Biology subjects

Siddiqui, Z.

Publications and source records attributed to Siddiqui, Z..

3 recordsLinked to original sources

bioRxiv2024

Cell identity revealed by precise cell cycle state mapping links data modalities

Several methods for cell cycle inference from sequencing data exist and are widely adopted. In contrast, methods for classification of cell cycle state from imaging data are scarce. We have for the first time integrated sequencing and imaging derived cell cycle pseudo-times for assigning 449 imaged cells to 693 sequenced cells at an average resolution of 3.4 and 2.4 cells for sequencing and imaging data respectively. Data integration revealed thousands of pathways and organelle features that are correlated with each other, including several previously known interactions and novel associations. The ability to assign the transcriptome state of a profiled cell to its closest living relative, which is still actively growing and expanding opens the door for genotype-phenotype mapping at single cell resolution forward in time.

bioinformatics↗

bioRxiv2021

Oxo-M and 4-PPBP Delivery via Multi-Domain Peptide Hydrogel Toward Tendon Regeneration

We have recently identified novel small molecules, Oxo-M and 4-PPBP, which specifically stimulates endogenous tendon stem/progenitor cells (TSCs) leading to potential regenerative healing of fully-transected tendons. Here we investigated an injectable, multi-domain peptide (MDP) hydrogel providing a controlled delivery of the small molecules for regenerative tendon healing. We investigated the release kinetics of Oxo-M and 4-PPBP from MDP hydrogels and the effect of MDP-released small molecules on tenogenic differentiation of TSCs and in vivo tendon healing. In vitro, MDP showed a sustained release of Oxo-M and 4-PPBP and a slower degradation compared to fibrin. In addition, tenogenic gene expression was significantly increased in TSC with MDP-released Oxo-M and 4-PPBP as compared to the fibrin-released. In vivo, MDP releasing Oxo-M and 4-PPBP significantly improved tendon healing, likely associated with prolonged effects of Oxo-M and 4-PPBP on suppression of M1 macrophages and promotion of M2 macrophages. Comprehensive analyses including histomorphology, digital image processing, and modulus mapping with nanoindentation consistently suggested that Oxo-M and 4-PPBP delivered via MDP further improved tendon healing as compared to fibrin-based delivery. In conclusion, MDP delivered with Oxo-M and 4-PPBP may serve as an efficient regenerative therapeutic for in situ tendon regeneration and healing.

bioengineering↗

bioRxiv2019

Multiplexed direct detection of barcoded protein reporters on a nanopore array

Genetically encoded reporter proteins are a cornerstone of molecular biology. While they are widely used to measure many biological activities, the current number of uniquely addressable reporters that can be used together for one-pot multiplexed tracking is small due to overlapping detection channels such as fluorescence. To address this, we built an expanded library of orthogonally-barcoded Nanopore-addressable protein Tags Engineered as Reporters (NanoporeTERs), which can be read and demuxed by nanopore sensors at the single-molecule level. By adapting a commercially available nanopore sensor array platform typically used for real-time DNA and RNA sequencing (Oxford Nanopore Technologies MinION), we show direct detection of NanoporeTER expression levels from unprocessed bacterial culture with no specialized sample preparation. These results lay the foundations for a new class of reporter proteins to enable multiplexed, real-time tracking of gene expression with nascent nanopore sensor technology.

synthetic biology↗