Biology subjects

Copeland, A.

Publications and source records attributed to Copeland, A..

14 recordsLinked to original sources

bioRxiv2026

Cortical gray matter density at age five associated with preceding early longitudinal language profiles: A Voxel-based morphometry analysis of the FinnBrain Birth Cohort Study

Previous studies exploring the connection between early language development and brain anatomy have shown that cortical areas relating to individual differences in language skills are diverse and vary depending on the age of child. However, due to lack of large longitudinal samples, current literature is limited in answering the extent to which individual differences in language development prior to school age are reflected in areas of the cortex. To fill this gap, we compared gray matter density between participants that belonged to different longitudinally defined language profiles from 14 months to five years of age in a large population-based sample. Participants were 166 children from the FinnBrain Birth Cohort Study who had longitudinal language data from 14 months to five years of age and magnetic resonance imaging data at five years of age. Three groups of language development were used as per our prior study: persistent low, stable average, and stable high. Voxel-based morphometry metrics were calculated using SPM12 and the three language profile groups were compared to one another. Covariates included sex and age at brain scan. The statistics were thresholded at p < 0.01 and false discovery rate corrected at the cluster level. Of the three longitudinal language profiles, the stable high group had higher gray matter density than the persistent low group in the right superior frontal gyrus. No differences were found between the stable average and stable high groups, nor persistent low and stable average groups. The identified superior frontal cortical area belongs to executive functions neural network. This finding adds to the cumulating evidence that individual differences in language development are reflected in growth of gray matter supporting general processing ability rather than specialized language regions. The results suggest that cognitive development and early language development are linked through shared principles of neural growth, identifiable already at age five. Key pointsO_LIAn association between early language development from 14 months to five years of age and gray matter density differences of the right superior frontal gyrus was found at the age of five years. Children following the strongest language trajectory were more likely to exhibit higher gray matter density of the right superior frontal gyrus than children following the weakest trajectory. C_LIO_LIAs the superior frontal gyrus is part of executive functions network, we propose that individual differences in early language development are more defined by general learning mechanisms supported by those networks, rather than language specific pathways. C_LI

neuroscience↗

bioRxiv2025

Exposure to Maternal Pre- and Postnatal Psychological Distress: Associations with Brain Structure in 5-year-old Children

BackgroundMaternal mental health is an important contributor to child neurodevelopment. While there are multiple studies on prenatal exposure, early postnatal exposure has received little attention in neuroimaging research. Methods5-year-old children (n = 173) were recruited from the FinnBrain Birth Cohort study. Maternal distress was assessed using questionnaires on depressive and anxiety symptoms at 14, 24 and 34 gestational weeks and postnatally at 3, 6 and 24 months. T1-weighted structural images were processed using a voxel-based morphometry pipeline to map associations between maternal distress exposure and regional gray matter (GM) volumes, while accounting for potential confounders. ResultsWe found widespread associations between maternal distress symptoms and offspring brain morphology. Higher prenatal distress at 14 gestational weeks was positively associated with regional GM volume in the right superior parietal lobe and precuneus. In contrast, postnatal distress at 3 months was negatively associated with GM volumes in multiple motor regions, the left anterior insula, right superior frontal areas and supramarginal gyrus. Postnatal distress at 6 months demonstrated a positive relationship with GM volumes in the right calcarine and lingual gyri, while distress at 24 months was negatively associated with GM volumes in the left supramarginal and right superior frontal gyri. ConclusionsThis study provides support for hypotheses proposing that fetal and early life exposure to maternal distress can influence the structural development of the brain. Furthermore, it highlights the role of early postnatal period and calls for further research into this so far overlooked period and pathways that explain the associations.

neuroscience↗

bioRxiv2025

Structural Brain Correlates of Speech Disfluency in Early Childhood: A Dimensional Analysis in a Non-Clinical Cohort

Most neuroimaging studies of speech disfluency have compared individuals who stutter with fluent controls. However, treating speech disfluency as a continuous, dimensional trait offers new insights into the neural basis of fluency during early childhood. This study aimed to investigate whether naturally occurring variation in speech disfluency is associated with grey matter structure in a non-clinical, population-based sample of 5-year-old children. The study included 120 participants (65M, 55F) from the FinnBrain Birth Cohort study. Speech disfluency was evaluated as a continuous measure from audiovisual speech samples, with transcription and analysis conducted using the SALT software. Ambrose & Yairi (1999) classification system was used to categorize speech disfluencies into stuttering-like (SLD) and other disfluency types. T1-weighted images obtained through magnetic resonance imaging were analyzed using voxel-based morphometry (VBM) with the CAT12 toolbox and complemented by surface-based morphometry with FreeSurfer. Whole-brain statistical analysis was employed to examine the association between grey matter metrics and speech disfluency. We found that VBM-derived proportional grey matter volume in the left middle frontal gyrus, left posterior cerebellum, and right superior frontal gyrus was positively associated with speech disfluency, specifically SLD, in children (p <.001; p=.002; p <.001, FDR corrected). No significant associations were found for cortical thickness or surface area. Additionally, no notable sex differences were observed. Our findings suggest that speech disfluency in early childhood is linked to localized structural differences in regions supporting motor planning and cognitive control, without broader changes in cortical thickness or surface area. Importantly, similar brain regions have been implicated in studies comparing children who stutter to those who do not, suggesting that normal variation in disfluency captures meaningful neurobiological differences even in non-clinical populations. This supports the value of treating speech disfluency as a spectrum and underscores the importance of longitudinal, multimodal research to clarify how these structural features evolve and influence later fluency outcomes.

neuroscience↗

bioRxiv2024

Effortful control and cortical brain structure in 5-year-old children: findings from the FinnBrain birth cohort study

The aim of this study was to explore the associations between an aspect of self-regulation (SR), effortful control (EC), and cortical brain structure in 5-year-old children. Efficient EC is a predictor of many attributes and important outcomes in life, such as social-emotional functioning, psychiatric and somatic health, finance, and criminal activity. The early brain correlates of EC are not widely studied, while a better understanding of them would aid in recognizing individuals at risk for maladaptive outcomes. Participants (N = 155) were a part of the FinnBrain Birth Cohort Study in Finland. T1-weighted brain magnetic resonance images were processed using FreeSurfer. The data was statistically analysed with a vertex-wise general linear model. At the age of 5 years, EC and its subscales, Attentional focusing, Inhibitory control (INH), Low intensity pleasure (LIP) and perceptual sensitivity, were assessed via parental report using The Childrens Behaviour Questionnaire. We found positive associations between overall EC and cortical volume in the left superior parietal region and in the right inferior temporal region. We also found positive associations between EC and surface area on the left hemisphere in the superior parietal region. The findings were driven by the EC subscales of INH and LIP with INH linking positively with left surface area and volume, and LIP linking with left cortical volume. We extended the previous literature by shedding light on early structural brain correlates of EC in a large sample of typically developing 5-year-olds. The results differed significantly from previous findings in older children, highlighting the need for longitudinal studies to better understand the neural underpinnings of SR throughout development.

neuroscience↗

bioRxiv2024

Pre- and postnatal maternal depressive symptoms associate with localconnectivity of the left amygdala in 5-year-olds.

BackgroundMaternal depressive symptoms can influence brain development in offspring, prenatally through intrauterine programming, and postnatally through caregiving related mother-child interaction. MethodsThe participants were 5-year-old mother-child dyads from the FinnBrain Birth Cohort Study (N = 68; 28 boys, 40 girls). Maternal depressive symptoms were assessed with the Edinburgh Postnatal Depression Scale (EPDS) at gestational week 24, 3 months, 6 months, and 12 months postnatal. Childrens brain imaging data were acquired with task-free functional magnetic resonance imaging (fMRI) at the age of 5 years in 7 min scans while watching the Inscapes movie. The derived brain metrics included whole brain regional homogeneity (ReHo) and seed-based connectivity maps of the bilateral amygdalae. ResultsWe found that maternal depressive symptoms were positively associated with ReHo values of the left amygdala. The association was highly localised and strongest with the maternal depressive symptoms at three months postnatal. Seed-based connectivity analysis did not reveal associations between distal connectivity of the left amygdala region and maternal depressive symptoms. ConclusionsThese results suggest that maternal depressive symptoms soon after birth may influence offsprings neurodevelopment in the local functional coherence in the left amygdala. They underline the potential relevance of postnatal maternal distress exposure on neurodevelopment that has received much less attention than prenatal exposures. These results offer a possible thus far understudied pathway of intergenerational effects of perinatal depression that should be further explored in future studies.

neuroscience↗

bioRxiv2023

Global Biogeography of the Soil Virosphere

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and comprised of 616,935 uncultivated viral genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

ecology↗

bioRxiv2023

Structural brain correlates of non-verbal cognitive ability in 5-year-old children: findings from the FinnBrain Birth Cohort study

Non-verbal cognitive ability predicts multiple important life outcomes, e.g., school and job performance. It has been associated with parieto-frontal cortical anatomy in prior studies in adult and adolescent populations, while young children have received relatively little attention. We explored the associations between cortical anatomy and non-verbal cognitive ability in 165 5-year-old participants (mean scan age 5.40 years, SD 0.13; 90 males) from the FinnBrain Birth Cohort study. T1-weighted brain magnetic resonance images were processed using FreeSurfer. Non-verbal cognitive ability was measured using the Performance Intelligence Quotient (PIQ) estimated from the Block Design and Matrix Reasoning subtests from the Wechsler Preschool And Primary Scale Of Intelligence (WPPSI-III). In vertex-wise general linear models, PIQ scores associated positively with volumes in left caudal middle frontal and right pericalcarine regions, as well as surface area in left caudal middle frontal, left inferior temporal, and right lingual regions. There were no associations between PIQ and cortical thickness. To the best of our knowledge, this is the first study to examine structural correlates of non-verbal cognitive ability in a large sample of typically developing 5-year-olds. The findings are generally in line with prior findings from older age groups.

neuroscience↗

bioRxiv2023

Sex differences, asymmetry and age-related white matter development in infants and 5-year-olds as assessed with Tract-Based Spatial Statistics

The rapid white matter (WM) maturation of first years of life is followed by slower yet long-lasting development, accompanied by learning of more elaborate skills. By the age of five years, behavioural and cognitive differences between females and males, and functions associated with brain lateralization such as language skills are appearing. Diffusion tensor imaging (DTI) can be used to quantify fractional anisotropy (FA) within the WM and increasing values correspond to advancing brain development. To investigate the normal features of WM development during early childhood, we gathered a DTI data set of 166 healthy infants (mean 3.8 wk, range 2-5wk; 89 males; born on gestational week 36 or later) and 144 healthy children (mean 5.4 years, range 5.1-5.8 years; 76 males). The sex differences, lateralization patterns and age-dependent changes were examined using tractbased spatial statistics (TBSS). In 5-year-olds, females showed higher FA in wide-spread regions in the posterior and the temporal WM and more so in the right hemisphere, while sex differences were not detected in infants. Gestational age showed stronger association with FA values compared to age after birth in infants. Additionally, child age at scan associated positively with FA around the age of 5 years in the body of corpus callosum, the connections of which are important especially for sensory and motor functions. Lastly, asymmetry of WM microstructure was detected already in infants, yet significant changes in lateralization pattern seems to occur during early childhood, and in 5-year-olds the pattern already resembles adult-like WM asymmetry. HighlightsO_LIWhite matter tract integrity shows widespread sex differences at the age of 5 years. C_LIO_LIWhite matter structure is highly lateralized during early childhood, and changes in asymmetry occur between the birth and 5 years of age. C_LIO_LIThe white matter lateralization pattern of 5-year-olds, unlike of infants, resembles asymmetry observed in adults. C_LI

neuroscience↗

bioRxiv2021

Subcortical brain segmentation in 5-year-old children: validation of FSL-FIRST and FreeSurfer against manual segmentation

Developing accurate subcortical volumetric quantification tools is crucial for neurodevelopmental studies, as they could reduce the need for challenging and time-consuming manual segmentation. In this study the accuracy of two automated segmentation tools, FSL-FIRST (with three different boundary correction settings) and FreeSurfer were compared against manual segmentation of subcortical nuclei, including the hippocampus, amygdala, thalamus, putamen, globus pallidus, caudate and nucleus accumbens, using volumetric and correlation analyses in 80 5-year-olds. Both FSL-FIRST and FreeSurfer overestimated the volume on all structures except the caudate, and the accuracy varied depending on the structure. Small structures such as the amygdala and nucleus accumbens, which are visually difficult to distinguish, produced significant overestimations and weaker correlations with all automated methods. Larger and more readily distinguishable structures such as the caudate and putamen produced notably lower overestimations and stronger correlations. Overall, the segmentations performed by FSL-FIRSTs Default pipeline were the most accurate, while FreeSurfers results were weaker across the structures. In line with prior studies, the accuracy of automated segmentation tools was imperfect with respect to manually defined structures. However, apart from amygdala and nucleus accumbens, FSL-FIRSTs agreement could be considered satisfactory (Pearson correlation > 0.74, Intraclass correlation coefficient (ICC) > 0.68 and Dice Score coefficient (DSC) > 0.87) with highest values for the striatal structures (putamen, globus pallidus and caudate) (Pearson correlation > 0.77, ICC > 0.87 and DSC > 0.88, respectively). Overall, automated segmentation tools do not always provide satisfactory results, and careful visual inspection of the automated segmentations is strongly advised.

neuroscience↗

bioRxiv2021

Feasibility of FreeSurfer processing for T1-weighted brain images of 5-year-olds: semiautomated protocol of FinnBrain Neuroimaging Lab

Pediatric neuroimaging is a quickly developing field that still faces important methodological challenges. One key challenge is the use of many different atlases, automated segmentation tools, manual edits in semiautomated protocols, and quality control protocols, which complicates comparisons between studies. In this article, we present our semiautomated segmentation protocol using FreeSurfer v6.0, ENIGMA consortium software, and the quality control protocol that was used in FinnBrain Birth Cohort Study. We used a dichotomous quality rating scale for inclusion and exclusion of images, and then explored the quality on a region of interest level to exclude all regions with major segmentation errors. The effects of manual edits on cortical thickness values were minor: less than 2% in all regions. Supplementary materials cover registration and additional edit options in FreeSurfer and comparison to the computational anatomy toolbox (CAT12). Overall, we conclude that despite minor imperfections FreeSurfer can be reliably used to segment cortical metrics from T1-weighted images of 5-year-old children with appropriate quality assessment in place. However, custom templates may be needed to optimize the results for the subcortical areas. Our semiautomated segmentation protocol provides high quality pediatric neuroimaging data and could help investigators working with similar data sets.

neuroscience↗

bioRxiv2020

The DOE JGI Metagenome Workflow

The DOE JGI Metagenome Workflow performs metagenome data processing, including assembly, structural, functional, and taxonomic annotation, and binning of metagenomic datasets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) comparative analysis system (I. Chen, K. Chu, K. Palaniappan, M. Pillay, A. Ratner, J. Huang, M. Huntemann, N. Varghese, J. White, R. Seshadri, et al, Nucleic Acids Rsearch, 2019) and provided for download via the Joint Genome Institute (JGI) Data Portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here we describe the different tools, databases, and parameters used at different steps of the workflow, to help with interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a Workflow Description Language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl.git). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, H. Katta, A. Mojica, I Chen, and N. Kyrpides, and T. Reddy, Nucleic Acids Research, 2018). IMPORTANCEThe DOE JGI Metagenome Workflow is designed for processing metagenomic datasets starting from Illumina fastq files. It performs data pre-processing, error correction, assembly, structural and functional annotation, and binning. The results of processing are provided in several standard formats, such as fasta and gff and can be used for subsequent integration into the Integrated Microbial Genome (IMG) system where they can be compared to a comprehensive set of publicly available metagenomes. As of 7/30/2020 7,155 JGI metagenomes have been processed by the JGI Metagenome Workflow.

bioinformatics↗

bioRxiv2020

Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil

As the world population increases, improvements in crop growth and yield will be needed to meet rising food demands, especially in countries that have not developed agricultural practices optimized for their own soils and crops. In many African countries, farmers improve agricultural productivity by applying synthetic fertilizers and pesticides to crops, but their continued use over the years has had serious environmental consequences including air and water pollution as well as loss of soil fertility. To reduce the overuse of synthetic amendments, we are developing inocula for crops that are based on indigenous soil microbes, especially those that enhance plant growth and improve agricultural productivity in a sustainable manner. We first isolated environmental DNA from soil samples collected from an agricultural region to study the composition of the soil microbiomes and then used Vigna unguiculata (cowpea), an important legume crop in Botswana and other legumes as "trap" plants using the collected soil to induce nitrogen-fixing nodule formation. We have identified drought-tolerant bacteria from Botswana soils that stimulate plant growth; many are species of Bacillus and Paenibacillus. In contrast, the cowpea nodule microbiomes from plants grown in these soils house mainly rhizobia particularly Bradyrhizobium, but also Methylobacterium spp. Hence, the nodule microbiome is much more limited in non-rhizobial diversity compared to the soil microbiome, but also contains a number of potential pathogenic bacteria.

microbiology↗

bioRxiv2020

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

microbiology↗

bioRxiv2019

Impact of soil salinity on the cowpea nodule-microbiome and the isolation of halotolerant PGPR strains to promote plant growth under salinity stress

Four soil samples (SS-1--SS-4) isolated from semi-arid soils in Punjab, Pakistan were used as inocula for cowpea (Vigna unguiculata L.) grown under salinity stress to analyze the composition of bacteria in the rhizosphere and within nodules through cultivation-dependent and cultivation-independent methods. Two cowpea varieties, 603 and the salt-tolerant CB 46, were each inoculated with four different native soil samples, and data showed that plants inoculated with soil samples SS-2 and SS-4 grew better than plants inoculated with soil samples SS-1 and SS-3. Bacteria were isolated from both soils and nodules, and 34 of the 51 original isolates tested positive for PGPR traits in plate assays with many exhibiting multiple plant growth-promoting properties. A number of isolates were positive for all PGPR traits tested. For the microbiome studies, environmental DNA (eDNA) was isolated from SS-1 and SS-4, which represented the extremes of the Pakistan soils to which the plants responded, and by 16S rRNA gene sequencing analysis were found to consist mainly of Actinobacteria, Firmicutes, and Proteobacteria. However, sequencing analysis of eDNA isolated from cowpea nodules established by the trap plants grown in the four Pakistan soils indicated that the nodule microbiome consisted almost exclusively of Proteobacterial sequences, particularly Bradyrhizobium. Yet, many other bacteria including Rhizobium, Mesorhizobium, Pseudomonas, as well as Paenibacillus, Bacillus as well as non-proteobacterial genera were isolated from the nodules of soil-inoculated cowpea plants. This discrepancy between the bacteria isolated from cowpea nodules (Proteobacteria and non-Proteobacteria) versus those detected in the nodule microbiome (Proteobacteria) needs further study.

plant biology↗