Biology subjects

Smith, H. J.

Publications and source records attributed to Smith, H. J..

12 recordsLinked to original sources

bioRxiv2026

Single-probe, amplification-free multiplex mRNA PNA-FISH maps bacterial gene expression in intact three-dimensional biofilms

Biofilms are spatially structured communities in which local microenvironments drive physiological differentiation, yet mapping gene expression inside intact three-dimensional biofilms remains challenging. Bacterial spatial transcriptomics methods typically rely on tiled probe sets, sequential hybridization rounds, or signal amplification. Here, we show that a single short, directly labelled peptide nucleic acid (PNA) probe per target is sufficient to quantify bacterial mRNA in situ without amplification. With all probes designed for a common hybridization condition, a transcript panel is resolved in one hybridization on a standard confocal microscope, in unmodified cells while preserving biofilm architecture. Benchmarked against the biphasic cycle of Legionella pneumophila, multiplex mRNA PNA-FISH recovers the expected transcriptional switch and agrees quantitatively with RT-qPCR in planktonic and biofilm populations. In flow-cell biofilms, it shows that sessile populations do not recapitulate the planktonic program and that transcriptional differences follow cellular aggregation state rather than depth.

molecular biology↗

bioRxiv2026

Neural correlates of novel word-form learning in developmental language disorder

Children with developmental language disorder (DLD) have persistent language learning difficulties and often perform poorly on pseudoword repetition, a task that probes phonological, memory, and speech-motor processes that support vocabulary acquisition. Research on the neural basis of pseudoword repetition in DLD is limited. We used whole-brain functional MRI (fMRI) to examine pseudoword repetition and repetition-based learning in 46 children with DLD (ages 10-15 years) and 71 age-matched children with typical language development. During scanning, children heard and repeated pseudowords paired with visual referents, allowing us to track learning-related changes in neural activity across repetitions. Repeated pseudoword production yielded comparable behavioural learning across groups, with faster productions by later repetitions. Post-scan, form-referent recognition was comparable across groups, whereas pseudoword repetition accuracy was lower in DLD. Pseudoword repetition engaged a distributed neural network, including inferior frontal cortex bilaterally (greater on the left), premotor and sensorimotor cortex, and posterior temporal and occipital regions. Group differences emerged primarily in regions where activity was task negative (i.e., below baseline or deactivated): lateral occipito-parietal cortex (posterior angular gyrus), medial parieto-occipital cortex (retrosplenial), and right posterior cingulate cortex. Learning-related decreases in activity were similar across groups, but region-of-interest analyses showed reduced leftward lateralisation of activity in inferior frontal gyrus in DLD. These findings suggest weaker disengagement of the default mode network during a linguistically demanding task in DLD. Although repetition-based pseudoword learning recruited similar neural mechanisms in both groups, these mechanisms may operate less efficiently in DLD, alongside reduced hemispheric specialisation in inferior frontal cortex. HighlightsO_LISimilar repetition-related neural attenuation across groups during pseudoword learning. C_LIO_LIReduced default-mode network suppression during pseudoword repetition in DLD. C_LIO_LIReduced left-hemisphere specialisation of inferior frontal cortex in DLD. C_LIO_LIRepetition-based learning in DLD supported by less efficient neural networks. C_LI

neuroscience↗

bioRxiv2023

Mixed Waste Contamination Selects for a Mobile Genetic Element Population Enriched in Multiple Heavy Metal Resistance Genes

Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal contaminated regions of the Oak Ridge Reservation (ORR) subsurface. This meta-mobilome was compared to one derived from samples collected from unimpacted regions of the ORR subsurface. We assembled 1,615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

microbiology↗

bioRxiv2023

Differences in cortical surface area in developmental language disorder

Approximately seven per cent of children have developmental language disorder (DLD), a neurodevelopmental condition associated with persistent language learning difficulties without a known cause. Our understanding of the neurobiological basis of DLD is limited. Here, we used FreeSurfer to investigate cortical surface area and thickness in 54 children and adolescents with DLD and 74 age-matched controls aged 10-16 years. We also examined cortical asymmetries in DLD using an automated surface-based technique. Those with DLD showed smaller surface area bilaterally in the inferior frontal gyrus extending to the anterior insula, in the posterior temporal and ventral occipito-temporal cortex, and in portions of the anterior cingulate and superior frontal cortex. There were no differences in cortical thickness, nor in asymmetry of these cortical metrics. Post-hoc exploratory analyses revealed that surface area in the left fusiform and inferior frontal cortex related to childrens reading and non-word repetition scores, respectively. This study highlights the importance of distinguishing between surface area and cortical thickness in investigating the brain basis of neurodevelopmental disorders and suggests the development of cortical surface area to be of importance to DLD. Future longitudinal studies are required to understand the developmental trajectory of these cortical differences in DLD and how they relate to language maturation.

neuroscience↗

bioRxiv2023

Microstructural Properties of the Cerebellar Peduncles in Children with Developmental Language Disorder

Children with developmental language disorder (DLD) struggle to learn their native language for no apparent reason. While research on the neurobiological underpinnings of the disorder has focused on the role of cortico-striatal systems, little is known about the role of the cerebellum in DLD. Cortico-cerebellar circuits might be involved in the disorder as they contribute to complex sensorimotor skill learning, including the acquisition of spoken language. Here, we used diffusion-weighted imaging data from 77 typically developing and 54 children with DLD and performed probabilistic tractography to identify the cerebellums white matter tracts: the inferior, middle, and superior cerebellar peduncles. Children with DLD showed lower fractional anisotropy (FA) in the inferior cerebellar peduncles (ICP), fiber tracts that carry motor and sensory input via the inferior olive to the cerebellum. Lower FA in DLD was driven by lower axial diffusivity. Probing this further with more sophisticated modeling of diffusion data, we found higher orientation dispersion but no difference in neurite density in the ICP of DLD. Reduced FA is therefore unlikely to be reflecting microstructural differences in myelination in this tract, rather the organization of axons in these pathways is disrupted. ICP microstructure was not associated with language or motor coordination performance in our sample. We also found no differences in the middle and superior peduncles, the main pathways connecting the cerebellum with the cortex. To conclude, it is not cortico-cerebellar but atypical olivocerebellar white matter connections that characterize DLD and suggest the involvement of the olivocerebellar system in speech acquisition and development.

neuroscience↗

bioRxiv2022

Antimicrobial resistance and virulence characteristics of Klebsiella pneumoniae isolates in Kenya

Klebsiella pneumoniae is a globally significant opportunistic pathogen causing healthcare-associated and community-acquired infections. This study examined the epidemiology and the distribution of resistance and virulence genes in clinical K. pneumoniae strains in Kenya. Eighty-nine K. pneumoniae isolates were collected over six years from five counties in Kenya and were analyzed using whole genome sequencing and bioinformatics. These isolates were obtained from community-acquired (62/89) and healthcare-associated infections (21/89), and the hospital environment (6/89). Genetic analysis revealed the presence of blaNDM-1 and blaOXA-181 carbapenemase genes and the armA and rmtF genes known to confer pan-aminoglycoside resistance. The most abundant extended-spectrum beta-lactamase genes identified were blaCTX-M-15 (36/89), blaTEM (35/89), and blaOXA (18/89). In addition, one isolate had a mobile colistin resistance gene (mcr-8). Fluoroquinolone resistance-conferring mutations in gyrA and parC genes were also observed. The most notable virulence factors were those associated with hyper-virulence (rmpA/A2 and magA), yersiniabactin (ybt), salmochelin (iro), and aerobactin (iuc and iutA). Thirty-eight distinct sequence types were identified, including known global lineages ST14, ST15, ST147, and ST307, and a regional clone ST17 implicated in regional outbreaks. In addition, this study genetically characterized two potential hypervirulent isolates and two community-acquired ST147 high-risk clones that contained carbapenemase genes, yersiniabactin, and other multidrug resistance genes. These results demonstrate that the resistome and virulome of Kenyan clinical and hospital environmental K. pneumoniae isolates are diverse. The reservoir of high risk-clones capable of spreading resistance and virulence factors have the potential to cause unmanageable infection outbreaks with high morbidity and mortality. AUTHOR SUMMARYKlebsiella pneumoniae is one of the human-disease-causing bacteria that easily acquires and spreads antibiotic resistance genes and is thus a serious threat to human health. We studied both the antibiotic resistance genes and the genes it uses to cause disease (virulence). Forty-two percent of our isolates were multidrug resistant (MDR). They carried several resistance and virulence genes bound in mobile circular DNA molecules called plasmids which easily migrate and spread the genes between bacteria. We identified 38 distinct K. pneumoniae strains (STs) distributed within the study sites. Fifteen isolates were classified under the groups of K. pneumoniae strains known to cause global infection outbreaks such as ST14, ST15 and ST147 collected from Nairobi and Kisumu, hotspot areas for spread of resistance. In particular, two ST147 isolates were resistant to carbapenems and one isolate to colistin, which are last line antibiotics. We also identified two isolates with the potential to cause high levels of disease. We concluded that the presence of highly resistant and virulent strains in the hospital and community demonstrates a need for the continuous monitoring and management of MDR K. pneumoniae infections to prevent disease outbreaks that are difficult to control and that lead to high death rate.

microbiology↗

bioRxiv2021

Efficacy of longevity interventions in C. elegans is determined by early life activity of RNA splicing factors

Geroscience aims to target the aging process to extend healthspan. However, even isogenic individuals show heterogeneity in natural aging rate and responsiveness to pro-longevity interventions, limiting translational potential. Using in vivo mini gene reporters in isogenic C. elegans, we show that alternative splicing of mRNAs related to lipid metabolism in young animals is coupled to subsequent life expectancy. Further, activity of RNA splicing factors REPO-1 and SFA-1 early in life modulates effectiveness of specific longevity interventions via POD-2/ACC1 and regulation of lipid utilization. In addition, early inhibition of REPO-1 renders animals refractory to late onset suppression of the TORC1 pathway. Together these data suggest that activity of RNA splicing factors and the metabolic landscape early in life can modulate responsiveness to longevity interventions and may explain variance in efficacy between individuals. One Sentence SummaryEfficacy of pro-longevity interventions in C. elegans is determined by the activity of splicing factors and the lipid metabolic landscape early in the life of the individual.

genetics↗

bioRxiv2021

Quantitative MRI reveals differences in striatal myelin in children with DLD

AbstractDevelopmental Language Disorder (DLD) is a common neurodevelopmental disorder characterised by receptive or expressive language difficulties or both. While theoretical frameworks and empirical studies support the idea that there may be neural correlates of DLD in frontostriatal loops, findings are inconsistent across studies. Here, we use a novel semiquantitative imaging protocol - multiparameter mapping (MPM) - to investigate microstructural neural differences in children with DLD. The MPM protocol allows us to reproducibly map specific indices of tissue microstructure. In 56 typically developing children and 33 children with DLD, we derived maps of: 1) longitudinal relaxation rate R1 (1/T1); 2) the transverse relaxation rate R2* (1/T2*); and 3) Magnetization Transfer Saturation (MTsat). R1 and MTsat predominantly index myelin, while R2* is sensitive to iron content. Children with DLD showed reductions in MTsat values in the caudate nucleus bilaterally, as well as in the left ventral sensorimotor cortex and Heschls gyrus. They also had globally lower R1 values. No group differences were noted in R2* maps. Differences in MTsat and R1 were coincident in the caudate nucleus bilaterally. These findings support our hypothesis of corticostriatal abnormalities in DLD and indicate abnormal levels of myelin in the dorsal striatum in children with DLD.

neuroscience↗

bioRxiv2021

Subsurface Hydrocarbon Degradation Strategies in Low- and High-Sulfate Coal Seam Communities Identified with Activity-Based Metagenomics

Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways were observed but with a predominance of aerobic dioxygenases. The putative low-molecular weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study--subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes--offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon. One Sentence SummaryIdentifying hydrocarbon degradation strategies across different redox conditions via metagenomic analysis of environmental and translationally active (BONCAT-FACS) samples from subsurface coal beds.

microbiology↗

bioRxiv2021

Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction in C. elegans

One of the most robust and reproducible methods to prolong lifespan in a variety of organisms is inhibition of the mTORC1 (mechanistic target of rapamycin complex 1) pathway. mTORC1 is a metabolic sensor that promotes anabolic growth when nutrients are abundant. Inhibition of mTORC1 extends lifespan, but also frequently has other effects such as stunted growth, slowed development, reduced fertility, and disrupted metabolism. It has long been assumed that suppression of anabolism and resulting phenotypes such as impaired growth and reproduction may be causal to mTORC1 longevity, but this hypothesis has not been directly tested. RAGA-1 is an upstream activator of TORC1. Previous work from our lab using a C. elegans model of mTORC1 longevity, the long-lived raga-1 null mutant, found that the presence of raga-1 only in the neurons suppresses longevity of the null mutant. Here, we use the auxin-inducible degradation (AID) system to test whether neuronal mTORC1 inhibition is sufficient for longevity, and whether any changes in lifespan are also linked to stunted growth or fertility. We find that life-long AID of RAGA-1 either in all somatic tissue or only in the neurons of C. elegans is sufficient to extend lifespan. We also find that AID of RAGA-1 or LET-363/mTOR beginning at day 1 of adulthood extends lifespan to a similar extent. Unlike somatic degradation of RAGA-1, neuronal degradation of RAGA-1 doesnt impair growth, slow development, or decrease the reproductive capacity of the worms. Lastly, while AID of LET-363/mTOR in all somatic cells shortens lifespan, neuronal AID of LET-363/mTOR slows aging. This work demonstrates that targeting mTORC1 specifically in the neurons uncouples longevity from growth and reproductive impairments, challenging previously held ideas about the mechanisms of mTORC1 longevity and elucidating the promise of tissue-specific aging therapeutics.

genetics↗

bioRxiv2019

Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated environments. To provide site assessment for a larger study, we processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater from the ENIGMA Field Research Site at the United States Department of Energy (DOE) Oak Ridge Reservation (ORR). We compared fresh core sediments by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including contaminants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. This environmental systems approach provided detailed site-specific biogeochemical information from the various properties of subsurface media to reveal the influences of solid, liquid, and gas phases. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate- reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. This suggested that groundwater predominantly flowed through preferential paths with high flux and little mixing with water in the interstices of sediment particles, which could impact microbial activity. The abundant clay minerals with high surface area and high water-holding capacity of micro-pores of the fine clay rich layer suggest suppression of nutrient supply to microbes from the surface. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of highly toxic elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.

systems biology↗

bioRxiv2017

Cortico-Cerebellar Networks Drive Sensorimotor Learning in Speech

The motor cortex and cerebellum are thought to be critical for learning and maintaining motor behaviours. Here we use tDCS to test the role of the motor cortex and cerebellum in sensorimotor learning in speech. During productions of head, bed, and dead, the first formant of the vowel sound was altered in real-time towards the first formant of the vowel sound in had, bad, and dad. Compensatory changes in first and second formant production were used as a measure of motor adaptation. TDCS to either the motor cortex or the cerebellum improved sensorimotor learning in speech compared to sham stimulation. However, in the case of cerebellar tDCS, production changes were restricted to the source of the acoustical error (i.e. the first formant). Motor cortex tDCS drove production changes that offset errors in the first formant, but, unlike cerebellar tDCS, adaptive changes in the second formant also occurred. The results suggest that motor cortex and cerebellar tDCS have both shared and dissociable effects on motor adaptation. The study provides initial causal evidence in speech production that the motor cortex and the cerebellum support different aspects of sensorimotor learning. We propose that motor cortex tDCS drives sensorimotor learning towards previously learned patterns of movement, while cerebellar tDCS focuses sensorimotor learning on error correction.

neuroscience↗