Biology subjects

Monks, J.

Publications and source records attributed to Monks, J..

4 recordsLinked to original sources

bioRxiv2026

MyoNet and AlveoliNet: A hybrid 3D neural-net pipeline for the instance segmentation and scoring of epithelial cells in intact mammary alveoli

Recent advances in tissue clearing protocols such as DISCO, CUBIC, Clarity, FUnGI, and PEGASOS have revolutionized our ability to label and image intact 3-dimensional (3D) biological structures using fluorescence microscopy. The lactating mammary gland particularly benefits from clearing due to its high degree of tissue opacity. Cleared mammary gland images are strikingly beautiful and complicated but are difficult to fully interpret without developing a series of quantitative techniques and assays to analyze and compare them. These approaches will ultimately be as varied as the biology each scientist wishes to study. Here, we present one strategy based on a modular, hybrid, deep-learning approach and classical image processing that can segment and measure alveoli, cell nuclei and myoepithelial cells in intact mammary tissue. We have developed two original, three-dimensional (3D) U-shaped encoder-decoder networks (U-Nets), AlveoliNet and MyoNet, and combined these with CellPose3 nuclear instance segmentation and SlideBook/SlideBook Synergy binary mask operations. This approach can be used to easily score 100,000s of cells in intact tissue and differentiated glands at different developmental stages, genetic backgrounds, or treatments. We demonstrate the utility of this approach for quantifying the change in proportion of myoepithelial cells over the pregnancy-lactation transition, driven by endoreplication in the gland postpartum. We present a complete methods pipeline for other laboratories to utilize our approach in their own studies using standard desktop computers.

developmental biology↗

bioRxiv2026

Neotaphonomic characteristics of vertebrate site formation in underwater caves

Recovering well-preserved vertebrate remains from underwater caves has provided critical insights into archaeological and palaeontological records worldwide. However, understanding how bone assemblages form and are modified in underwater environments remains limited due to stable low energy burial conditions that produce time-averaged deposits, and underwater settings that hinder traditional recording and recovery methods. This study applies an actualistic taphonomic framework to three assemblages of domesticate animal bones (N = 231) from two underwater caves, Green Waterhole and Gouldens Sinkhole, near Mount Gambier, South Australia, encompassing known submerged (wet; N = 134) and dry (N = 97) burial conditions. The assemblages were examined to assess how wet and dry cave environments impact bone distribution, surface and microstructural modification. Radiocarbon dating of 41 specimens indicates that domesticate fauna were deposited over decadal and centennial timescales, allowing taphonomic signatures to be contextualised through time. Statistically significant differences were identified between wet and dry burial contexts. Bones recovered from wet contexts exhibit mostly better preservation, including skeletal elemental completeness, surface, and microstructure, than those from dry caves. However, some of the submerged specimens also have elevated frequencies of bone surface corrosion with macroscopic evidence for heterogenous black biological staining, algal or biofilm attack, and a distinctive form of circular etching. Histotaphonomy further reveals patterns of peripheral cyanobacterial tunnelling across most bones recovered from submerged contexts. Bones from dry environments were dominated by terrestrially linked tunnelling across all regions of the bone cortex. These findings can be explained by variation in light availability across different cave zones which influences biological activity and, in turn, the expression of taphonomic markers on bone externally and at the microstructural level. This is the first study to provide a benchmark bone dataset for reconstructing depositional histories and post-depositional reworking in underwater cave environments under a taphonomic framework.

paleontology↗

bioRxiv2023

Comparative Proteomic Analysis of Paired Human Milk Fat Globules and Membranes and Mouse Milk Fat Globules Identifies Core Cellular Systems Contributing to Mammary Lipid Trafficking and Secretion

Human milk delivers critical nutritional and immunological support to the infant. The milk fat globule and its membrane contain many bioactive components, yet the mechanism of milk fat secretion and how milk fat globule (MFG) components are regulated are poorly defined. In this study, we perform quantitative proteomic profiling of milk fat globules from human and mouse milk, as well as from isolated membranes physically disrupted from human milk fat globules. Using paired analyses of the human samples we report membrane enrichment of the proteins involved in docking/tethering the lipid droplet to the membrane as well as minor components involved in the signaling pathway for secretion. Comparing abundance between human and mouse milk fat globules we find that 8 of 12 major milk fat globule proteins are shared between the two species. Comparative pathway enrichment analyses between human and mouse samples reveal similarities in shared membrane trafficking and signaling pathways involved in milk fat secretion. Our results advance knowledge of the composition and relative quantities of proteins in human and mouse milk fat globules in greater detail, provide a quantitative profile of specifically enriched human milk fat globule membrane proteins, and identify core cellular systems involved in milk lipid secretion.

cell biology↗

bioRxiv2018

Selective roles of vertebrate PCF11 in premature and full-length transcript termination

The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including: mNET-seq, 3 mRNA-seq, chromatin RNA-seq and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and downstream gene silencing. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto-regulatory mechanism involving premature termination of its own transcript, and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination.

molecular biology↗