Biology subjects

Mai, G.

Publications and source records attributed to Mai, G..

7 recordsLinked to original sources

bioRxiv2026

What makes a banana false? How the genome of Ethiopian orphan staple Ensete ventricosum differs from the banana A and B sub-genomes

BackgroundEnsete ventricosum, also known as the "tree against hunger" plays a key role in Ethiopian food security and farming systems, feeding more than 20 million people. Since domestication via clonal selection in the south-west Ethiopian highlands, todays diverse enset landraces contribute multiple benefits including food, fibre by-product, animal bedding and cattle fodder to farmers and local communities. Improved genomic resources for this highly drought-tolerant plant are essential to supplement the conventional clonal selection-based breeding programme and pave the way towards targeted breeding. ResultsWe sequenced the genome of enset landrace Mazia, which is partially resistant/tolerant to Xanthomonas wilt and predicted 38,940 protein-coding genes. The Mazia assembly (540.14 Mb) is more complete than the previously published genome assembly of landrace Bedadeti (451.28 Mb) and displayed 1.41% heterozygosity and 64.64% repetitive DNA content. Comparative analyses with the Bedadeti assembly and chromosome-level genome sequences of the two main banana progenitors (Musa acuminata, AA genome; Musa balbisiana, BB genome) unexpectedly revealed [~]25% of the Mazia genome is unique to enset. Gene Ontology (GO) and sequence similarity search analysis of enset-specific protein-coding genes identified distinct functional signatures that underpin the lifestyle, adaptation, and corm productive quality of enset, including functions related to DNA integration, carbohydrate metabolism, disease resistance and transcriptional regulation. In contrast, Musa-specific genes showed enrichment for defence response, protein phosphorylation and fruit development pathways. Focusing on the classical nucleotide binding site leucine rich repeat (NLR) disease resistance genes, we identified and characterised NLRs in enset and Musa species genomes, revealing a considerable expansion in the Musa acuminata genome. We also identified unique genes in enset and banana genomes whose functional and evolutionary roles are yet to be determined. ConclusionsHere, we report a de novo genome assembly for the enset (Ensete ventricosum) landrace Mazia and provide a high-quality annotation of both Mazia and the previously published assembly of the landrace Bedadeti. Collectively, these genomic resources provide a valuable foundation for comparative genomics within the Musaceae family and open new opportunities for the development of marker-assisted breeding strategies to accelerate the improvement of agronomically important traits in enset.

bioinformatics↗

bioRxiv2026

PathoResist AI: A One-Click Web Platform for Rapid Pathogen Resistance Analysis Based on the all_ratio Algorithm

This study introduces a one-stop analysis platform named "PathoResistAI" (https://www.resistpath.com/), which can be used to solve the technical bottlenecks of pathogenic microorganism detection and antimicrobial resistance analysis. The platform is based on nanopore sequencing and the innovative all-ratio algorithm, which integrates four-dimensional parameters (sequence similarity, abundance, matching number, and matching length), significantly improving the detection accuracy of low-abundance pathogens and drug-resistance genes. The platform adopts four layers of modular design (input layer, core engine, dual-channel output, and visualization layer). Users only need to upload data in FASTQ format, and they can obtain automated reports, including pathogen identification and drug-resistance gene prediction within 30 min. The verification results show that the platform can accurately identify bacteria (e.g., Staphylococcus aureus and Serratia marcescens), viruses (e.g., Ebola virus), and drug-resistance genes (e.g., SdeY), which are consistent with the published literature results. Limitations include only supporting long-read sequencing data, small sample size (fewer than 50 cases), and lack of real clinical sample verification. In general, this platform represents the application and exploration of nanopore sequencing in the field of rapid detection of pathogenic microorganisms, and provides a new tool for microbial pathogen or AMR detection research.

bioinformatics↗

bioRxiv2025

Neural entrainment to pitch changes of auditory targets in noise

Neural entrainment to certain acoustic features can predict speech-in-noise perception, but these features are difficult to separate. We measured neural responses to both natural speech-in-noise and stimuli (auditory figure-ground) that simulate speech-in-noise without any acoustic or linguistic confound such as stress contour and semantics. The figure-ground stimulus is formed by multiple temporally coherent pure-tone components embedded in a random tone cloud. Previous work has shown that discrimination of dynamic figure-ground based on the fundamental frequency (F0) of natural speech predicts speech-in-noise recognition independent of hearing and age. In this study, we compared the brain substrate for the figure-ground analysis based on the F0 contour and a statistically similar 1/f contour with speech-in-noise. We used the temporal response function to predict the electroencephalography responses to the frequency trajectories of the auditory targets. We demonstrate that the brain significantly tracked the pitch changes in both AFG conditions (F0 and 1/F tracking) and a sentence-in-noise condition (F0 tracking) at similar latencies, but at similar magnitudes only when tracking the F0 contour. The pitch-tracking accuracy was consistently high across the delta and theta bands for the AFG condition but not for speech. Sensor-space analysis revealed that speech-in-noise performance correlated with the positive peak amplitude of the F0 figure-ground at 100 ms. Source-space analysis revealed bilateral temporal lobe and hippocampal generators, and strong tracking in the superior parietal lobe for auditory figures and natural speech. In conclusion, our findings demonstrate that the human brain reliably tracks the F0 trajectory of both speech and a non-linguistic figure in noise, with speech tracking showing reduced accuracy in the theta band compared to figure-ground tracking. Despite the difference in prediction accuracy, we reveal striking similarities in neural entrainment patterns and source locations between the two paradigms. These results suggest that neural entrainment engages high-level cortical mechanisms independent of linguistic content. Furthermore, we show that TRF peak amplitude serves as a potential biomarker for speech-in-noise ability, highlighting possible clinical applications.

neuroscience↗

bioRxiv2023

Neuroplasticity of speech-in-noise processing in older adults assessed by functional near-infrared spectroscopy (fNIRS)

Functional near-infrared spectroscopy (fNIRS), a non-invasive optical neuroimaging technique that is portable and acoustically silent, has become a promising tool for evaluating auditory brain functions in hearing- vulnerable individuals. This study, for the first time, used fNIRS to evaluate neuroplasticity of speech-in-noise processing in older adults. Ten older adults, most of whom had moderate-to-mild hearing loss, participated in a 4-week speech-in-noise training. Their speech-in-noise performances and fNIRS brain responses to speech (auditory sentences in noise), non-speech (spectrally-rotated speech in noise) and visual (flashing chequerboards) stimuli were evaluated pre- (T0) and post-training (immediately after training, T1; and after a 4-week retention, T2). Behaviourally, speech-in-noise performances were improved after retention (T2 vs. T0) but not immediately after training (T1 vs. T0). Neurally, we intriguingly found brain responses to speech vs. non-speech decreased significantly in the left auditory cortex after retention (T2 vs. T0 and T2 vs. T1) for which we interpret as suppressed processing of background noise during speech listening alongside the significant behavioural improvements. Meanwhile, functional connectivity within and between multiple regions of temporal, parietal and frontal lobes was significantly enhanced in the speech condition after retention (T2 vs. T0). We also found neural changes before the emergence significant behavioural improvements. Compared to pre-training, responses to speech vs. non-speech in the left frontal/prefrontal cortex were decreased significantly both immediately after training (T1 vs. T0) and retention (T2 vs. T0), reflecting possible alleviation of listening efforts. Finally, connectivity was significantly decreased between auditory and higher-level non-auditory (parietal and frontal) cortices in response to visual stimuli immediately after training (T1 vs. T0), indicating decreased cross-modal takeover of speech-related regions during visual processing. The results thus showed that neuroplasticity can be observed not only at the same time, but also before behavioural changes in speech-in- noise perception. To our knowledge, this is the first fNIRS study to evaluate speech-based auditory neuroplasticity in older adults. It thus provides important implications for current research by illustrating the promises of detecting neuroplasticity using fNIRS in hearing-vulnerable individuals.

neuroscience↗

bioRxiv2020

Causal relationship between the right auditory cortex and speech-evoked frequency-following response: Evidence from combined tDCS and EEG

Speech-evoked envelope-following response (EFR) reflects brain encoding of speech periodicity that serves as a biomarker for pitch and speech perception and various auditory and language disorders. While EFR is thought to originate from the subcortex, recent research illustrated a right-hemispheric cortical contribution to EFR. However, it is unclear whether this contribution is causal. This study aimed to establish this causality by combining transcranial direct current stimulation (tDCS) and measurement of EFR (pre- and post-tDCS) via scalp-recorded electroencephalography (EEG). We applied tDCS over the left and right auditory cortices in right-handed normal-hearing participants and examined whether altering cortical excitability via tDCS causes changes in EFR during monaural listening to speech syllables. We showed significant changes in EFR magnitude when tDCS was applied over the right auditory cortex compared to sham stimulation for the listening ear contralateral to the stimulation site. No such effect was found when tDCS was applied over the left auditory cortex. Crucially, we further observed a hemispheric laterality where after-effect was significantly greater for tDCS applied over the right than the left auditory cortex in the contralateral ear condition. Our finding thus provides the first evidence that validates the causal relationship between the right auditory cortex and EFR.

neuroscience↗

bioRxiv2019

Relationship between neural phase-locked responses to speech and speech-in-noise perception in young and older adults

Auditory phase-locked responses are affected by aging and it has been proposed that this increases the challenges experienced during speech perception in noise (SPiN). However, this proposal lacks direct support. This issue was addressed by measuring speech-evoked phase-locked responses at subcortical (frequency-following responses, FFRs) and cortical (theta-band phase-locking, {theta}-PLV) levels, and studying the relationship between these phase-locked responses and SPiN (word report accuracies of sentences listened to in noise) in adults across a wide age-range (19-75 years old). It was found that: (1) FFR magnitudes declined with age after hearing loss was controlled for; (2) {theta}-PLV increased with age, suggesting cortical hyperexcitability in audition; (3) SPiN correlated positively with FFR magnitudes obtained in quiet and with {theta}-PLV obtained in noise, suggesting that impacts of aging (smaller FFR magnitudes and greater {theta}-PLV) on SPiN differ at subcortical and cortical levels. Thus, the current study provided evidence for different mechanisms at subcortical and cortical levels through which age affects speech-evoked phase-locked activities and SPiN.

neuroscience↗

bioRxiv2019

Delta and theta neural entrainment during phonological and semantic processing in speech perception

Neural entrainment of acoustic envelopes is important for speech intelligibility in spoken language processing. However, it is unclear how it contributes to processing at different linguistic hierarchical levels. The present EEG study investigated this issue when participants responded to stimuli that dissociated phonological and semantic processing (real-word, pseudo-word and backward utterances). Multivariate Temporal Response Function (mTRF) model was adopted to map speech envelopes from multiple spectral bands onto EEG signals, providing a direct approach to measure neural entrainment. We tested the hypothesis that entrainment at delta (supra-syllabic) and theta (syllabic and sub-syllabic) bands take distinct roles at different hierarchical levels. Results showed that both types of entrainment involve speech-specific processing, but their underlying mechanisms were different. Theta-band entrainment was modulated by phonological but not semantic contents, reflecting the possible mechanism of tracking syllabic- and sub-syllabic patterns during phonological processing. Delta-band entrainment, on the other hand, was modulated by semantic information, indexing more attention-demanding, effortful phonological encoding when higher-level (semantic) information is deficient. Interestingly, we further demonstrated that the statistical capacity of mTRFs at the delta band and theta band to classify utterances is affected by their semantic (real-word vs. pseudo-word) and phonological (real-word and pseudo-word vs. backward) contents, respectively. Moreover, analyses on the response weighting of mTRFs showed that delta-band entrainment sustained across neural processing stages up to higher-order timescales (~ 300 ms), while theta-band entrainment occurred mainly at early, perceptual processing stages (< 160 ms). This indicates that, compared to theta-band entrainment, delta-band entrainment may reflect increased involvement of higher-order cognitive functions during interactions between phonological and semantic processing. As such, we conclude that neural entrainment is not only associated with speech intelligibility, but also with the hierarchy of linguistic (phonological and semantic) content. The present study thus provide a new insight into cognitive mechanisms of neural entrainment for spoken language processing. HighlightsO_LILow-frequency neural entrainment was examined via mTRF models in EEG during phonological and semantic processing. C_LIO_LIDelta entrainment take roles in effortful listening for phonological recognition C_LIO_LITheta entrainment take roles in tracking syllabic and subsyllabic patterns for phonological processing C_LIO_LIDelta and theta entrainment sustain at different timescales of neural processing C_LI

neuroscience↗