Biology subjects

De, R.

Publications and source records attributed to De, R..

11 recordsLinked to original sources

bioRxiv2026

Investigating the significance of iron levels in influencing megakaryocytic commitment in megakaryocyte-erythroid progenitors

AimThe present study investigated the significance of iron in regulating megakaryopoiesis, by a diet-based intervention in an in-vivo model. MethodsMale C57BL/6 mice, aged 4-5 weeks were fed on varying iron diets. Following sacrifice, blood samples collected in EDTA tubes were used to analyse haematological parameters, and iron content of liver and spleen was assessed by biochemical analyses. Megakaryocyte-erythroid progenitors (MEPs) were isolated from bone marrow by magnetic bead-based selection. RNA isolated from bone marrow cells and MEPs were used for gene expression analyses, and RNA Sequencing to identify differentially expressed genes (DEGs) and associated pathways. ResultsMice fed on an iron-deficient diet had reduced hepatic iron content after 5 weeks (p < 0.01), while both the hepatic and spleen iron content increased after 3 weeks in mice on an iron-rich diet (p < 0.05) and developed iron overloading. Hb and RBC counts increased (p < 0.05) in iron-rich mice and decreased in iron-deficient mice (p < 0.05), which also showed elevated platelet counts (p < 0.01). This may be explained by increased expression of Gata1, Tal1 (p < 0.01) Mds1 and Pdpk1 (p < 0.05) in bone marrow cells from iron-deficient mice. MEPs isolated from these mice showed elevated expression of genes associated with megakaryocytic differentiation, platelet functions, and genes encoding TGF-{beta}R1 and Smad 2,3 and 4. ConclusionsIron deficiency may activate TGF-{beta} signalling and downstream Smad-mediated transcriptional programs within MEPs. This may promote a shift in lineage commitment towards megakaryopoiesis through elevated expression of megakaryopoiesis related genes.

molecular biology↗

bioRxiv2024

Exploring the link between extended red blood cell parameters and platelet indices in voluntary blood donors

BackgroundAs regular blood donors are prone to iron deficiency, importance of extended red blood cell (eRBC) parameters in identifying donors with depleted iron stores was investigated. Thrombocytosis has been well documented in patients affected with IDA. Thus, significance of eRBC parameters in identifying iron deficiency associated thrombocytosis was also examined in this cohort. MethodsBlood samples were collected in EDTA tubes from consenting donors for analyses of routine haematological and eRBC parameters. Serum samples were isolated for estimation of iron parameters. ResultsIron deficient donors had significantly altered eRBC parameters. Among them, Ret-He with a cut-off of [≥]32 pg had high AUC (0.822) and showed relatively high sensitivity & specificity in detecting iron deficiency. Combination of Ret-He with CCI increased sensitivity & specificity to 90.6% and 98.2%, in detection of donors affected with iron restricted erythropoiesis. This cohort had increased platelet counts, which showed significant association with Ret-He ({beta}= -0.373), RBC-He ({beta}= -0.384), CCI ({beta}= 0.384), Hypo-He ({beta}=0.494) and Micro-R ({beta}= 0.299). Elevated platelet counts also showed significant correlations with these eRBC parameters, which was absent in iron replete donors. ConclusionseRBC parameters are sensitive indicators of non-anaemic iron deficiency, which may be enhanced by combining them. Their significant association with elevated platelet counts in iron deficient donors, highlights their importance in reflecting iron deficiency associated thrombocytosis. Impact StatementThe present study discusses utility of eRBC parameters in detecting non-anaemic iron deficiency, in regular voluntary blood donors. Previous reports have investigated the importance of these parameters in identifying IDA in blood donors. The present study is the first one which indicates combining different eRBC parameters such as Ret-He and CCI increases their accuracy of detection. They were also significantly associated with elevated platelet counts in iron deficient donors, which was absent in iron replete individuals. This link between eRBC parameters and higher platelet counts in healthy donors affected with non-anaemic iron deficiency has not been reported before.

bioinformatics↗

bioRxiv2024

Investigating the influence of iron parameters in regulating platelet recovery in Apheresis Platelet Donors

IntroductionThe present study investigates changes in haematological parameters in the donor during apheresis and following donation. Effect of iron parameters in influencing platelet recovery was studied. MethodsBlood samples were collected in EDTA tubes for analyses of haematological parameters. Serum samples were isolated for estimation of iron parameters. ResultsHb, RBC count and Hct increased during apheresis, but no significant changes were observed after 48 hrs post donation. Platelet recovery rates increased from 78 % after 48 hours to > 100% on day 10 (p < 0.001). Ferritin, serum iron & Transferrin saturation initially increased and subsequently declined from day 7 post donation, which may influence platelet recovery. Recovery rates were also higher in donors with lower iron stores. ConclusionsChanges in haematological parameters during plateletpheresis are transient and optimal time required for platelet recovery is dependent on pre-donation counts. Recovery of platelet counts may be positively regulated by donor iron parameters.

molecular biology↗

bioRxiv2024

Stably-Inverted Apical-Out Human Upper Airway Organoids for SARS-CoV-2 Infection and Therapeutic Testing

While breakthroughs with organoids have emerged as next-generation in vitro tools, standardization for drug discovery remains a challenge. This work introduces human airway organoids with reversed biopolarity (AORBs), cultured and analyzed in a high-throughput, single-organoid-per-well format, enabling milestones towards standardization. AORBs exhibit a spatio-temporally stable apical-out morphology, facilitating high-yield direct intact-organoid virus infection. Single-cell RNA sequencing and immunohistochemistry confirm the physiologically relevant recapitulation of differentiated human airway epithelia. The cellular tropism of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains along with host response differences between Delta, Washington, and Omicron variants, as observed in transcriptomic profiles, also suggest clinical relevance. Dose-response analysis of three well-studied SARS-CoV-2 antiviral compounds (remdesivir, bemnifosbuvir, and nirmatrelvir) demonstrates that AORBs efficiently predict human efficacy, comparable to gold-standard air-liquid interface cultures, but with higher throughput ([~]10-fold) and fewer cells ([~]100-fold). This combination of throughput and relevance allows AORBs to robustly detect false negative results in efficacy, preventing irretrievable loss of promising lead compounds. While this work leverages the SARS-CoV-2 study as a proof-of-concept application, the standardization capacity of AORB holds broader implications in line with regulatory efforts to push alternatives to animal studies.

bioengineering↗

bioRxiv2023

Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the prospective development of prognostic markers and probiotics to protect from diarrhea

A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted by employing 16s rRNA amplicon sequencing and subsequent analysis for taxonomic profiling of OTUs and abundance interpretation of reads. Significant differences in the structural composition of the two groups were observed. In both Firmicutes was the most abundant phylum in majority of the samples. B/F ratio was consistently <1 in all diarrheal samples. Significant difference in mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% diarrheal samples and where Streptococcaceae was suppressed, Bacteroideaceae and Nocardeaceae were the most abundant. In non-diarrheal samples where Streptococcaceae was almost completely suppressed Bifidobacteriaceae was the most abundant and suppressed other families significantly. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples while they were absent in diarrheal samples. The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. This is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, to our knowledge, and distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics for protecting the endemic population from diarrhea.

microbiology↗

bioRxiv2023

The gut microbiome of the healthy population in Kolkata, India, is a reservoir of antimicrobial resistance genes emphasizing the need of enforcing antimicrobial stewardship

Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes (ARGs) in the healthy gut microbiome. We found that it was a reservoir of ARGs against common antibiotics. A targeted PCR and sequencing-based ARGs detection against tetracyclines, macrolides, trimethoprim, sulfamethoxazole, aminoglycosides, amphenicol and mobile genetic element (MGE) markers was deployed in twenty-five fecal samples. Relative abundance and frequency of ARGs was calculated. We detected markers against all these classes of antibiotics. 100% samples carried aminoglycoside resistance marker and int1U. A comparison with our previously published diarrheal resistome from the same spatial and temporal frame revealed that a higher diversity of ARGs were detected in the community and a higher rate of isolation of tetC, msrA, tmp and sul-2 was found. The presence of common markers in the two cohorts proves that the gut microbiome has been contaminated with ARGs and which are being disseminated among different ecosystems. This is an issue of discerning concern for public health. The study raises an alarming picture of the AMR crisis in low-middle and emergent economies. It emphasizes the strict enforcement of AS in the community.

microbiology↗

bioRxiv2022

Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2

Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2 site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants. One sentence summaryBroadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.

immunology↗

bioRxiv2021

Growth kinetics and power laws indicate distinct mechanisms of cell-cell interactions in the aggregation process

Cellular aggregation is a complex process orchestrated by various kinds of interactions depending on its environments. Different interactions give rise to different pathways of cellular rearrangement and the development of specialized tissues. To distinguish the underlying mechanisms, in this theoretical work, we investigate the spontaneous emergence of tissue patterns from an ensemble of single cells on a substrate following three leading pathways of cell-cell interactions, namely, direct cell adhesion contacts, matrix mediated mechanical interaction, and chemical signalling. Our analysis shows that the growth kinetics of the aggregation process is distinctly different for each pathway and bears the signature of the specific cell-cell interactions. Interestingly, we find that the average domain size and the mass of the clusters exhibit a power law growth in time under certain interaction mechanisms hitherto unexplored. Further, as observed in experiments, the cluster size distribution can be characterized by stretched exponential functions showing distinct cellular organization processes.

biophysics↗

bioRxiv2021

Efficient Flocking: Metric Versus Topological Interactions

Flocking is a fascinating phenomenon observed across a wide range of living organisms. We investigate, based on a simple self-propelled particle model, how the emergence of ordered motion in a collectively moving group is influenced by the local rules of interactions among the individuals, namely, metric versus topological interactions as debated over in the current literature. In the case of the metric ruling, the individuals interact with the neighbours within a certain metric distance; in contrast, in the topological ruling, interaction is confined within a number of fixed nearest neighbours. Here, we explore how the range of interaction versus the number of fixed interacting neighbours affects the dynamics of flocking in an unbounded space, as observed in natural scenarios. Our study reveals the existence of a certain threshold value of the interaction radius in the case of metric ruling and a threshold number of interacting neighbours for the topological ruling to reach an ordered state. Interestingly, our analysis shows that topological interaction is more effective in bringing the order in the group, as observed in field studies. We further compare how the nature of the interactions affects the dynamics for various sizes and speeds of the flock.

biophysics↗

bioRxiv2021

Does cellular adaptation to force loading rate determine the biphasic vs monotonic response of actin retrograde flow with substrate rigidity?

The transmission of cytoskeletal forces to the extracellular matrix through focal adhesion complexes is essential for a multitude of biological processes such as cell migration, differentiation, tissue development, cancer progression, among others. During migration, focal adhesions arrest the actin retrograde flow towards the cell interior, allowing the cell front to move forward. Here, we address a puzzling observation of the existence of two distinct phenomena: a biphasic relationship of the retrograde flow and cell traction force with increasing substrate rigidity, with maximum traction force and minimum retrograde flow velocity being present at an optimal substrate stiffness; in contrast, a monotonic relationship between them where the retrograde flow decreases and traction force increases with substrate stiffness. We propose a theoretical model for cell-matrix adhesions at the leading edge of a migrating cell, incorporating a novel approach in force loading rate sensitive binding and reinforcement of focal adhesions assembly and the subsequent force-induced slowing down of actin flow. Our model unravels both biphasic and monotonic responses of the retrograde flow and cell traction force with increasing substrate rigidity, owing to the cells ability to sense and adapt to the fast-growing forces. Moreover, we also elucidate how the viscoelastic properties of the substrate regulate these nonlinear responses and alter cellular behaviours.

biophysics↗

bioRxiv2019

Stick-Slip Dynamics of Migrating Cells on Viscoelastic Substrates

Stick-slip motion, a common phenomenon observed during crawling of cells, is found to be strongly sensitive to the substrate stiffness. Stick-slip behaviours have previously been investigated typically using purely elastic substrates. For a more realistic understanding of this phenomenon, we propose a theoretical model to study the dynamics on a viscoelastic substrate. Our model based on a reaction-diffusion framework, incorporates known important interactions such as retrograde flow of actin, myosin contractility, force dependent assembly and disassembly of focal adhesions coupled with cell-substrate interaction. We show that consideration of a viscoelastic substrate not only captures the usually observed stick-slip jumps, but also predicts the existence of an optimal substrate viscosity corresponding to maximum traction force and minimum retrograde flow which was hitherto unexplored. Moreover, our theory predicts the time evolution of individual bond force that characterizes the stick-slip patterns on soft versus stiff substrates. Our analysis also elucidates how the duration of the stick-slip cycles are affected by various cellular parameters.

biophysics↗