Biology subjects

Adams, B. A.

Publications and source records attributed to Adams, B. A..

4 recordsLinked to original sources

bioRxiv2026

Ambient humidity and temperature influence physicochemical drift during laboratory storage of field-collected mosquito breeding water

The use of field water for laboratory rearing of mosquitoes could offer a better representation of the natural aquatic environment than laboratory tap or deionised water. For logistical reasons, such water may be stored in the laboratory environment for an extended period, but its stability is poorly documented. This study evaluated the influence of laboratory storage conditions on the kinetics of physicochemical parameters of breeding water collected from a field habitat. To capture within-habitat variability, water was collected from multiple spatial points from a breeding site and transferred into plastic containers for storage under laboratory conditions. Water physicochemical parameters were measured in the field to establish baseline readings, while laboratory measurements were done at 2-3-day intervals over 2 months to evaluate temporal changes. A linear mixed-effects model was fitted to evaluate the determinants of changes in physicochemical parameters under laboratory storage. Most parameters exhibited high stability; however, water temperature increased significantly by an average of [~]1.5 (p= 0.046) relative to the field. Water pH demonstrated a long-term rise over the 2-month storage period with a transient, significant dip of 0.71 units after a week of storage (p< 0.001). Overall, LMM analyses revealed that ambient relative humidity was the strongest statistical predictor of change in all water parameters except pH (p< 0.05). Ambient temperature correlated positively with water temperature and ammonium nitrogen (NH4-N) (p<0.002), and negatively with dissolved oxygen (p< 0.002). These results indicate that stored field water is highly sensitive to the laboratory microclimate. Specifically, water temperature, pH, and NH4-N serve as candidate indicators for storage-related physicochemical drift. We recommend the rigorous standardisation of insectary humidity and temperature, and monitoring of water parameters, which are likely relevant for bioassay reproducibility.

ecology↗

bioRxiv2024

Application of Elevated Atmospheric Pressure and Hypoxia Enhance Pluripotency and Stem Cell Differentiation

Physical forces regulate stem cell differentiation in-vivo, however few simple and precise methods exist to better understand this biology in-vitro. Here we describe the use of a novel bioreactor that enables addition of physical force in the form of elevated atmospheric pressure during reprogramming of human fibroblasts and culture of human induced pluripotent stem cell (iPSC) and neural stem cell (NSC) lines. We demonstrate that elevated atmospheric pressure and hypoxia can positively regulate reprogramming of human fibroblasts to iPSCs across multiple donors. Prolonged culture of iPSCs in elevated atmospheric pressure (+ 2 PSI) and 15% oxygen exhibited progressive differentiation with concomitant metabolic and epigenetic gene expression changes. Furthermore, elevated atmospheric pressure positively regulates differentiation of iPSCs to neural-ectodermal and hematopoietic lineages when combined with appropriate soluble factors and oxygen concentration. In summary, these results demonstrate the significance of applied atmospheric pressure for stem cell applications and warrants further investigation.

developmental biology↗

bioRxiv2022

Functional antibodies exhibit light chain coherence

The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies binding particular antigens1. In most mammals, antibodies are composed of a heavy and a light chain which are sequentially generated by recombination of V, D (for heavy chains), J, and C gene segments. Each chain contains three complementarity-determining regions (CDR1-3), contributing to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-21. We considered pairs of B cells sharing the same heavy chain V gene and CDRH3 amino acid sequence and isolated from different donors, also known as public clonotypes22,23. We show that for naive antibodies (not yet adapted to antigens), the probability that they use the same light chain V gene is [~]10%, whereas for memory (functional) antibodies it is [~]80%. This property of functional antibodies is a phenomenon we call light chain coherence. We also observe it when similar heavy chains recur within a donor. Thus, though naive antibodies appear to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.

immunology↗

bioRxiv2022

enclone: precision clonotyping and analysis of immune receptors

Half a billion years of evolutionary battle forged the vertebrate adaptive immune system, an astonishingly versatile factory for molecules that can adapt to arbitrary attacks. The history of an individual encounter is chronicled within a clonotype: the descendants of a single fully rearranged adaptive immune cell. For B cells, reading this immune history for an individual remains a fundamental challenge of modern immunology. Identification of such clonotypes is a magnificently challenging problem for three reasons: O_LIThe cell history is inferred rather than directly observed: the only available data are the sequences of V(D)J molecules occurring in a sample of cells. C_LIO_LIEach immune receptor is a pair of V(D)J molecules. Identifying these pairs at scale is a technological challenge and cannot be done with perfect accuracy--real samples are mixtures of cells and fragments thereof. C_LIO_LIThese molecules can be intensely mutated during the optimization of the response to particular antigens, blurring distinctions between kindred molecules. C_LI It is thus impossible to determine clonotypes exactly. All solutions to this problem make a trade-off between sensitivity and specificity; useful solutions must address actual artifacts found in real data. We present enclone1, a system for computing approximate clonotypes from single cell data, and demonstrate its use and value with the 10x Genomics Immune Profiling Solution. To test it, we generate data for 1.6 million individual B cells, from four humans, including deliberately enriched memory cells, to tax the algorithm and provide a resource for the community. We analytically determine the specificity of enclones clonotyping algorithm, showing that on this dataset the probability of co-clonotyping two unrelated B cells is around 10-9. We prove that using only heavy chains increases the error rate by two orders of magnitude. enclone comprises a comprehensive toolkit for the analysis and display of immune receptor data. It is ultra-fast, easy to install, has public source code, comes with public data, and is documented at bit.ly/enclone. It has three "flavors" of use: (1) as a command-line tool run from a terminal window, that yields visual output; (2) as a command-line tool that yields parseable output that can be fed to other programs; and (3) as a graphical version (GUI).

immunology↗