Biology subjects

Micklem, G.

Publications and source records attributed to Micklem, G..

4 recordsLinked to original sources

bioRxiv2026

LAS3R: A simple, secure, scalable, and robust framework fordeploying lab automation devices

Laboratory automation can greatly accelerate experiments and data collection, yet building automated systems often requires substantial programming and electronics expertise, and few frameworks are targeted at deploying many devices. We present LAS3R, a low-cost, open-source framework that enables researchers with minimal technical expertise to rapidly prototype, deploy, remotely control, and collect data from multiple custom-built laboratory devices while maintaining strong security and reliability throughout the process--from early prototyping to routine operation. The system is built around a central hub to which multiple lab devices connect. This hub can be set up on a Raspberry Pi (a small, low-cost single-board computer) in under fifteen minutes. In the setup process, code is automatically generated for ESP32 microcontroller boards that control the hardware. Users can choose from a list of preconfigured ESP32 devices, for example a bioreactor, or use a template that provides base code for many common automation tasks, which they can then easily customise using the beginner-friendly Arduino platform. The ESP32 devices connect through a secure Wi-Fi network hosted by the Raspberry Pi that encrypts communication, and ensures only authorised hardware can join, helping safeguard experimental data and institutional networks, even while prototyping. We demonstrate the framework with two applications--a turbidostat bioreactor and a light-level controller--and show that it can simultaneously manage eight devices with 24 sensors. Robustness was evaluated through single-point-of-failure analysis, confirming continued operation during mains power or network interruptions. Comprehensive documentation, aimed at wet lab researchers, enables users to understand, build, and adapt the system, making it both a practical laboratory automation platform, including for those in low-resource settings, and a teaching resource. This paper is intended to be a technical evaluation of the architecture. Those wishing to deploy the system should refer to the online documentation at kavihshah.github.io/LAS3R.

bioengineering↗

bioRxiv2023

Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs

In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related sister cell type to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 23 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Twelve are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Six are electrosensory-restricted on the head (Irx5, Insm1, Sp5, Satb2, MafA and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a shark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.

developmental biology↗

bioRxiv2022

HumanMine: advanced data searching, analysis and cross-species comparison.

HumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration and analysis of data compiled from experimental, computational and curated data sources. Built using the InterMine data integration platform, HumanMine includes genes, proteins, pathways, expression levels, SNPs, diseases and more, integrated into a single searchable database. HumanMine promotes integrative analysis, a powerful approach in modern biology that allows many sources of evidence to be analysed together. The data can be accessed through a user-friendly web interface as well as a powerful, scriptable web service API to allow programmatic access to data. The web interface includes a useful identifier resolution system, sophisticated query options and interactive results tables that enable powerful exploration of data, including data summaries, filtering, browsing and export. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other biological entities. HumanMine can be used for integrative multi-staged analysis that can lead to new insights and uncover previously unknown relationships. Database URL: https://www.humanmine.org

genomics↗

bioRxiv2017

Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution

Bdelloid rotifers are microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasized desiccation as the cause of several unusual genomic features in this group. Here, we evaluate the relative effects of asexuality and desiccation tolerance on genome evolution by comparing whole genome sequences for three bdelloid species: Adineta ricciae (desiccation tolerant), Rotaria macrura and Rotaria magnacalcarata (both desiccation intolerant) to the only published bdelloid genome to date, that of Adineta vaga (also desiccation tolerant). We find that tetraploidy is conserved among all four bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is low, well within the range observed between alleles in obligately sexual, diploid animals. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. These findings are contrary to current understanding of the role of desiccation in shaping the bdelloid genome, and indicate that various features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred non-metazoan genes encoded in both desiccating and non-desiccating bdelloid species, and show that this is a unique feature of bdelloids among related animal phyla. Comparisons within bdelloids and to other desiccation-tolerant animals, however, again call into question the purported role of desiccation in horizontal transfer.

evolutionary biology↗