Biology subjects

Noble, K.

Publications and source records attributed to Noble, K..

10 recordsLinked to original sources

bioRxiv2026

A single-cell transcriptomic atlas of the periventricular proliferative zone in the late gestation fetal brain in the pigtail macaque

BackgroundThe fetal brain undergoes rapid changes in late gestation, when waves of neurogenesis and gliogenesis shape cortical circuitry. The periventricular proliferative region and adjacent white matter are enriched in neuroprogenitor cells, newborn neurons, and interneurons, which is challenging to study in the late gestation human fetal brain. The nonhuman primate (NHP) provides a powerful translational model to overcome this limitation, given its close similarity to human neurodevelopmental trajectories. The study objective was to construct a single-cell RNA-Seq (scRNA-Seq) atlas of the late-gestation fetal brain of the pigtail macaque (Macaca nemestrina), focused on the periventricular proliferative zone. MethodsA sample of the lateral ventricular wall, subventricular zone, and overlying white/gray matter was dissociated into single cells and processed through the 10X Genomics pipeline, followed by SoupX removal of ambient RNA, and Seurats pipeline to aggregate, cluster and annotate single-cell populations. Monocle3 was used to determine pseudotime and map lineage progression. ResultsThis analysis captured diverse populations of neuroprogenitors, newborn neurons, developing lineages of excitatory and inhibitory neurons, oligodendrocyte and astrocyte lineages, and resident immune and endothelial cells. ConclusionsSingle-cell populations from the third-trimester nonhuman primate fetal brain are highly similar to those in the human fetus. This late-gestation single-cell atlas of the periventricular proliferative zone provides a unique reference for progenitor, neuronal, glial, vascular, and immune cell states during a critical window of primate neurodevelopment, enabling mechanistic interrogation of how inflammatory, infectious, or hypoxic insults disrupt vulnerable neurogenic niches.

genomics↗

bioRxiv2025

MtrAB activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae

The MtrAB two-component system is a master regulator of antibiotic biosynthesis in Streptomyces species. MtrA is also required for sporulation under certain growth conditions, which means that on some growth media {Delta}mtrA mutant colonies do not produce aerial hyphae or spores. These mutants are referred to as (conditionally) bald because they lack the hairy appearance of wild-type colonies. Here we report that S. venezuelae NRRL B-65442 {Delta}mtrA is bald on R2YE agar but sporulates normally on MYM agar and we demonstrate that this is caused by the presence of 10.2% sucrose in R2YE. Consistent with this, we found that adding 10.2% sucrose to MYM agar also inhibits sporulation of the {Delta}mtrA mutant. Proteomics combined with DNA binding studies revealed that MtrA directly activates the expression of the key developmental regulator genes bldM and whiI on R2YE but not MYM agar. BldM and WhiI work together to activate genes required for aerial hyphae production and sporulation. Crucially, over-expression of bldM-whiI in the {Delta}mtrA mutant restored normal sporulation in the presence of 10.2% sucrose. We hypothesised that MtrAB must sense and respond to osmotic stress and consistent with this we found that MtrA directly activates biosynthesis of the compatible solute and osmoprotectant ectoine on growth media containing 10.2% sucrose. We propose a model in which high concentrations of sucrose induce osmotic stress in Streptomyces species and this activates MtrAB. The response regulator MtrA then directly activates expression of the ectABCD operon to switch on ectoine biosynthesis and expression of bldM and whiI to trigger entry into sporulation. Impact statementStreptomyces species have complex developmental life cycles that start with spore germination and outgrowth of an actively growing substrate mycelium. Environmental stresses including nutrient starvation and osmotic stress trigger the production of aerial hyphae that undergo cell division to form spores. These spores are more resistant to environmental stresses and can stay viable in the soil until conditions improve. Here we show that MtrAB is responsible for sensing and responding to osmotic stress and we demonstrate that it directly controls the biosynthesis of ectoine and the developmental transition to sporulation through direct activation of BldM and WhiI. This work provides new insight into how environmental cues control the development of Streptomyces bacteria. Data summaryThe S. venezuelae NRRL B-65442 genome sequence is available at NCBI (Reference Sequence NZ_CP018074.1) and can be viewed at http://strepDB.streptomyces.org.uk (select vnz chromosome from the drop-down list). The ChIP-seq data (GEO accession number CP018074) used to map MtrA binding sites on the S. venezuelae NRRL B-65442 chromosome and the differential RNA-seq data (accession number GSE81104) used to map global transcript start sites throughout the life cycle were generated for earlier studies (1,2). The tandem mass tag proteomics data are available via ProteomeXchange with identifier PXD069151. The ReDCaT SPR data is included in the manuscript and the supplementary information. Protocols are freely available at http://actinobase.org (3) and strains and plasmids are available from http://streptomyces.org.uk/strepstrains. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2025

Redox control of antibiotic biosynthesis

Streptomyces bacteria make diverse specialised metabolites that form the basis of [~]55% of clinically used antibiotics. Despite this, only 3% of their encoded specialised metabolites have been matched to molecules and understanding how their biosynthesis is controlled is essential to fully exploit their potential. Here we use Streptomyces formicae and the formicamycin biosynthetic pathway as a model to understand the complex regulation of specialised metabolism. We analysed all three pathway-specific regulators and found that biosynthesis is subject to negative feedback and redox control via two MarR-family proteins while activation of the pathway is dependent on a cytoplasmic two-component system. Like many Streptomyces antibiotics, formicamycins are only produced in solid culture and biosynthesis is switched off in aerated liquid cultures. Here, we demonstrate that a redox-sensitive repressor named ForJ senses oxygen via a single cysteine residue that is required to repress formicamycin biosynthesis in liquid cultures.

molecular biology↗

bioRxiv2023

Cancer Prevalence Across Vertebrates

Cancer is pervasive across multicellular species, but what explains differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades (amphibians, sauropsids and mammals) we found that neoplasia and malignancy prevalence increases with adult weight (contrary to Petos Paradox) and somatic mutation rate, but decreases with gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%) the black-footed penguin (<0.4%), ferrets (63%) and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Statement of SignificanceEvolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.

cancer biology↗

bioRxiv2022

Jovian enables direct inference of germline haplotypes from short reads via sequence-to-sequence modeling

Detection of germline variants in next-generation sequencing data is an essential component of modern genomics analysis. Variant detection tools typically rely on statistical algorithms such as de Bruijn graphs, Hidden Markov Models and regression models, often coupled with heuristic techniques and thresholds to identify variants. Here we describe a new approach that replaces these handcrafted statistical methods with a single, end-to-end deep learning model that directly infers germline haplotypes from short read pileups. Our model, called Jovian, frames variant detection as a sequence-tosequence modeling task, akin to language translation, and employs a transformer-based architecture to translate alignment columns into two predicted haplotype sequences. After training with 17 whole genome sequences from Genome-in-a-Bottle cell lines, we demonstrate that this method learns to realign complex and ambiguous read mappings to produce accurate haplotype predictions, predicts variant genotypes and phase accurately, and leverages the local read context to inform predictions about a given position. We also demonstrate that a 2-dimensional positional encoding significantly improved precision of the detected variants. Compared to other callers, sensitivity and precision is higher than GATK HaplotypeCaller, but lower than DeepVariant and Strelka2.

bioinformatics↗

bioRxiv2022

Peripheral Auditory Nerve Impairment in a Mouse Model of Syndromic Autism

Dysfunction of the peripheral auditory nerve (AN) contributes to dynamic changes throughout the central auditory system, resulting in abnormal auditory processing, including hypersensitivity. Altered sound sensitivity is frequently observed in autism spectrum disorder (ASD), suggesting that AN deficits and changes in auditory information processing may contribute to ASD-associated symptoms, including social communication deficits and hyperacusis. The MEF2C transcription factor is associated with risk for several neurodevelopmental disorders, and mutations or deletions of MEF2C produce a haploinsufficiency syndrome characterized by ASD, language and cognitive deficits. A mouse model of this syndromic ASD (i.e., Mef2c+/- or Mef2c-Het) recapitulates many of the MEF2C Haploinsufficiency syndrome-linked behaviors including communication deficits. We show here that Mef2c-Het mice exhibit functional impairment of the peripheral AN and a modest reduction in hearing sensitivity. We find that MEF2C is expressed during development in multiple AN and cochlear cell types, and in Mef2c-Het mice, we observe multiple cellular and molecular alterations associated with the AN, including abnormal myelination, neuronal degeneration, neuronal mitochondria dysfunction, and increased macrophage activation and cochlear inflammation. These results reveal the importance of MEF2C function in inner ear development and function and the engagement of immune cells and other non-neuronal cells, which suggests that microglia/macrophages and other non-neuronal cells might contribute, directly or indirectly, to AN dysfunction and ASD-related phenotypes. Finally, our study establishes a comprehensive approach for characterizing AN function at the physiological, cellular, and molecular levels in mice, which can be applied to animal models with a wide range of human auditory processing impairments. Significance StatementThis is the first report of peripheral auditory nerve (AN) impairment in a mouse model of human MEF2C haploinsufficiency syndrome that has well-characterized ASD related behaviors including communication deficits, hyperactivity, repetitive behavior, and social deficits. We identify multiple underlying cellular, sub-cellular, and molecular abnormalities that may contribute to peripheral AN impairment. Our findings also highlight the important roles of immune cells (e.g., cochlear macrophages) and other non-neuronal elements (e.g., glial cells and cells in the stria vascularis) in auditory impairment in ASD. The methodological significance of the study is the establishment of a comprehensive approach for evaluating peripheral AN function and impact of peripheral AN deficits with minimal hearing loss.

neuroscience↗

bioRxiv2021

Sampling of Structure and Sequence Space of Small Protein Folds

Nature only samples a small fraction in sequence space, yet many more amino acid combinations can fold into stable proteins. Furthermore, small structural variations in a single fold, which may only be a few amino acids different from the next homolog, define their molecular function. Hence, to design proteins with novel molecular functionalities, such as molecular recognition, methods to control and sample shape diversity are necessary. To explore this space, we developed and experimentally validated a computational platform that can design a wide variety of small protein folds while sampling high shape diversity. We designed and evaluated about 30,000 de novo protein designs of 7 different folds. Among these designs, about 6,200 stable proteins were identified, with predicted structures having first-of-its-kind minimalized thioredoxin. Obtained data revealed more protein folding rules, such as helix connecting loops, which were in nature. Beyond providing a resource database for protein engineering, our data presents a large training data set for machine learning. We developed a high-accuracy classifier to predict the stability of our designed proteins. The methods and the wide range of new protein shapes provide a basis for the design of new protein function without compromising stability.

bioengineering↗

bioRxiv2020

Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)

Robber flies or assassin flies (Diptera: Asilidae) are a diverse family of venomous predators. The most recent classification organizes Asilidae into 14 subfamilies based on a comprehensive morphological phylogeny, but many of these have not been supported in a subsequent molecular study using traditional molecular markers. To address questions of monophyly in Asilidae, we leveraged the recently developed Diptera-wide UCE baitset to compile seven datasets comprising 151 robber flies and 146 - 2,508 loci, varying in the extent of missing data. We also studied the behavior of different nodal support metrics, as the non-parametric bootstrap is known to perform poorly with large genomic datasets. Our ML phylogeny was fully resolved and well-supported, but partially incongruent with the coalescent phylogeny. Further examination of the datasets suggested the possibility that GC bias had influenced gene tree inference and subsequent species tree analysis. The subfamilies Brachyrhopalinae, Dasypogoninae, Dioctriinae, Stenopogoninae, Tillobromatinae, Trigonomiminae, and Willistonininae were not recovered as monophyletic in either analysis, consistent with a previous molecular study. The inter-subfamily relationships are summarized as follows: Laphriinae and Dioctriinae (in part) are successively sister to the remaining subfamilies, which form two clades; the first consists of a grade of Stenopogoninae (in part), Willistonininae (in part), Bathypogoninae+Phellinae, Stichopogoninae, Leptogastrinae, Ommatiinae, and Asilinae; the second clade consists of a thoroughly paraphyletic assemblage of genera from Dioctriinae (in part), Trigonomiminae, Stenopogoninae (in part), Tillobromatinae, Brachyrhopalinae, and Dasypogoninae. We find that nodal support does not significantly vary with missing data. Furthermore, the bootstrap appears to overestimate nodal support, as has been reported from many recent studies. Gene concordance and site concordance factors seem to perform better, but may actually underestimate support. We instead recommend quartet concordance as a more appropriate estimator of nodal support. Our comprehensive phylogeny demonstrates that the higher classification of Asilidae is far from settled, and it will provide a much-needed foundation for a thorough revision of the subfamily classification.

evolutionary biology↗

bioRxiv2020

Refactoring the formicamycin biosynthetic gene cluster to make high-level producing strains and new molecules

The formicamycins are promising antibiotics with potent activity against Gram-positive pathogens including VRE and MRSA and display a high barrier to selection of resistant isolates. They were first identified in Streptomyces formicae KY5, which produces the formicamycins at low levels on solid agar but not in liquid culture, thus hindering further investigation of these promising antibacterial compounds. We hypothesised that by understanding the organisation and regulation of the for biosynthetic gene cluster, we could rationally refactor the cluster to increase production levels. Here we report that the for biosynthetic gene cluster consists of 24 genes expressed on nine transcripts. Seven of these transcripts, including those containing all the major biosynthetic genes, are repressed by the MarR-regulator ForJ which also controls the expression of the ForGF two-component system that initiates biosynthesis. A third cluster-situated regulator, ForZ, autoregulates and controls production of the putative MFS transporter ForAA. Consistent with these findings, deletion of forJ increased formicamycin biosynthesis 5-fold, while over-expression of forGF in the {Delta}forJ background increased production 10-fold compared to the wild-type. De-repression by deleting forJ also switched on biosynthesis in liquid-culture and induced the production of two novel formicamycin congeners. By combining mutations in regulatory and biosynthetic genes, six new biosynthetic precursors with antibacterial activity were also isolated. This work demonstrates the power of synthetic biology for the rational redesign of antibiotic biosynthetic gene clusters both to engineer strains suitable for fermentation in large scale bioreactors and to generate new molecules. ImportanceAntimicrobial resistance is a growing threat as existing antibiotics become increasingly ineffective against drug resistant pathogens. Here we determine the transcriptional organisation and regulation of the gene cluster encoding biosynthesis of the formicamycins, promising new antibiotics with activity against drug resistant bacteria. By exploiting this knowledge, we construct stable mutant strains which over-produce these molecules in both liquid and solid culture whilst also making some new compound variants. This will facilitate large scale purification of these molecules for further study including in vivo experiments and the elucidation of their mechanism of action. Our work demonstrates that understanding the regulation of natural product biosynthetic pathways can enable rational improvement of the producing strains.

microbiology↗

bioRxiv2019

Neural correlates of experience with CCTV surveillance of naturalistic prosocial and antisocial interactions: a reverse correlation analysis

Previous research using reverse correlation to explore the relationship between brain activity and presented image information found that Face Fusiform Area (FFA) activity could be related to the appearance of faces during free viewing of the Hollywood movie \"The Good, the Bad, and the Ugly\" (Hasson, et al, 2004). We applied this approach to the naturalistic viewing of unedited footage of city-centre closed-circuit television (CCTV) surveillance. Two 300 second videos were used, one containing prosocial activities and the other antisocial activities. Brain activity revealed through fMRI as well as eye movements were recorded while fifteen expert CCTV operators with a minimum of 6 months experience of CCTV surveillance alongside an age and gender matched control group of fifteen novice viewers were scanned while watching the videos. Independent scans functionally localized FFA and posterior Superior Temporal Sulcus (pSTS) activity using faces/houses and intact/scrambled point-light biological motion displays respectively. Reverse correlation revealed peaks in FFA and pSTS brain activity corresponding to the expert and novice eye movements directed towards faces and biological motion across both videos. In contrast, troughs in activation corresponded to camera-induced motion when a clear view of visual targets were temporarily not available. Our findings, validated by the eye movement data, indicate that the predicted modulation of brain activity occurs as a result of salient features of faces and biological motion embedded within the naturalistic stimuli. The examination of expertise revealed that in both pSTS and FFA the novices had significantly more activated timeframes than the experienced observers for the prosocial video. However, no difference was found for the antisocial video. The modulation of brain activity, as well as the effect of expertise gives a novel insight into the underlying visual processes in an applied real-life task.

neuroscience↗