Thomas Michael Maynard

Background: The emergence of accessible spatial transcriptomic platforms such as 10x Genomics Visium HD and Xenium has created demand for analysis tools that can handle the complexity and scale of spatial datasets. Current frameworks approach spatial data primarily as an extension of single-cell RNA-seq pipelines, where spatial coordinates are retained as metadata rather than treated as a first-class organizing principle. As a result, common tasks such as multi-modal data alignment, region-of-interest selection, and cross-resolution visualization require manually managing disparate data types, coordinates, and scales, making spatial analysis unnecessarily time-consuming and error-prone. Results: We present platpy ( p ipeline for layered a nalysis of transcriptomics), a Python-based “spatial-first” framework that treats absolute physical micron coordinates as the organizing principle for all data types. All data – morphology images, transcript point clouds, expression matrices, segmented cells, and user-defined regions – are stored as typed objects (“Channels”) that carry their own spatial metadata, keeping all layers in automatic registration regardless of platform, resolution, or analysis operation. Two complementary interfaces simplify access to underlying data: the ViewPort , a compositing engine for efficient multi-channel visualization, and the DataPort , which extracts raw data in its native format for downstream analysis. A set of spatial analysis tools demonstrates the practical benefits of the framework, including ROI-based expression binning, cortical unfolding, and sub-micron fine alignment of transcript and image data. The use of modern Python data management methods helps maintain the efficiency of the framework, allowing for quick visualizations and analysis with a low memory footprint. Conclusions: Platpy is designed to complement rather than replace widely used tools in the spatial analysis ecosystem (scanpy, squidpy, CellPose, StarDist), by handling the spatial mechanics of large datasets so that the analyst can focus on the biology. Platpy is freely available under the MIT license at https://github.com/maynardt/platpy .

We characterized cellular and molecular mechanisms underlying the therapeutic response in vitro and in vivo to the antioxidant N-acetyl cysteine (NAC), which in the LgDel 22q11.2 Deletion Syndrome mouse model restores growth and connectivity of upper layer cortical projection neurons (Layer 2/3 PNs) and improves cognitive performance. NAC treatment of primary cultured LgDel L 2/3 PNs does not restore these neurons to a wild type (WT) state. Rather than returning to the bimodal dendrite and axon size distribution seen in WT, LgDel L 2/3 PN dendrite and axon growth in vitro increases unimodally in response to NAC. In parallel, altered expression of 22q11-deleted genes and presumed downstream targets are unchanged. Instead, novel antioxidant defense and neuronal growth genes are differentially expressed: some generally NAC-regulated, others responsive only in the context of 22q11 deletion. Apparently, NAC ameliorates L 2/3 PN developmental pathology without restoring WT cell states or typical expression of mutant genes or their downstream targets. NAC also elicits differential expression of antioxidant defense genes in 22q11-deleted L 2/3 PN - but not L 5/6 counterparts - in the developing postnatal LgDel mouse cortex, rather than modulating 22q11 genes or downstream targets. These NAC-dependent, L 2/3 PN-selective in vivo cellular and transcriptional changes differ substantially from those in primary culture. Thus, despite some in vitro and in vivo parallels, the NAC therapeutic response that diminishes oxidative stress-related L 2/3 PN circuit and behavioral pathology due to 22q11 deletion has a unique in vivo signature.

Heterozygous deletion of multiple contiguous genes associated with 22q11.2 Deletion Syndrome (22q11DS), a developmental disorder with significant risk for autistic spectrum disorder (ASD) and schizophrenia (Scz), selectively compromises neurogenic capacities of a temporally distinct cohort of cerebral cortical basal progenitors (bPs), prefiguring diminished frequency, divergent times of origin, positions, and identities of a subset of Layer 2/3 projection neuron (PN) progeny in the LgDel 22q11DS mouse model. LgDel bPs express 24/28 contiguous murine 22q11 gene orthologues at diminished levels; in parallel, cell cycle kinetics, modes of division, gene expression levels, and DNA methylation states are aberrant in LgDel bPs but not their apical progenitor precursors. Accordingly, targeted disruption of bP proliferative and transcriptional states selectively alters Layer 2/3 PN identities and frequencies, prefiguring atypical association cortico-cortical connections and behavioral deficits associated with ASD and Scz pathology in a mouse model of 22q11DS.

Heterozygous deletion of multiple contiguous genes associated with 22q11.2 Deletion Syndrome (22q11DS), a developmental disorder with significant risk for autistic spectrum disorder (ASD) and schizophrenia (Scz), selectively compromises neurogenic capacities of a temporally distinct cohort of cerebral cortical basal progenitors (bPs), prefiguring diminished frequency, divergent times of origin, positions, and identities of a subset of Layer 2/3 projection neuron (PN) progeny in the LgDel 22q11DS mouse model. LgDel bPs express 24/28 contiguous murine 22q11 gene orthologues at diminished levels; in parallel, cell cycle kinetics, modes of division, gene expression levels, and DNA methylation states are aberrant in LgDel bPs but not their apical progenitor precursors. Accordingly, targeted disruption of bP proliferative and transcriptional states selectively alters Layer 2/3 PN identities and frequencies, prefiguring atypical association cortico-cortical connections and behavioral deficits associated with ASD and Scz pathology in a mouse model of 22q11DS.

The genesis of a mature complement of neurons is thought to require, at least in part, precursor cell lineages in which neural progenitors have distinct identities recognized by exclusive expression of one or a few molecular markers. Nevertheless, limited progenitor types distinguished by specific markers and lineal progression through such subclasses cannot easily yield the magnitude of neuronal diversity in most regions of the nervous system. The late Verne Caviness, to whom this edition of Developmental Neuroscience is dedicated, recognized this mismatch. In his pioneering work on the histogenesis of the cerebral cortex, he acknowledged the additional flexibility required to generate multiple classes of cortical projection and interneurons. This flexibility may be accomplished by establishing cell states in which levels rather than binary expression or repression of individual genes vary across each progenitor’s shared transcriptome. Such states may reflect local, stochastic signaling via soluble factors or coincidence of cell surface ligand/receptor pairs in subsets of neighboring progenitors. This probabilistic, rather than determined, signaling could modify transcription levels via multiple pathways within an apparently uniform population of progenitors. Progenitor states, therefore, rather than lineal relationships between types may underlie the generation of neuronal diversity in most regions of the nervous system. Moreover, mechanisms that influence variation required for flexible progenitor states may be targets for pathological changes in a broad range of neurodevelopmental disorders, especially those with polygenic origins.

Facial dysmorphology is a hallmark of 22q11.2 deletion syndrome (22q11DS). Nearly all affected individuals have facial features characteristic of the syndrome: a vertically long face with broad nasal bridge, narrow palpebral fissures and mild micrognathia, sometimes accompanied by facial skeletal and oropharyngeal anomalies. Despite the frequency of craniofacial dysmorphology due to 22q11.2 deletion, there is still incomplete understanding of the contribution of individual 22q11 genes to craniofacial and oropharyngeal development. We asked whether homozygous or heterozygous loss of function of single 22q11 genes compromises craniofacial and/or oropharyngeal morphogenesis related to these 22q11DS phenotypes. We found that Ranbp1, a 22q11DS gene that mediates nucleocytoplasmic protein trafficking, is a dosage-dependent modulator of craniofacial development. Ranbp1^−/− embryos have variably penetrant facial phenotypes, including altered facial morphology and cleft palate. This 22q11DS-related dysmorphology is particularly evident in the midline of the facial skeleton, as evidenced by a robustly quantifiable dysmorphology of the vomer, an unpaired facial midline bone. 22q11DS-related oropharyngeal phenotypes reflect Ranbp1 function in both the cranial neural crest and cranial ectoderm based upon tissue-selective Ranbp1 deletion. Analyses of genetic interaction show that Ranbp1 mutation disrupts BMP signaling-dependent midline gene expression and BMP-mediated craniofacial and cranial skeletal morphogenesis. Finally, midline defects that parallel those in Ranbp1 mutant mice are observed at similar frequencies in the LgDel 22q112DS mouse model. Apparently, Ranbp1 is a modulator of craniofacial development, and in the context of broader 22q11 deletion, Ranbp1 mutant phenotypes mirror key aspects of 22q11DS midline facial anomalies.

Background The maintenance of phosphate and calcium homeostasis alongside optimal vitamin D status is essential for bone health. Moreover, low vitamin D is associated with an increased risk of stress fracture, impaired muscular remodelling and increased risk of upper respiratory tract infections. Objective The primary objective was to assess the efficacy of an individualised in-season vitamin D supplementation programme. The secondary aim was to observe for regression of vitamin D levels during the longer daylight months (April-October) in players where vitamin D was not routinely supplemented. Design Serum 25 Hydroxyvitamin D (Serum 25[OH]D) levels were collected twice a year (October and April). Levels were categorised as: deficient (175). Players with sufficient levels were given a maintenance protocol (20,000iu once weekly) October-April. Players who were deficient/insufficient were given a loading regimen (20,000iu twice weekly for three weeks) and the maintenance protocol thereafter. Setting A category one Premier League Elite Player Performance Plan (EPPP) youth football academy. Participants 13 participants from the u23s and u18s squads. Interventions Serum 25[OH]D levels were collected (via venous blood sample) twice a year (October and April). Levels were categorised as: deficient 175nmol/l. Players with sufficient or insufficient levels were given a maintenance protocol (20,000IU once weekly) during October-April. Players who were deficient were given a loading regimen (20,000iu twice weekly for three weeks) and the maintenance protocol for the remainder of winter (22 weeks). Oral supplementation was administered using Synergy Biologics LTD Pro D3 Sport 20k (UK). Results There was no significant increase in serum 25[OH]D during the supplementation period (October-April). However, 20,000iu of supplemental Vitamin D over a 25-week period was sufficient to maintain vitamin D status. Baseline serum 25[OH]D was not significantly increased after a period of supplemental vitamin D during winter months. Further studies in this population group would be beneficial to assess the effects of longer term season-on-season supplementation.

We defined a temporal dimension of precursor diversity and lineage in the developing mouse olfactory epithelium (OE) at mid-gestation that results in genesis of distinct cell classes. Slow, symmetrically dividing Meis1+/ Pax7+ progenitors in the early differentiating lateral OE give rise to small numbers of Ascl1+ precursors in the dorsolateral and ventromedial OE. Few of the initial progeny of the Ascl1+ precursors immediately generate olfactory receptor neurons (ORNs). Instead, most early progeny of this temporally defined precursor cohort, labeled via temporally discreet tamoxifen-dependent Ascl1 ^Cre -driven recombination, populate a dorsomedial OE domain comprised of proliferative Ascl1+ as well as Ascl1-cells from which newly generated ORNs are mostly excluded. The most prominent early progeny of these Ascl1+ OE precursors are migratory mass cells associated with the nascent olfactory nerve (ON) in the frontonasal mesenchyme. These temporal, regional and lineage distinctions are matched by differences in proliferative capacity and modes of division in isolated, molecularly distinct lateral versus medial OE precursors. By late gestation, the progeny of the temporally and spatially defined Ascl1+ precursor cohort include few proliferating precursors. Instead, these cells generate a substantial subset of OE sustentacular cells, spatially restricted ORNs, and ensheathing cells associated with actively growing as well as mature ON axons. Accordingly, from the earliest stages of OE differentiation, distinct temporal and spatial precursor identities provide a template for acquisition of subsequent OE and ON cellular diversity.

Rapid and widespread testing of severe acute respiratory coronavirus 2 (SARS-CoV-2) is essential for an effective public health response aimed at containing and mitigating the coronavirus disease 2019 (COVID-19) pandemic. Successful health policy implementation relies on early identification of infected individuals and extensive contact tracing. However, rural communities, where resources for testing are sparse or simply absent, face distinctive challenges to achieving this success. Accordingly, we report the development of an academic, public land grant University laboratory-based detection assay for the identification of SARS-CoV-2 in samples from various clinical specimens that can be readily deployed in areas where access to testing is limited. The test, which is a quantitative reverse transcription polymerase chain reaction (RT-qPCR)-based procedure, was validated on samples provided by the state laboratory and submitted for FDA Emergency Use Authorization. Our test exhibits comparable sensitivity and exceeds specificity and inclusivity values compared to other molecular assays. Additionally, this test can be re-configured to meet supply chain shortages, modified for scale up demands, and is amenable to several clinical specimens. Test development also involved 3D engineering critical supplies and formulating a stable collection media that allowed samples to be transported for hours over a dispersed rural region without the need for a cold-chain. These two elements that were critical when shortages impacted testing and when personnel needed to reach areas that were geographically isolated from the testing center. Overall, using a robust, easy-to-adapt methodology, we show that an academic laboratory can supplement COVID-19 testing needs and help local health departments assess and manage outbreaks. This additional testing capacity is particularly germane for smaller cities and rural regions that would otherwise be unable to meet the testing demand.