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Byrne, E.

Publications and source records attributed to Byrne, E..

8 recordsLinked to original sources

Human Peripheral Nerve-on-a-Chip on a Multiwell Microelectrode Array as a Scalable Preclinical Neurotoxicity Assay

Reliable human-relevant models of peripheral nerve function remain a critical unmet need in preclinical drug development, particularly for predicting neurotoxicity and bridging the gap to clinical translation. Here, we introduce a next generation Nerve-on-a-Chip, PNS-3D organoids, as a novel human-cell-based 3D peripheral nerve microphysiological system (MPS) that recapitulates key functional and structural features of native nerves, including long-distance axonal outgrowth, physiological myelination, and clinically translational population level electrophysiology. The platform integrates iPSC-derived human sensory neurons and primary human Schwann cells within a spatially organized 3D environment, coupled to a custom embedded electrode array that enables high-content, longitudinal, and clinically translatable functional assessments. As a proof of concept, we evaluated the platforms predictive power using vincristine, a chemotherapeutic agent known to cause chemotherapy-induced peripheral neuropathy (CIPN). PNS-3D organoids captured dose- and time-dependent deficits in nerve conduction velocity, compound action potential amplitude, and axonal degeneration, with IC values in line with human clinical exposures-- outperforming traditional 2D cultures and in vivo benchmarks. Transcriptomic and morphological analyses further revealed neuron-specific degeneration consistent with axonopathy. These results validate the platform as a human-relevant, clinically translation, and scalable solution, enabling mechanistic safety assessment and drug discovery for neurotoxic and neuroprotective therapeutics.

pharmacology and toxicology↗

An arch worth revisiting: A study on the feline humeral supracondylar foramen and its evolutionary significance

The supracondylar foramen with a seemingly osseous peripheral arch noticed on the medio-distal feline humeri had remained disputed among anatomists. Some scholars have argued in favor of homology between this foramen and the supracondyloid foramen formed in the presence of the ligament of Struthers in humans. Other theories include its presence as a retinaculum holding the median nerve and brachial artery to their anatomical position in a flexed elbow. Unfortunately, these theories lack investigative rigor. The emergence of non-invasive imaging modalities, such as micro-computed tomography, has enabled researchers to inspect the internal anatomy of bones without dismantling. Thus, a micro-computed tomographic investigation was conducted on three feline humeri specimens while the internal anatomy of the supracondylar foramina was examined. Unlike the humerus, the thin peripheral arch of the feline supracondylar foramen failed to elicit any osseous trabeculae or foci of calcification. While adhering to the humeral periosteum at its origin, the non-osseous arch, typical of a muscular tendon or a ligament, inserts into a bony spur attached to the medial humeral epicondyle suggestive of a ligament or aponeurotic extension of a (vestigial) brachial muscle, with the coracobrachialis longus emerging to be the most likely candidate.

evolutionary biology↗

Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations

This paper presents an extension to a heuristic method for phasing and imputation of genotypes of descendants in bi-parental populations so that it can phase and impute genotypes of parents of bi-parental populations that are fully ungenotyped or partially genotyped. The imputed genotypes of the parent are then used to impute low-density genotyped descendants of the bi-parental population to high-density. The extension works in three steps. First, it identifies whether a parent has no or low-density genotypes available and it identifies all of its relatives that have high-density genotypes. Second, using the high-density information of relatives, it determines whether the parent is homozygous or heterozygous for a given locus. Third, it phases heterozygous positions of the parent by matching haplotypes to its relatives. We implemented the new algorithm in an extension of the AlphaPlantImptue software and tested its accuracy of imputing missing parent genotypes in simulated bi-parental populations from different scenarios. We also tested the accuracy of imputation of the missing parents descendants using the true genotype of the parent and compared this to using the imputed genotypes of the parent. Our results show that across all scenarios, the accuracy of imputation of a parent, measured as the correlation between true and imputed genotypes, was > 0.98 and did not drop below [~] 0.96. The imputation accuracy of a parent was always higher when it was inbred than when it was outbred and when it had low-density genotypes. Including ancestors of the parent at HD, increasing the number of crosses and the number of high-density descendants all increased the accuracy of imputation. The high imputation accuracy achieved for the parent across all scenarios translated to little or no impact on the accuracy of imputation of its descendants at low-density. Key MessageNew fast and accurate method for phasing and imputation of SNP chip genotypes within diploid bi-parental plant populations.

genetics↗

Conditional GWAS analysis identifies putative disorder-specific SNPs for psychiatric disorders

Substantial genetic liability is shared across psychiatric disorders but less is known about risk variants that are specific to a given disorder. We used multi-trait conditional and joint analysis (mtCOJO) to adjust GWAS summary statistics of one disorder for the effects of genetically correlated traits to identify putative disorder-specific SNP associations. We applied mtCOJO to summary statistics for five psychiatric disorders from the Psychiatric Genomics Consortium - schizophrenia (SCZ), bipolar disorder (BIP), major depression (MD), attention-deficit hyperactivity disorder (ADHD) and autism (AUT). Most genom-wide significant variants for these disorders had evidence of pleiotropy (i.e., impact on multiple psychiatric disorders) and hence have reduced mtCOJO conditional effect sizes. However, subsets of genome-wide significant variants had larger conditional effect sizes consistent with disorder-specific effects: 15 of 130 genome-wide significant variants for schizophrenia, 5 of 40 for major depression, 3 of 11 for ADHD and 1 of 2 for autism. In addition, we identified a number of variants that approached genome-wide significance in the original GWAS and have larger conditional effect sizes after conditioning on the other disorders. We show that decreased expression of VPS29 in the brain may increase risk to SCZ only and increased expression of CSE1L is associated with SCZ and MD, but not with BIP. Likewise, decreased expression of PCDHA7 in the brain is linked to increased risk of MD but decreased risk of SCZ and BIP.

genetics↗

The effects of training population design on genomic prediction accuracy in wheat

Genomic selection offers several routes for increasing genetic gain or efficiency of plant breeding programs. In various species of livestock there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeders equation. Accurate predictions of genomic breeding value are central to this and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable accurate predictions.\n\nTo quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F2:4 bi- and triparental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25,000 segregating single nucleotide polymorphism markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Within cross genomic prediction accuracies of yield BLUEs were 0.125 - 0.127 using two different cross-validation approaches, and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasize the importance of the training set design in relation to the genetic material to which the resulting prediction model is to be applied.

genetics↗

A heuristic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi-parental plant populations

This paper presents a new heuristic method for phasing and imputation of genomic data in diploid plant species. Our method, called AlphaPlantImpute, explicitly leverages features of plant breeding programs to maximise the accuracy of imputation. The features are a small number of parents, which can be inbred and usually have high-density genomic data, and few recombinations separating parents and focal individuals genotyped at low-density (i.e. descendants that are the imputation targets). AlphaPlantImpute works roughly in three steps. First, it identifies informative low-density genotype markers in parents. Second, it tracks the inheritance of parental alleles and haplotypes to focal individuals at informative markers. Finally, it uses this low-density information as anchor points to impute focal individuals to high-density.\n\nWe tested the imputation accuracy of AlphaPlantImpute in simulated bi-parental populations across different scenarios. We also compared its accuracy to existing software called PlantImpute. In general, AlphaPlantImpute had better or equal imputation accuracy as PlantImpute. The computational time and memory requirements of AlphaPlantImpute were tiny compared to PlantImpute. For example, accuracy of imputation was 0.96 for a scenario where both parents were inbred and genotyped at 25,000 markers per chromosome and a focal F2 individual was genotyped with 50 markers per chromosome. The maximum memory requirement for this scenario was 0.08 GB and took 37 seconds to complete.

genomics↗

Infants’ neural oscillatory processing of theta-rate speech patterns exceeds adults’

During their early years, infants use the temporal statistics of the speech signal to boot-strap language learning, but the neural mechanisms that facilitate this temporal analysis are poorly understood. In adults, neural oscillatory entrainment to the speech amplitude envelope has been proposed to be a mechanism for multi-time resolution analysis of adult-directed speech, with a focus on Theta (syllable) and low Gamma (phoneme) rates. However, it is not known whether developing infants perform multi-time oscillatory analysis of infant-directed speech with the same temporal focus. Here, we examined infants processing of the temporal structure of sung nursery rhymes, and compared their neural entrainment across multiple timescales with that of well-matched adults (their mothers). Typical infants and their mothers (N=58, median age 8.3 months) viewed videos of sung nursery rhymes while their neural activity at C3 and C4 was concurrently monitored using dual-electroencephalography (dual-EEG). The accuracy of infants and adults neural oscillatory entrainment to speech was compared by calculating their phase-locking values (PLVs) across the EEG-speech frequency spectrum. Infants showed better phase-locking than adults at Theta (~4.5 Hz)and Alpha (~9.3 Hz) rates, corresponding to rhyme and phoneme patterns in our stimuli. Infant entrainment levels matched adults for syllables and prosodic stress patterns (Delta,~1-2 Hz). By contrast, infants were less accurate than adults at tracking slow (~0.5 Hz) phrasal patterns. Therefore, compared to adults, language-learning infants temporal parsing of the speech signal shows highest relative acuity at Theta-Alpha rates. This temporal focus could support the accurate encoding of syllable and rhyme patterns during infants sensitive period for phonetic and phonotactic learning. Therefore, oscillatory entrainment could be one neural mechanism that supports early bootstrapping of language learning from infant-directed speech (such as nursery rhymes).

neuroscience↗

Speaker gaze changes information coupling between infant and adult brains

When infants and adults communicate, they exchange social signals of availability and communicative intention such as eye gaze. Previous research indicates that when communication is successful, close temporal dependencies arise between adult speakers and listeners neural activity. However, it is not known whether similar neural contingencies exist within adult-infant dyads. Here, we used dual-electroencephalography to assess whether direct gaze increases neural coupling between adults and infants during screen-based and live interactions. In Experiment 1 (N=17), infants viewed videos of an adult who was singing nursery rhymes with (a) Direct gaze (looking forward); (b) Indirect gaze (head and eyes averted by 20{degrees}); or (c) Direct-Oblique gaze (head averted but eyes orientated forward). In Experiment 2 (N=19), infants viewed the same adult in a live context, singing with Direct or Indirect gaze. Gaze-related changes in adult-infant neural network connectivity were measured using Partial Directed Coherence. Across both experiments, the adult had a significant (Granger)-causal influence on infants neural activity, which was stronger during Direct and Direct-Oblique gaze relative to Indirect gaze. During live interactions, infants also influenced the adult more during Direct than Indirect gaze. Further, infants vocalised more frequently during live Direct gaze, and individual infants who vocalized longer also elicited stronger synchronisation from the adult. These results demonstrate that direct gaze strengthens bi-directional adult-infant neural connectivity during communication. Thus, ostensive social signals could act to bring brains into mutual temporal alignment, creating a joint-networked state that is structured to facilitate information transfer during early communication and learning.

neuroscience↗