Biology subjects

Kiran, A.

Publications and source records attributed to Kiran, A..

8 recordsLinked to original sources

bioRxiv2026

Phytochemical profiling and antioxidant potential of freshwater algal extracts from Lahore, Pakistan, with preliminary evaluation of cytotoxic activity

Freshwater algae represent an underexplored source of naturally occurring bioactive metabolites with potential applications in pharmaceutical and biomedical research. This study investigated the phytochemical composition, antioxidant capacity, and preliminary cytotoxic potential of ethanolic and n-hexane extracts of freshwater algal species collected at Jilani Park, Lahore, Pakistan. Algal species were identified morphologically by Dr. Ghazal Yasmeen (Institute of Botany, Punjab University, Lahore). Extracts were analyzed using gas chromatography-mass spectrometry (GC-MS) and qualitative phytochemical screening. Antioxidant activity was evaluated using DPPH radical scavenging, hydrogen peroxide scavenging, and reducing power assays. Cytotoxic potential was assessed using MTT and cell adhesion assays on HeLa and SF767 cell lines as preliminary indicators of bioactivity. GC-MS analysis identified 25 compounds, including sterols, fatty acid esters, terpenoids, phenolic compounds, and volatile metabolites. Phytochemical screening confirmed the presence of flavonoids, phenolics, tannins, and terpenoids in the extracts. Among the tested extracts, the n-hexane fraction demonstrated comparatively higher antioxidant activity across multiple assays. Ethanolic extracts showed moderate reductions in HeLa cell viability, whereas limited effects were observed in SF767 cells. These findings suggest that freshwater algae are promising natural reservoirs of antioxidant metabolites with potential relevance for future isolation and characterization of bioactive compounds for biomedical applications. Further purification and mechanistic studies are required to identify specific active constituents.

biochemistry↗

bioRxiv2025

Macrophage chemotaxis steered by complex self-generated gradients of complement C5a

Macrophages rely on efficient chemotaxis to locate sites of infection and tissue damage. One general strategy that enhances chemotactic accuracy is the use of self-generated gradients, where cells locally deplete attractants to create or sharpen guidance cues. Here we show that mouse bone marrow-derived macrophages (BMDMs) migrate toward the complement component C5a using this strategy. Cells actively deplete C5a from their surroundings, establishing local gradients as fresh attractant diffuses inward. We visualized this process in real time with fluorescent C5a and reproduced its dynamics using computational models. C5a depletion is mediated primarily by C5aR1-dependent endocytosis. This mechanism produces complex responses, with different C5a concentrations inducing temporally distinct waves of migration, and maximal chemotaxis occurring below 10 nM C5a. As expected, increasing C5a concentrations recruit more cells. In contrast, human macrophages inactivate C5a mainly through carboxypeptidase-mediated enzymatic degradation, yielding a higher optimal concentration ([~]30 nM) and distinct migratory dynamics. Both species also deplete externally imposed C5a gradients, sharpening them and enhancing guidance. These findings identify C5a degradation as a critical mechanism by which macrophages extract directional information from their environment. Self-generated gradient formation, despite different mechanisms across species, emerges as a conserved and versatile strategy for immune navigation.

immunology↗

bioRxiv2023

Pan-genome study underling the extent of genomic variation of invasive Streptococcus pneumoniae in Malawi

AbstractStreptococcus pneumoniae is a common cause of acute bacterial infections in Malawi. Understanding the molecular mechanisms underlying its invasive behavior is crucial for designing new therapeutic strategies. We conducted a pan-genome analysis to identify potential virulence genes in S. pneumoniae by comparing the gene pool of isolates from carriers nasopharyngeal secretions to isolates from the blood and cerebrospinal fluid of patients. Our analysis involved 1,477 pneumococcal isolates from Malawi, comprising 825 samples from carriers (nasopharyngeal swab) and 652 from patients (368 from blood and 284 from cerebrospinal fluid). We identified 56 serotypes in the cohort. While most serotypes exhibited a similar prevalence in both carriage and disease groups, serotypes 1 and 5, the most abundant serotypes in the entire cohort, were significantly more commonly detected in specimens from patients compared to the carriage group. This difference is presumably due to their shorter nasopharyngeal colonization period. Furthermore, these serotypes displayed genetic distinctiveness from other serotypes. A magnificent genetic difference was observed in the absence of genes from the RD8a genomic island in serotypes 1 and 5 compared to significantly prevalent serotypes in the nasopharynx. RD8a genes play pivotal roles in binding to epithelial cells and performing aerobic respiration to synthesize ATP through oxidative phosphorylation. The absence of RD8a from serotypes 1 and 5 may be associated with a shorter duration in the nasopharynx, theoretically due to a reduced capacity to bind to epithelial cells and access free oxygen molecules required for aerobic respiration (essential to maintain the carriage state). Serotypes 1 and 5, significantly harbor operons that encode phosphoenolpyruvate phosphotransferase systems, which might relate to transporting carbohydrates, relying on phosphoenolpyruvate as the energy source instead of ATP. In conclusion, serotypes 1 and 5 as the most prevalent invasive pneumococcal strains in Malawi, displayed considerable genetic divergence from other strains, which may offer insights into their invasiveness and potential avenues for further research. Author summaryDespite introducing the pneumococcal conjugate vaccine in 2011, Streptococcus pneumoniae remains a major cause of bacterial infection in Malawi. Whilst some pneumococcal strains harmlessly colonize the nasopharynx, others find their way into normally sterile sites, such as lungs, blood, and nervous system, resulting in serious illness. Our study identified specific pneumococcal serotypes as the most invasive in Malawi, characterized by a short colonization period and significant genetic distinctiveness from other strains. This genetic divergence notably included the absence of several genes associated with aerobic respiration and the presence of genes facilitating ATP-independent carbohydrate transport. The presence or absence of these genes may underlie their heightened invasiveness and shorter colonization period. This hypothesis positions these genes as potential candidates for future therapeutic research. We propose that the specific gene gain and/or loss in invasive versus other serotypes may be linked to the development of invasive pneumococcal diseases. Impact StatementOur research applied pan-genomics principles to comprehensively assess diversity within the pneumococcus genome, with the primary objective of identifying pneumococcal virulence genes for advancing vaccine design and drug development. Within this study, we identified Serotypes 1 and 5 as the predominant and highly invasive pneumococcal strains in Malawi, characterized by a short nasopharyngeal colonization period, suggesting their potential for rapid infection of sterile sites within the human body such as blood and the central nervous system. These serotypes exhibited significant genetic divergence from other serotypes in Malawi, notably lacking key genes within the RD8a operon while harboring transporters functioning independently of ATP. Its important to note that these findings are based on computational analysis, and further validation through laboratory experiments is essential to confirm their biological significance and potential clinical applications. The implications of our research offer potential avenues for more effective pneumococcal disease prevention and treatment, not only in Malawi but also in regions facing similar challenges.

microbiology↗

bioRxiv2021

KnowMore: An Automated Knowledge Discovery Tool for the FAIR SPARC Datasets

This manuscript provides the methods and outcomes of KnowMore, the Grand Prize winning automated knowledge discovery tool developed by our team during the 2021 NIH SPARC FAIR Data Codeathon. The National Institutes of Health Stimulating Peripheral Activity to Relieve Conditions (NIH SPARC) program generates rich datasets from neuromodulation researches, curated according to the Findable, Accessible, Interoperable, and Reusable (FAIR) SPARC data standards. These datasets are publicly available through the SPARC Data Portal at sparc.science. Currently, the process of simultaneously comparing and analyzing multiple SPARC datasets is tedious because it requires investigating each dataset of interest individually and downloading all of them to conduct cross-analyses. It is crucial to enhance this process to enable rapid discoveries across SPARC datasets. To fill this need, we created KnowMore, a tool integrated into the SPARC Portal that only requires the user to select their datasets of interest to launch an automated discovery process. KnowMore uses several SPARC resources (Pennsieve, o2S2PARC, SciCrunch, protocols.io, Biolucida), data science methods, and machine learning algorithms in the back end to generate various visualizations in the front end intended to help the user identify potential similarities, differences, and relations across the datasets. These visualizations can lead to a new discovery, new hypothesis, or simply guide the user to the next logical step in their discovery process. The outcome of this project is a SPARC portal-ready code architecture that helps researchers to use SPARC datasets more efficiently and fully leverages their FAIR characteristics. The tool has been built and documented such that more data analysis methods and visualization items could be easily added. The potential for automated discoveries from SPARC datasets is huge given the unique SPARC data ecosystem promoting FAIR data practices, and KnowMore has only demonstrated a small highlight of what could be achieved to speed up discoveries from SPARC datasets.

bioinformatics↗

bioRxiv2021

Mechanism of tissue expansion in the early stage of the migration

The collective cell migration is observed in many biological processes such as wound healing, embryogenesis, and cancer metastasis. Despite extensive theoretical and experimental studies on collective cell motion, there is no unified mechanism to explain it. In this work, we experimentally report the collectively growing cell colonies in the sub-marginal region of a freely expanding cell monolayer. These colonies could be responsible for the highly aligned collective cell migration observed in front cell rows. Our results provide a basic framework to understand the physical mechanism responsible for collective cell migration in the freely expanding monolayer.

biophysics↗

bioRxiv2020

SARS-CoV2 genome analysis of Indian isolates and molecular modelling of D614G mutated spike protein with TMPRSS2 depicted its enhanced interaction and virus infectivity

COVID-19 that emerged as a global pandemic is caused by SARS-CoV-2 virus. The virus genome analysis during disease spread reveals about its evolution and transmission. We did whole genome sequencing of 225 clinical strains from the state of Odisha in eastern India using ARTIC protocol-based amplicon sequencing. Phylogenetic analysis identified the presence of all five reported clades 19A, 19B, 20A, 20B and 20C in the population. The analyses revealed two major routes for the introduction of the disease in India i.e. Europe and South-east Asia followed by local transmission. Interestingly, 19B clade was found to be much more prevalent in our sequenced genomes (17%) as compared to other genomes reported so far from India. The haplogroup analysis for clades showed evolution of 19A and 19B in parallel whereas the 20B and 20C appeared to evolve from 20A. Majority of the 19A and 19B clades were present in cases that migrated from Gujarat state in India suggesting it to be one of the major initial points of disease transmission in India during month of March and April. We found that with the time 20A and 20B clades evolved drastically that originated from central Europe. At the same time, it has been observed that 20A and 20B clades depicted selection of four common mutations i.e. 241 C>T (5UTR), P323L in RdRP, F942F in NSP3 and D614G in the spike protein. We found an increase in the concordance of G614 mutation evolution with the viral load in clinical samples as evident from decreased Ct value of spike and Orf1ab gene in qPCR. Molecular modelling and docking analysis identified that D614G mutation enhanced interaction of spike with TMPRSS2 protease, which could impact the shedding of S1 domain and infectivity of the virus in host cells.

genomics↗

bioRxiv2020

Understanding the diversity of DNA methylation in Mycobacterium tuberculosis

Although Mycobacterium tuberculosis (Mtb) strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity in Mtb are not well understood but epigenetic variation is thought to contribute. At present the methylome of Mtb has not been completely characterized. We completed methylomes of 18 Mycobacterium tuberculosis (Mtb) clinical isolates from Malawi representing the largest number of Mtb genomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date. We replicate and confirm four methylation disrupting mutations in lineages of Mtb. For the first time we report complete loss of methylation courtesy of C758T (S253L) mutation in the MamB gene of Indo-oceanic lineage of Mtb. We also conducted a genomic and methylome comparison of the Malawian samples against a global sample. We confirm that methylation in Mtb is lineage specific although some unresolved issues still remain.

genomics↗

bioRxiv2018

CAN NEUROPATHIC PAIN PREDICT RESPONSE TO ARTHROPLASTY IN KNEE OSTEOARTHRITIS? A PROSPECTIVE OBSERVATIONAL COHORT STUDY.

A significant proportion of patients with knee osteoarthritis (OA) continue to have severe ongoing pain following knee replacement surgery. Central sensitization and features suggestive of neuropathic pain before surgery may result in a poor outcome post-operatively. In this prospective observational study of patients undergoing primary knee arthroplasty (n=120), the modified PainDETECT score was used to divide patients, with primary knee OA, into nociceptive (<13), unclear (13-18) and neuropathic -like pain (>18) groups pre-operatively. Response to surgery was compared between groups using the Oxford Knee Score (OKS) and the presence of moderate to severe long-term pain 12 months after arthroplasty. The analyses were replicated in a larger independent cohort study (n=404). 120 patients were recruited to the main study cohort: 63 (52%) nociceptive pain; 32 (27%) unclear pain; 25 (21%) neuropathic-like pain. Patients with neuropathic-like pain had significantly worse OKS pre and post-operatively, compared to the nociceptive pain group, independent of age, sex and BMI. At 12-months post-operatively the mean OKS was 4 points lower in the neuropathic-like group compared with the nociceptive group in the study cohort (non-significant); with a difference of 5 points in the replication cohort (p<0.001). Moderate to severe long-term pain after arthroplasty at 12-months was present in 50% of the neuropathic-like pain group versus 24% in the nociceptive pain group, in the replication cohort (p<0.001). Neuropathic pain is common and targeted therapy pre, peri and post-operatively may improve treatment response.

epidemiology↗