Biology subjects

Smith, T.

Publications and source records attributed to Smith, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Neural populations in the dorsal and ventral cervical spinal cord share temporal dynamics during reach

Neural population dynamics provide a popular framework for studying motor cortex function. However, whether such dynamics reflect stage-specific computations or are shared across the input and output stages of a sensorimotor circuit is unknown. In the spinal cord, afferent inputs and motor outputs are segregated by anatomical depth. Here we developed depth-resolved Neuropixels recordings from the rat cervical spinal cord during targeted reaching behavior. Across our recordings, population activity was low-dimensional and organized into transient, rotational and target-specific dynamical motifs. Despite differences in single-neuron activity by depth, dorsal and ventral populations expressed nearly identical dynamics across targets and animals. The dominant target-invariant component was strikingly synchronized across depths, whereas other components, including the target-specific component, showed condition-dependent ventral-to-dorsal delays with timing consistent with movement-related feedback. Thus, cervical spinal population dynamics span sensory and motor territories, and may reflect shared coordination of activity rather than purely state-specific local processing.

neuroscience↗

bioRxiv2026

Choreographed morphogenetic events underlie early foregut development in the mouse embryo

Between embryonic days 7.5 and 8.5, the mouse embryo undergoes a dramatic rearrangement of its entire anterior, a process known as ventral folding: the near-simultaneous morphogenesis of the cardiac crescent, cranial headfolds, and anterior foregut that together establish the antero-ventral body plan. While cardiac morphogenesis has been studied in detail, the cellular and mechanical basis of foregut involution remains largely undefined. Using combined light-sheet and spinning-disk live imaging spanning the full window of foregut formation, we show that involution proceeds through a stereotyped morphological programme that does not require actomyosin contractility for its initiation. Additionally, involution is preceded by a spatiotemporally restricted wave of apoptosis in embryonic visceral endoderm (emVE) cells, which extrude bidirectionally. A lineage- and stage-resolved bulk RNA-sequencing of emVE, definitive endoderm, and epiblast populations identifies a differential-adhesion and cell-cycle signature underlying this behaviour. Revisiting a visceral-endoderm-specific Bmp2 knock-out mutant, we find that BMP2 controls involution indirectly, by directing notochord positioning and thereby the geometry of the surrounding heart and headfold mechanics. Together, these findings reframe ventral folding as a single coordinated geometric process rather than a set of independent organ forming events.

developmental biology↗

bioRxiv2026

Post-transcriptional glucocorticoid receptor signalling synchronises circadian rhythms

Keeping cellular circadian clocks synchronised is critical for cellular and physiological health. Glucocorticoid (GC) hormones are the most potent systemic timing signal for cellular clocks, acting via the glucocorticoid receptor (GR), a transcription factor conventionally thought to synchronise cells by translocating into the nucleus and activating the transcription of clock genes. Our findings overturn this model: acute changes in GR translocation and nascent transcription are both dispensable for GC-resetting of the circadian clock. Instead, physiological GC pulses act post-transcriptionally to rapidly increase Period1 mRNA through enhanced RNA processing, not synthesis. This elevates PER1 protein production which, alone, is sufficient to reset the clock. Yet each pulse resets only a subset of cells, explaining why, in vivo, repeated daily hormonal cues are required for full re-entrainment after jet lag or shift work. We propose a new model for hormonal signalling to the circadian clock and identify RNA processing kinetics as a general regulatory lever for nuclear receptor signalling.

molecular biology↗

bioRxiv2026

Divergent Pathogenic PR-DUB Complex Variants Converge Functionally Via PRC2 Displacement From Chromatin

The PR-DUB complex is responsible for erasing the repressive histone modification, H2AK119ub1. ASXL1-3 proteins are mutually exclusive catalytic partners of BAP1 in the PR-DUB complex. Somatic heterozygous ASXL1-3 variants are associated with cancer, including myeloid malignancies, while de novo germline variants cause neurodevelopmental disorders such as Bohring-Opitz syndrome. These pathogenic variants are almost exclusively nonsense and frameshift and have been proposed to act as gain-of-function. However, the precise catalytic impact and mechanism of variant ASXL1-3 remains elusive. Using an isogenic embryonic stem cell model we have discovered that ASXL1 BOS variants drive reductions - but not global ablations - in H2AK119ub1, consistent with gain-of-function. This catalytic change occurs through the production of a truncated ASXL1 protein with enhanced stability. Hyper-stabilised ASXL1 drives a stoichiometric shift in PR-DUB assembly away from ASXL2 complexes. The drop in H2AK119ub1 levels ultimately reduces PRC2 binding and H3K27me3 deposition. Surprisingly, this phenotype is shared across PR-DUB loss-of-function models and indeed is emerging as a common phenotype across genetically and mechanistically distinct Polycomb-related chromatinopathies.

genetics↗

bioRxiv2026

Whole-genome pre-amplification as a viable approach for genomic screening of FFPE-derived DNA samples

Whole-genome sequencing (WGS) enables comprehensive analysis of tumour genomes, but its use in formalin-fixed paraffin-embedded (FFPE) samples is limited by DNA fragmentation and low yields. Whole-genome amplification (WGA) methods such as multiple displacement amplification (MDA) can boost DNA availability but distort copy-number alteration (CNA) profiles. DNA ligation-mediated MDA (DLMDA) mitigates this bias by reconstituting fragmented templates, yet its performance in FFPE-derived DNA remains uncertain. We compared paired DLMDA pre-amplified (2h, 8h) and non-pre-amplified FFPE prostate tumour samples from 22 archival blocks (5, 15 and 20 years old). DLMDA increased DNA yield by 42- to 86-fold, with global CNA patterns largely preserved. However, DLMDA significantly reduced the number of detected CNA deletions and amplifications. These effects were independent of both block age and reaction time. CNA dropouts were randomly distributed across the genome, indicating that DLMDA does not introduce regional bias. Our results show that DLMDA enables robust DNA yield recovery and avoids false-positive CNA artefacts, but at the cost of reduced CNA sensitivity. While suitable for CNA screening pipelines through WGS, further improvements are required to minimise the false-negative risk and improve the techniques sensitivity for FFPE-based genomics.

molecular biology↗

bioRxiv2026

The historical domestication of a Clostridium botulinum strain used for the industrial production of botulinum neurotoxin

Laboratory production of botulinum neurotoxin (BoNT) began more than 90 years ago for medical, military, and later pharmaceutical applications, creating one of the longest-running examples of microbial cultivation under sustained human control. A single Clostridium botulinum Group I lineage, Army Hall A (AHA), was established by the U.S. military in 1942 and later gave rise to Hall A-hyper (HAH), the strain widely used for pharmaceutical BoNT production. We analyzed more than 1,000 C. botulinum genomes to identify AHAs closest relatives and to infer the most recent common ancestor (MRCA) shared with its nearest wild lineage. Relative to this MRCA, AHA accumulated nearly 100 genetic changes, including 46 single-nucleotide substitutions, 44 small insertions or deletions, and several large deletions and structural variants that led to the loss of more than 80 genes. A nonsense mutation in mutS generated a hypermutator phenotype that accelerated mutation rates and increased genetic diversity. This event occurred early in the lineages domestication and appears to have facilitated laboratory-adaptive traits, including the lack of sporulation and increased BoNT yield. Competition experiments under standard growth conditions confirmed substantial laboratory adaptation, with AHA exhibiting a strong fitness advantage over a close wild relative. Together, these results reconstruct the genomic trajectory of a bacterium evolving under prolonged human-mediated selection and provide a genome-resolved example of microbial domestication. The findings show how laboratory conditions, industrial selection, and changing mutation rates can jointly shape bacterial evolution, and they offer a general framework for understanding domestication and laboratory adaptation across microbial systems. SignificanceHuman-mediated species domestication has been central to the development of civilization, with well-known examples in plants and animals. Microbes have also been domesticated, often unintentionally and before the advent of modern microbiology. The military and pharmaceutical applications of botulinum neurotoxin led to the sustained cultivation and eventual domestication of a high toxin-producing Clostridium botulinum strain that remains widely used today. We reconstruct the genomic changes along this trajectory and identify a key early mutation that generated a hypermutator phenotype, increasing genetic variation available for human-directed selection. These findings reveal fundamental evolutionary processes shaping bacterial genomes under long-term human control. This genome-resolved example of microbial domestication offers a general framework for understanding laboratory adaptation in both evolutionary and applied microbiology.

microbiology↗

bioRxiv2026

Microbiological Survey of the San Pedro Basin Subseafloor

Marine subseafloor sediments host extensive microbial communities that drive global biogeochemical processes. Despite its proximity to one of the most densely populated and economically important coastal regions in the world, the sub benthic ecology of the San Pedro Channel, the waterway separating Los Angeles County from Santa Catalina Island, remains largely uncharacterized. To establish the foundational knowledge required for future impact assessment studies, we initiated a sediment coring survey that generated a water and sediment depth standardized transect across the sloping flanks of the San Pedro Basin. Here, we describe the early development of an integrated subseafloor microbiological catalogue for this region of intense maritime activity incorporating molecular ecology, microbial isolation and cultivation, and physiological assays. This initial effort is designed not as a direct comparison between basin flanks, but as a baseline assessment that captures ecological and microbiological variation across paired sides matched in water column depth and sediment depth beneath seafloor. Accordingly, we provide a cross channel coordinated dataset of subseafloor microbial communities and cultivated representatives from San Pedro Basin sediment, offering a critical starting point for understanding natural variability and for detecting potential signatures of environmental or anthropogenic disturbance. Ultimately, this baseline will support long{square}term monitoring efforts and supply a curated collection of isolates for future experimental microbiology and comparative genomics research.

ecology↗

bioRxiv2025

Early intervention with a PACAP lactoside following repetitive mild traumatic brain injury prevents persistent LHb hyperactivity and motivational deficits in male mice

Mild traumatic brain injury (mTBI) often leads to long-lasting mood disorders and motivational deficits, significantly decreasing quality of life. The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) has known neuroprotective effects and is often deficient in neurological conditions, but its role in preventing mTBI's long-term effects on mood circuits remains unclear. Our previous studies of repetitive closed-head mTBI in murine models found that the lateral habenula (LHb) is a key area for post-injury impairments. These impairments are characterized by mTBI-induced LHb hyperactivity and mood-related behavioral deficits. Here we investigated if a novel PACAP type I receptor (PAC1R) agonist, TES2320, could prevent or treat these long-term mTBI effects. The drug is based on a truncated glycoside analogue of PACAP that is stable and brain penetrant. Using RNAscope, we first found that mTBI caused a persistent and widespread reduction in PACAP mRNA within the LHb, suggesting a possible mTBI-related PACAP signaling deficiency in LHb circuits. We then used two intervention strategies in young adult male mice: an early intervention administered immediately after injury and a late intervention given as a single injection one-month post-injury. One month after injury, we measured LHb activity and self-care grooming motivation. Both early and late PAC1 agonist interventions almost completely normalized the mTBI-induced increases in LHb spontaneous tonic activity and hyperexcitability. However, only the early intervention improved the delayed initiation of grooming seen in mTBI mice. Unfortunately, a single late PAC1R agonist injection not only failed to reverse the grooming delay, but also significantly reduced total grooming behavior 24 hours after treatment. This finding points to a potential behavioral side effect of late PAC1R agonist administration on grooming. Overall, our findings confirm that an early PAC1R agonist intervention effectively prevents mTBI-induced LHb hyperactivity and associated motivational deficits, likely by restoring the persistent PACAP signaling deficiency in the LHb and its related circuits. This preclinical study provides strong evidence that novel PAC1R agonists could be a valuable preventive therapy for mTBI-related depression and anti-reward circuit dysfunction.

neuroscience↗

bioRxiv2025

Nesting behaviour drives the evolution of heat tolerance and climate vulnerability in bees

Species vulnerability to climate change depends in part on their capacity to evolve in response to increasing heat1. Within terrestrial ectotherms, heat tolerance generally corresponds weakly to current climates, which has led many to conclude that this trait is evolutionarily constrained2-4. However, most studies have not accounted for the role of microclimates, potentially obscuring signals of local adaptation. We examined heat tolerance in 95 species of wild bees that varied in nesting behaviour across the latitudinal extent of Australia. Species nest (ground, wooden cavities, or plant stems) micro-climate temperatures predicted heat tolerance evolution, where stem nesters evolved the highest heat tolerances, and ground nesters evolved the lowest heat tolerances due to their ability to evade extreme heat. A moderate level of phylogenetic inertia in heat tolerance was explained by patterns of related species sharing nesting behaviours. This indicated repeated adaptive evolution of similar heat tolerances, rather than strong evolutionary constraints on heat tolerance. Finally, incorporating nesting behaviour into assessments of climate change vulnerability changed the rank order of which species were most at risk. This underscores the need to understand what drives the evolution of heat tolerance across species to better identify the taxa most at risk to climate change.

ecology↗

bioRxiv2025

Optimal TELSAM-Target Protein Linker Character is TargetProtein-Dependent

Fusing a variant of the sterile alpha motif domain of the human translocation ETS leukaemia protein (TELSAM) to a protein of interest has been shown to significantly enhance crystallization propensity. TELSAM is a pH-dependent, polymer-forming protein crystallization chaperone which, when covalently fused to a protein of interest, forms a stable, well-ordered crystal lattice. However, despite its success, a challenge persists in that crystal quality and diffraction limits appear to be heavily dependent on the choice of linker between TELSAM and the protein of interest, with identification of a functional linker relying on trial-and-error methods. Likewise, previous studies revealed that the 10xHis tag at the TELSAM N-terminus can either facilitate or hinder the ordered crystallization of target proteins attached via flexible or semi-flexible linkers. To address these challenges, we designed multiple constructs with several types of linkers--rigid (helical fusion), semi-flexible (Pro-Alan), and flexible (poly-Gly)--of varying lengths to fuse a designed ankyrin repeat protein (DARPin) to the TELSAM C-terminus. Semi-flexible and flexible linker constructs were made with and without the 10xHis tag. Our findings indicate that short semi-flexible and rigid linkers consistently yield large crystals within 24 hours with a DARPin target protein, but that flexible linkers perform best with a TNK1 UBA domain target protein. Removing the 10xHis tag enhanced crystallization rates, improved crystal morphology, and increased the crystallization propensity of semi-flexible and flexible linker constructs. While removing the His tag did not have a significant effect on crystal size, it improved the diffraction limits and crystal quality of the 1TEL-PA-DARPin construct. These results suggest that the ideal linker selection primarily depends on the properties of the target protein. Our data support the recommendation to use a short yet flexible or semi-flexible linker between TELSAM and the target protein to facilitate protein crystallization and high-resolution structure determination. SynopsisIn this study, we examine the effect of short to medium-length flexible, semi-flexible, and rigid linkers on the crystallization of a DARPin fused to the 1TEL protein crystallization chaperone, demonstrating that while rigid linkers impair crystallization and reduce diffraction quality, the ideal linker character remain target-protein dependent. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/672704v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@b90d1org.highwire.dtl.DTLVardef@1508e7dorg.highwire.dtl.DTLVardef@1baf0d1org.highwire.dtl.DTLVardef@1843df_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

Electron cryomicroscopy (cryo-EM) allows high-resolution spatial visualization of biological specimens, however, it is challenging to chemically identify densities observed in cryo-EM. To overcome this, we combined cryo-EM with chemical imaging using focused ion beam secondary ion mass spectrometry (FIB-SIMS) for integrated spatio-chemical analysis of untagged specimens. We show that our correlative workflow permits sub-cellular localisation of molecules inside bacterial cells and is compatible with cryogenic light microscopy and FIB-milled lamellae of multicellular specimens. To highlight biological insights enabled by the workflow, we studied the uptake of Bisphenol-AF, a widespread chemical pollutant, by environmental bacteria, revealing the storage of these chemicals within cytosolic phase-separated aggregates in pollutant-exposed cells, where they cannot be removed by the bacterial efflux machinery despite its robust upregulation. These mechanistic insights were directly facilitated by the versatile cryo-EM-FIB-SIMS technique, showing that it is an effective avenue to map elemental and molecular signatures in near-native biological samples, which can be extended in the future for multiple applications in cell biology and imaging.

molecular biology↗

bioRxiv2025

An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome

Deciphering the regulatory syntax of the genome is essential to understand the genetic and molecular architecture of complex traits, as most trait-associated variants lie in non-coding regions. Yet, functional annotation of the bovine genome remains limited, hindering our ability to unravel the mechanisms underpinning complex traits of economic and ecological importance in cattle. Here, we present a comprehensive epigenetic atlas comprising 1,138 genome-wide epigenetic profiles, including chromatin accessibility, six histone modifications, CCCTC-binding factor (CTCF) transcription factor binding, DNA methylation, chromatin conformation, and transcriptomes across 53 adult tissues, five fetal tissues, and seven primary cell types. This atlas-level data enables us to annotate around 45% of the genome as putative regulatory elements exhibiting tissue- or cell-specific regulatory activity. Leveraging sequence-to-function deep learning models, we discovered 301 sequence motifs and predicted the functional impact of genetic variants through in silico mutagenesis, thereby facilitating the decoding of the regulatory syntax of the cattle genome and fine-mapping of GWAS loci for 22 complex traits. Cross-species analysis further revealed evolutionarily conserved features of regulatory architecture and provided evolutionary insights into complex traits and diseases in humans. Together, this atlas offers a foundational resource for advancing cattle functional genomics, sustainable breeding, and studies of regulatory evolution.

genomics↗

bioRxiv2025

Structural variants are enriched in deleterious visible phenotypes in Drosophila

Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore long reads. These assemblies enabled the creation of a pangenome graph containing comprehensive, nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncovered new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, we mapped the tarsal joint defect AblpeyD to an 8 kb Roo retrotransposon insertion into an intergenic enhancer, a finding validated via CRISPR-Cas9. The wing vein phenotype plexus (px1) was linked to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c1) wing phenotype was linked to a 7.5 kb DM412 retrotransposon inserted into the coding sequence of the muscle protein gene Strn-Mlck. We also unveiled 8 SV alleles of previously identified causal genes, including previously uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of the genes causing phenotypic changes harbored candidate SVs over 100 bp, whereas only 28% is expected based on euchromatic SVs. Our data, based on the 50 Drosophila phenotypes, 44 of which are strongly deleterious, suggests a disproportionately larger contribution of SVs to deleterious changes in visible phenotypes in Drosophila.

genomics↗

bioRxiv2025

Protective efficacy of mutant strains of Borrelia burgdorferi as potential reservoir host-targeted biologics against Lyme disease

Lyme disease (LD), caused by Borrelia burgdorferi (Bb), is the most common vector-borne disease in the United States. Novel strategies to control transmission of Bb to humans via ticks are critical for prevention of LD. One such strategy is to leverage non-infectious mutant strains of Bb for pathogen-derived biologics to block Bb transmission during the natural infectious cycle. Deletion of Borrelia host-adaptation Regulator ({Delta}badR) and replacement of 8 conserved residues with alanines in Carbon Storage Regulator A of Bb (8S) resulted in mutants, with upregulation of RpoS and several immunogenic lipoproteins, that were incapable of colonization in C3H/HeN mice. Intradermal vaccination of mice with the live mutant strains resulted in significant anti-borrelial antibody responses and a reduction in Bb acquisition by naive Ixodes scapularis larvae following needle challenge with Bb B31-A3. While vaccination with {Delta}badR mutant conferred significant reduction in the percentage of infected mice, ML23 and 8S mutants conferred variable levels of protection. Comparative proteomic analysis of Purified Borrelial Lipoproteins (PBLs) from parental and mutant strains revealed similar and unique antigenic components. Infection derived mouse serum and serum from Lyme disease patients exhibited reactivity to lysates and PBLs from these mutants. Immunization with PBLs from B31-A3 and 8S strains conferred significant protection against challenge with Bb infected nymphs, underscoring the utility of PBLs as protective formulations. Overall, non-infectious mutant strains, or their lipoproteins, can be exploited as biologics to block the acquisition of Bb by naive larvae from reservoir hosts, disrupting the enzootic transmission cycle of the agent of Lyme disease.

microbiology↗

bioRxiv2025

Hypoxia-induced extracellular matrix changes are conserved in cancer and directly impact radiotherapy benefit

Our overarching aim was to determine how hypoxia affects the extracellular matrix (ECM). Transcriptomic analysis (21,941 patients; 10 cancer types) identified ECM remodelling as the predominant pathway affected by hypoxia. Multi-omics confirmed that hypoxia impacts ECM organisation and collagen degradation; 53 ECM genes were affected, of which 74% were HIF1/HIF2-regulated. Spatial transcriptomics highlighted different hypoxia remodelling processes in tumour and stroma. Five ECM genes commonly affected in tumour and in vitro constituted a signature. This signature was independently prognostic and independently predictive of radiotherapy benefit in multiple malignancies. Patients within either high or low hypoxic-ECM score tertiles benefited from radiotherapy versus surgery. Hypoxic ECMs generated in vitro increased adhesion and decreased migration of cancer cells, an effect enhanced by irradiation. Immunofluorescence demonstrated that hypoxia decreased collagen fibre number, and irradiation decreased cell-ECM interactions. Taken together, these findings demonstrate hypoxia induces pan-cancer ECM changes, directly impacting radiotherapy benefit.

cancer biology↗

bioRxiv2024

Off-purpose activity of industrial and agricultural chemicals against human gut bacteria

Contamination by industrial and agricultural chemicals like pesticides are a cause of great concern due to the risk to human and environmental health. While these chemicals are often considered to have restricted activity and are labelled as such, there are concerns over a broader toxicity range. Here we report the impact of 1076 pollutants spanning diverse chemistries and indicated applications on 22 prevalent commensal gut bacteria. Our systematic investigation uncovered 588 interactions involving 168 chemicals, the majority of which were not previously reported to have antibacterial properties. Fungicides and industrial chemicals showed the largest impact with circa 30% exhibiting anti-commensal properties. We find that the sensitivity to chemical pollutants across species surprisingly correlates with that to human-targeted drugs, suggesting common susceptibility mechanisms. Using a genome-wide chemical-genetic screen, we identified membrane transport and fatty acid metabolism as major modulators of the off-target toxicity of chemicals. Mutants exhibiting chemical resistance include those defective in producing human-health-relevant metabolites like branched short-chain fatty acids, indicating that chronic exposure could lead to selection against production of beneficial metabolites. Toxicokinetic modelling suggested gut bacteria could be used as more sensitive in vitro toxicity indicators for chemicals of concern than animal models. Together, our data uncovers the off-target activity of industrial and agricultural chemicals with widespread exposure against human gut bacteria. Impact on the structure and function of the microbiota should therefore be considered in assessing chemical safety.

microbiology↗

bioRxiv2024

Ecological fNIRS in mobile children: Using short separation channels to correct for systemic contamination during naturalistic neuroimaging.

AbstractO_ST_ABSSignificanceC_ST_ABSThe advances and the miniaturization in functional Near Infrared Spectroscopy (fNIRS) instrumentation offers the potential to move the classical laboratory-based cognitive neuroscience investigations into more naturalistic settings. Wearable and mobile fNIRS devices also provide a novel child-friendly means to image functional brain activity in freely moving toddlers and preschoolers. Measuring brain activity in more ecologically valid settings with fNIRS presents additional challenges, such as the increased impact of physiological interferences. One of the most popular methods to minimize such interferences is to regress out short separation channels from the long separation channels (i.e., superficial signal regression or SSR). Whilst this has been extensively investigated in adults, little is known about the impact of systemic changes on the fNIRS signals recorded in children in either classical or novel naturalistic experiments. AimWe aim to investigate if extracerebral physiological changes occur in toddlers and preschoolers, and whether SSR can help minimize these interferences. ApproachWe collected fNIRS data from 3-to-7 years olds during a conventional computerized static task and in a dynamic naturalistic task in an immersive virtual reality (VR) continuous automatic virtual environment (CAVE). ResultsOur results show that superficial signal contamination data is present in both young children as in adults. Importantly, we find that SSR helps in improving the localization of functional brain activity, both in the computerized task and, to a larger extent, in the dynamic VR task. ConclusionsFollowing from these results, we formulate suggestions to advance the field of developmental neuroimaging with fNIRS, particularly in ecological settings.

neuroscience↗

bioRxiv2024

Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex

Bacterial conjugation is a process by which DNA is transferred unidirectionally from a donor cell to a recipient cell. It is the main means by which antibiotics resistance genes spread among bacterial populations. It is crucially dependent upon the elaboration of an extracellular appendage, termed "pilus", by a large double-membrane spanning secretion system termed conjugative "type IV secretion system". Here we present the structure of the conjugative pilus encoded by the R388 plasmid. We demonstrate that, as opposed to all conjugative pili produced so far for cryo-EM structure determination, that encoded by the R388 plasmid is greatly stimulated by the presence of recipient cells. Comparison of its cryo-EM structure with existing conjugative pilus structures highlights a number of important differences between the R388 pilus structure and that of its homologues, the most prominent being the highly distinctive conformation of its bound lipid.

microbiology↗