Biology subjects

Shivakumar, A.

Publications and source records attributed to Shivakumar, A..

3 recordsLinked to original sources

bioRxiv2026

Alternative polyadenylation and the sex-specific gene expression program in hemp

Hemp (Cannabis sativa) produces a wide array of medicinally significant compounds, including cannabidiol (CBD). These compounds are predominantly synthesized in female hemp inflorescences. The proposed research utilizes next-generation sequencing-based transcriptome analysis using a 3{square}-end-directed approach to identify differentially expressed genes between male and female hemp plants at the early vegetative stage. 886 differentially expressed genes (DEGs) were identified, a majority of which were upregulated in males compared to females. We hypothesized that alternative RNA processing contributes to sex-specific gene expression. To this end, 932 genes were identified that exhibited significant changes in poly(A) site usage when comparing males and females. These genes were much more likely to be differentially expressed, supportive of this hypothesis. Males tend to have longer 3 UTRs with canonical motifs found in the Near-Upstream Elements (NUE), compared to the shorter 3 UTRs in females, which have A-rich motifs near the cleavage site. This suggests that polyadenylation remodels hemp mRNAs with distal poly(A) sites being preferred in males. To further investigate when this sex-specific gene expression program is established, RNA was isolated from plants at various developmental stages, such as developing seeds, four-day-old seedlings, and different developmental stages up to four weeks after sowing. Diagnostic male-specific genes were analyzed using RT/PCR. The results indicate that sex-specific gene expression is not evident in seeds but rather is set during or after germination. SignificanceO_LIHemp males tend to have longer 3 UTRs with canonical motifs found in the Near-Upstream Elements (NUE), compared to the shorter 3 UTRs in females, which have A-rich motifs near the cleavage site. C_LIO_LIThe sex-specific gene expression program is not yet established in mature seed but is set in the time between germination and 4 days of growth. C_LI

plant biology↗

bioRxiv2025

The lag phase of seed development plays an important role in determining the maximum potential final seed weight in soybean (Glycine max L.)

Soybean (Glycine max L.) cultivars exhibit substantial variation in seed weight; however, the developmental and physiological mechanisms contributing to this variation remain incompletely characterized. Here, we investigated the relationship between early seed developmental dynamics and final seed weight by comparing two large-seeded and two small-seeded cultivars under control and depodding conditions. Depodding, achieved by retaining a single pod per node, minimized assimilate competition. Final seed weight was positively correlated with cotyledon cell number and duration of the lag phase, which is a key early stage of seed development. Large-seeded cultivars exhibited significantly longer lag phases and higher cotyledon pavement cell numbers than small-seeded cultivars, suggesting that extended lag phases promote enhanced cell proliferation, contributing to increased seed weight. Depodding further increased the cotyledon cell number; however, this response was associated with accelerated embryo development rather than an extension of the lag phase. These findings indicate that both the duration of the lag phase and the rate of early embryo development influence cotyledon cell proliferation and ultimately seed weight. Moreover, genetic factors and assimilate availability regulate developmental processes through distinct pathways. Together, our results highlight the importance of early seed developmental timing in determining final seed weight and provide new insights into the developmental basis of yield-related traits in soybean.

plant biology↗

bioRxiv2024

Brain-responsive music enables non-invasive, targeted and unobtrusive neurostimulation

ObjectiveWe are developing a new closed-loop brain stimulation method by embedding, within music, auditory elements that respond to the listeners brain activity. Here we show that this brain-responsive music has systematic and targeted effects on neural oscillations implicated in a variety of neurological and mental health disorders. ApproachWe recorded magnetoencephalogram (MEG) or electroencephalogram (EEG) signals from participants as they listened to music synthesized by commercial audio software. Brain signals were bandpass filtered, phase-shifted and used to control the timbre and/or timing of notes within the music. Main resultsListening to brain-responsive music induced peaks and troughs in spectral power at frequencies that depended systematically on the phase-shift applied to the brain signal. Phase-dependent modulation was greatest at the centre frequency of the filter. As a result, by calibrating these parameters we could achieve selective enhancement or suppression of either theta (5 Hz) or alpha (10 Hz) oscillations. Moreover, by chosing different sensor locations we could target power modulation to either frontal or temporal cortex. The phase-dependent power modulation observed with brain-responsive music was significantly attenuated when participants listened to identical music as a conventional, open-loop stimulus. Finally, we demonstrate that brain activity could be modulated by more complex compositions combining a variety of brain-responsive musical elements controlled by a wireless, wearable EEG headband suitable for home use. SignificanceBrain-responsive music provides an unobtrusive and targeted method of modulating neural oscillations in the listeners brain, and may enable both creative and therapeutic applications of Brain Computer Interface technologies.

neuroscience↗