Biology subjects

Wakefield, J.

Publications and source records attributed to Wakefield, J..

5 recordsLinked to original sources

bioRxiv2025

Accounting for Spatial Correlation in Graphical Analysis of SpatialTranscriptomics Data

Co-expression analysis is key for understanding disease mechanisms and gene regulatory and functional relationships. In spatial transcriptomics, estimating gene correlation is challenging due to correlation among cells, which can lead to spurious associations that obscure true biological associations. To address this, we propose SpaceDecorr, a method that adjusts gene expression for technical artifacts and spatial dependencies by modeling each gene independently using a Negative Binomial Generalized Additive Model (NB-GAM) with spatial splines. Co-expression is then estimated from the Pearson residuals, yielding decorrelated expression values suitable for downstream analysis. This method targets cell-intrinsic coordination, rather than clustering genes by shared spatial patterns, and supports multi-sample analysis trough independent per-sample adjustment. Across simulations and real datasets, it consistently reduces false-positive correlations and improves the functional coherence of co-expression modules.

genomics↗

bioRxiv2025

RNase H1 counteracts DNA damage and ameliorates SMN-dependent phenotypes in a Drosophila model of Spinal Muscular Atrophy

Spinal Muscular Atrophy (SMA) is caused by a deficiency of the Survival Motor Neuron (SMN) protein. Mutations in SMN disrupt mRNA splicing and translation, leading to maladaptive changes in transcriptomes, proteomes, neuroinflammation, and metabolism, which drive motor neuron degeneration in SMA patients. Using a Drosophila SMA model, we found that systemic depletion of Smn leads to accumulation of RNA:DNA hybrids (R-loops), increased DNA damage, dysregulation of amino acids and sugar metabolism and activation of the innate immune response, recapitulating key pathological features reported in mammalian models and severe SMA patients. Persistent DNA damage in Smn-deficient flies alters cell proliferation rates in larval brains and induces extensive cell death in the developing eye. Importantly here, we show that stimulating the resolution of RNA:DNA hybrids with transgenic human RNAse H1 prevents the accumulation of DNA damage and attenuates the transcriptome and amino acid alterations induced by Smn depletion, mitigating the Smn-dependent cellular and developmental abnormalities, in Smn-deficient flies. Our data suggest that depletion of Smn causes an accumulation of aberrant transcripts and chronic DNA damage, which--along with the altered metabolomic profiles associated with Smn deficiency--trigger systemic inflammatory responses, ultimately affecting neuronal function and survival.

genetics↗

bioRxiv2022

Estimating the distribution of livestock in space and time: a time-series contribution to livestock density mapping

More than one billion people rely on livestock for income, nutrition, and social cohesion, however livestock keeping can facilitate disease transmission and contribute to climate change. While data on the distribution of livestock thus have broad utility across a range of applications, efforts to map the distribution of livestock on a large scale are limited to the Gridded Livestock of the World (GLW) project. We present a complimentary effort to map the distribution of cattle and pigs in Malawi, Uganda, Democratic Republic of Congo (DRC), and South Sudan. In contrast to GLW, which uses dasymmetric modeling applied to census data to produce time-stratified estimates of livestock counts and spatial density, our work uses complex survey data and distinct modeling methods to generate a time-series of livestock distribution, defining livestock density as the ratio of animals to humans. In addition to favorable cross-validation results and general agreement with national density estimates derived from external data on national human and livestock populations, our results demonstrate extremely good agreement with GLW-3 estimates, supporting the validity of both efforts. Our results furthermore offer a high-resolution time series result and employ a definition of density which is particularly well-suited to the study of livestock-origin zoonoses.

ecology↗

bioRxiv2019

In vitro reconstitution of branched microtubule nucleation

Eukaryotic cell division requires the mitotic spindle, a microtubule (MT)-based structure which accurately aligns and segregates duplicated chromosomes. The dynamics of spindle formation are determined primarily by correctly localising the MT nucleator,{gamma} -Tubulin Ring Complex ({gamma}-TuRC)1-4, within the cell. A conserved MT-associated protein complex, Augmin, recruits{gamma} -TuRC to pre-existing spindle MTs, amplifying their number, in an essential cellular phenomenon termed \"branched\" MT nucleation5-9. Here, we purify endogenous, GFP-tagged Augmin and{gamma} -TuRC from Drosophila embryos to near homogeneity using a novel one-step affinity technique. We demonstrate that, in vitro, while Augmin alone does not affect Tubulin polymerisation dynamics, it stimulates{gamma} -TuRC-dependent MT nucleation in a cell cycle-dependent manner. We also assemble and visualise the MT-Augmin-{gamma}-TuRC-MT junction using light microscopy. Our work therefore conclusively reconstitutes branched MT nucleation. It also provides a powerful synthetic approach with which to investigate the emergence of cellular phenomena, such as mitotic spindle formation, from component parts.

cell biology↗

bioRxiv2019

Tissue specific vulnerability to mitotic defects caused by mutations in the Drosophila ASPM homologue, Asp

Misregulation of candidate stem cell marker ASPM, and its Drosophila homologue Asp, leads to either tumour formation or microcephaly, but the functional roles contributing to each are not understood. We reverse-engineered flies to express a version of Asp (AspLIE), predicted to have lost its ability to bind the phosphatase PP2A-B. Although AspLIE flies were viable, they exhibited splayed neural stem cell spindle poles under stress, and development was substantially delayed. A tissue-level analysis of microcephaly and midgut abnormalities in Asp mutants with a compromised spindle assembly checkpoint (SAC) demonstrates tissue-specific vulnerability to mitotic defects.

developmental biology↗