Biology subjects

Newman, A. J.

Publications and source records attributed to Newman, A. J..

5 recordsLinked to original sources

bioRxiv2026

Investigating fNIRS Test-Retest Reliability During Lexical Decision

SignificancefNIRS is highly suitable for the study of reading development, however, the reliability of its signals is not well understood during reading tasks. AimTherefore, this study assessed the test-retest reliability of the fNIRS signal during a common event-related reading paradigm. ApproachEnglish-speaking adults (n = 30) completed a lexical decision task during fNIRS recording twice, one week apart. ResultsOur results demonstrated contrast effects partially consistent with prior neuroimaging literature, insofar as for each contrast, at least one predicted region of interest was activated. However, we did not identify significant activation in all predicted brain areas. Regarding group level test-retest reliability, we observed poor reliability across predicted brain regions for most conditions, with the exception of fair test-retest reliability in the left posterior temporal lobe for coarse lexical tuning. At the single-subject level, test-retest reliability ranged from poor to excellent across subjects, but was poor for most subjects. ConclusionThese results suggest fNIRS can detect changes in brain activation during a fast event-related reading task at the group level. However, reliability does not appear sufficient to interpret individual-level data. Further research should explore reliability across a wider range of designs to assess the generalizability of these findings.

neuroscience↗

bioRxiv2024

Dissociable roles of neural pattern reactivation and transformation during recognition of words read aloud and silently: An MVPA study of the production effect

Recent work surrounding the neural correlates of episodic memory retrieval has focussed on the decodability of neural activation patterns elicited by unique stimuli. Research in this area has revealed two distinct phenomena: (i) neural pattern reactivation, which describes the fidelity of activation patterns between encoding and retrieval; (ii) neural pattern transformation, which describes systematic changes to these patterns. This study used fMRI to investigate the roles of these two processes in the context of the production effect, which is a robust episodic memory advantage for words read aloud compared to words read silently. Twenty-five participants read words either aloud or silently, and later performed old-new recognition judgements on all previously seen words. We applied multivariate analysis to compare measures of reactivation and transformation between the two conditions. We found that, compared with silent words, successful recognition of aloud words was associated with reactivation in the left insula and transformation in the left precuneus. By contrast, recognising silent words (compared to aloud) was associated with relatively more extensive reactivation, predominantly in left ventral temporal and prefrontal areas. We suggest that recognition of aloud words might depend on retrieval and metacognitive evaluation of speech-related information that was elicited during the initial encoding experience, while recognition of silent words is more dependent on reinstatement of visual-orthographic information. Overall, our results demonstrate that different encoding conditions may give rise to dissociable neural mechanisms supporting single word recognition.

neuroscience↗

bioRxiv2024

Differential weighting of information during aloud and silent reading: Evidence from representational similarity analysis of fMRI data

Single word reading depends on multiple types of information processing: readers must process low-level visual properties of the stimulus, form orthographic and phonological representations of the word, and retrieve semantic content from memory. Reading aloud introduces an additional type of processing wherein readers must execute an appropriate sequence of articulatory movements necessary to produce the word. To date, cognitive and neural differences between aloud and silent reading have mainly been ascribed to articulatory processes. However, it remains unclear whether articulatory information is used to discriminate unique words, at the neural level, during aloud reading. Moreover, very little work has investigated how other types of information processing might differ between the two tasks. The current work used representational similarity analysis (RSA) to interrogate fMRI data collected while participants read single words aloud or silently. RSA was implemented using a whole-brain searchlight procedure to characterize correspondence between neural data and each of five models representing a discrete type of information. Both conditions elicited decodability of visual, orthographic, phonological, and articulatory information, though to different degrees. Compared with reading silently, reading aloud elicited greater decodability of visual, phonological, and articulatory information. By contrast, silent reading elicited greater decodability of orthographic information in right anterior temporal lobe. These results support an adaptive view of reading whereby information is weighted according to its task relevance, in a manner that best suits the readers goals.

neuroscience↗

bioRxiv2020

psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation

Eight RNA helicases remodel the spliceosome to effect pre-mRNA splicing but their mechanism of action remains poorly understood. We have developed "purified spliceosome iCLIP" (psiCLIP) to define helicase-RNA contacts in specific spliceosomal states. psiCLIP reveals previously unappreciated dynamics of spliceosomal helicases. The binding profile of the helicase Prp16 is influenced by the distance between the branch-point and 3 splice site, while Prp22 binds diffusely on the intron before exon ligation but switches to more narrow binding downstream of the exon junction after exon ligation. Notably, depletion of the exon-ligation factor Prp18 destabilizes Prp22 binding to the pre-mRNA, demonstrating that psiCLIP can be used to study the relationships between helicases and auxiliary splicing factors. Thus, psiCLIP is sensitive to spliceosome dynamics and complements the insights from structural and imaging studies by providing crucial positional information on helicase-RNA contacts during spliceosomal remodeling.

molecular biology↗

bioRxiv2017

Post-catalytic spliceosome structure reveals mechanism of 3'-splice site selection

Introns are removed from eukaryotic mRNA precursors by the spliceosome in two transesterification reactions - branching and exon ligation. Following branching, the 5'-exon remains paired to U5 snRNA loop 1, but the mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7[A] cryo-EM structure of the yeast P complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognised through non-Watson-Crick pairing with the 5'-splice site and the branch point adenosine. A conserved loop of Prp18 together with the -finger and the RNaseH domain of Prp8 clamp the docked 3'-splice site and 3'-exon. The step 2 factors Prp18 and Slu7 and the C-terminal domain of Yju2 stabilise a conformation competent for 3'-splice site docking and exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides of the introns and provides insight into the catalytic mechanism of exon ligation.

molecular biology↗