Biology subjects

Sahni, G.

Publications and source records attributed to Sahni, G..

4 recordsLinked to original sources

bioRxiv2025

Scaffolded hiPSC liver organoids recapitulating bile duct tubulogenesis and periportal architecture.

Recapitulating the liver periportal area in vitro remains a major challenge due to its complex cellular composition and the coordinated development of both ductal and endothelial networks. Most existing bile duct organoid models fail to reproduce tubular extension and multicellular organization. We present a 3D ECM micro-rods system biofunctionalized with grafted growth factors mimicking fetal liver paracrine signaling to initiate and to coordinate the development of bile ducts, parenchymal cells, and vascular structures. Our system recapitulates key developmental stages, from the formation of the ductal plate to the emergence of elongated tubular ducts. The ECM rod alone provides the biophysical cues initiating the elongation of the bile ducts and the spatial structuration of the cellular organization, while the biofunctionalization with growth factors enhance the organization and maturation of the biliary and vascular systems. We further demonstrate that this approach is scalable and amenable to quantitative analysis through label-free Optical Coherence Tomography combined with AI-driven 3D segmentation.

cell biology↗

bioRxiv2025

Extracellular matrix deposition controls early differentiation patterns in human cardiac gastruloids

Amongst the various factors that affect differentiation and tissue organization, the autonomous deposition of extracellular matrix (ECM) has hardly been considered in the context of gastruloids. Using biofunctionalized colloidal particles as artificial organizing centers (aOCs), we patterned differentiation loci within 3D embryonic bodies. Our findings reveal that the spatial distribution of the aOCs induces various pattern organizations, mediated by endogenous deposition of ECM. We investigated how the interplay between meso-endoderm cell epithelial-to-mesenchymal transition, migration into germ layers, and the prolonged maintenance of local stem-cell niches orchestrates gastruloid structure and composition. These factors collectively regulate the complexity of emergent cardiac structures observed at later time points. This work uncovers a critical feedback loop between cell differentiation rates and endogenous ECM deposition patterns, which governs the differentiation paths in scaffolded cardiac gastruloids.

cell biology↗

bioRxiv2021

High content 3D imaging method for quantitative characterization of organoid development and phenotype.

Quantitative analysis on a large number of organoids can provide meaningful information from the morphological variability observed in 3D organotypic cultures, called organoids. Yet, gathering statistics of growing organoids is currently limited by existing imaging methods and subsequent image analysis workflows that are either restricted to 2D, limited in resolution, or with a low throughput. Here, we present an automated high content imaging platform synergizing high density organoid cultures with 3D live light-sheet imaging. The platform is an add-on to a standard inverted microscope. We demonstrate our capacity to collect libraries of 3D images at a rate of 300 organoids per hour, enabling training of artificial intelligence-based algorithms to quantify the organoid morphogenetic organization at multiple scales with subcellular resolution. We validate our approach on different organotypic cell cultures (stem, primary, and cancer), and quantify the development of hundreds of neuroectoderm organoids (from human Embryonic Stem Cells) at cellular, multicellular and whole organoid scales.

biophysics↗

bioRxiv2020

Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach

In the present study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community and antibiotic resistance genes. Utilizing data from Illumina platform, 4174 ([~]0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3602 reads, [~]86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium (128), Propionibacterium (71), Erwinia (70), Ralstonia (56) phages shows the highest abundance and account for approximately 90% of the total identified phages. Additionally, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria ([~]69.3%) dominates the microbial population structure. Primarily orders such as Caulobacterales ([~]28%), Burkholderiales ([~]13.9%), Actinomycetales ([~]13.7%), Pseudomonadales ([~]7.5%) signify the core section. Further, 21869 ([~]0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes) among which 4 ARG types namely multidrug resistance (MDR) (12041 reads, [~]55%), bacitracin (3202 reads, [~]15%), macrolide-lincosamide-streptogramin (MLS) (1744 reads, [~]7.98%), and fosmidomycin (990 reads, [~]4.53%) has the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15919 reads). The results unveil the distribution of (pro)-phages; microbial community and various ARGs in the Ganges river sediments. Further research on these identified phage(s) could be used in phage-based therapeutics against pathogenic bacteria.

genomics↗