Biology subjects

Woodruff, M.

Publications and source records attributed to Woodruff, M..

3 recordsLinked to original sources

bioRxiv2025

Development of a displacement-controlled uniaxial-strain bioreactor for high-throughput, dynamic in vitro cell culture

1Bone is a dynamic tissue that experiences a wide range of forces during regular daily locomotion. This environment of dynamic strain strongly influences the architecture of the extracellular matrix, and it can impact the rate that bone adapts or recovers after an injury [1], [2]. Cell research is commonly performed in mechanically static conditions in the base of well plates, yet this is a far cry from the conditions natural to osteoblasts. To better understand the behaviours of osteoblasts, it is important to ensure that platforms are available to perform cell culture experiments in mechanically dynamic environments [3]-[5]. For this reason, we have designed a bioreactor system that imparts tensile strain onto flat, cell-seeded scaffold constructs in vivo within custom well plates. The bioreactor system has 36 separated wells spread across four mechanical actuation units and can apply up to 30% tensile strain to a 15 by 9 mm area of the constructs, operating within an incubator. The wider body of mechanostimulation research also shows that different many cell types, from neurons [6] to cardiac tissue [7], [8] and more [2], [6], [9]-[11], can be stimulated with a range of stimulus and have a wide array of responses, and it is expected that the bioreactor will also be useful for this research. To be accessible to research groups, the bioreactor has predominantly been constructed from widely available components and materials. Most parts fabricated using 3D printing, and all of the electronics can be found within a typical 3D printer DIY assembly kit. The device was validated for use in a 28 day in-vitro dynamic culture of osteoblasts on melt-electrowritten polycaprolactone scaffolds. The cell constructs were strained to 4% at 0.5 Hz on days 25-27 and removed on the 28th day. Cells were observed to elongate and align within some regions of high local strain following the 3 days of stimulation.

bioengineering↗

bioRxiv2023

Advancing scaffold biomimicry: engineering mechanics in microfiber scaffolds with independently controlled architecture using melt electrowriting

Melt electrowriting (MEW) is an additive manufacturing technique characterized by its ability to fabricate micronscale fibers from molten polymers into highly controlled 3D microfiber scaffolds. This emerging technique is gaining traction in tissue engineering and biofabrication research, however limitations in the ability to develop advanced coding to program MEW printers to fabricate scaffolds with complex fiber architectures has inhibited the development of structures with tunable and biomimetic mechanical properties. This study reports a series of non-straight scaffold architectures with combinations of independently controlled X & Y fiber spacing, corrections for MEW jet lag, and characterizations of their influences on scaffold mechanics. Polycaprolactone scaffolds with an elastic modulus ranging from 0.3 to 7.3 MPa were fabricated utilizing scaffolds manufactured from 5 layers of 55 m fibers. The inclusion of scaffold design corrections in the gcode to compensate for decreasing deposition accuracy with increasing layer height enabled us to correct for discontinuous stress-strain mechanics and improved scaffold fabrication reproducibility. This study provides a comparison between a series of highly reproducible MEW scaffold architectures with non-straight fibers compared to the common crosshatch design to inform the development of more biomimetic scaffolds applicable to a variety of clinical applications. It further illustrates the significant effect toolpath correction has on reducing poor stress-strain mechanics, therefore improving the control, reproducibility, and biomimetic capacity of the MEW technique.

bioengineering↗

bioRxiv2018

GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data

B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. GLaMST constructs the minimum-spanning-tree (MST) to approximate the landscape of how observed BCR sequences are related, uses the MST to guide the interpolation of the closest unobserved sequence, updates the MST for the interpolation of additional unobserved sequences, and iterates until a full lineage tree is completed, where all observed sequences are connected by interpolated unobserved sequences and single base operations of mutations, insertions and deletions. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure.

bioinformatics↗