significantly high in association with P. falciparum monoinfection in 5–10 year age group. Similarly P. vivax monoinfection had greatest propensity to cause multiorgan dysfunction in 0–5 year age group (34.1% [17/41], P < 0.0001) in comparison to P. falciparum monoinfection, which had similar propensity in 5–10 year age group (36.8% [35/95], P = 0.039). Plasmodium vivax monoinfection was almost equally serious to cause significant mortality in comparison to P. falciparum (case fatality rate of severe P. vivax was 3.9% versus 3.2% of severe P. falciparum malaria; P = 1.0). This study reaffirms the evidence of severe P. vivax malaria in children in Bikaner.Item Clinical profiles of 13 children with Plasmodium vivax cerebral malaria(Taylor & Francis, 2011) Garg, Shilpi; Das, AshisBikaner region is endemic for both P. vivax and P. falciparum malaria. Usually, cerebral malaria is caused by P. falciparum but it has been reported recently also in P. vivax mono-infection. Epidemiologic studies and clinical descriptions of P. vivax cerebral malaria in children are rare.