Biology subjects

Kalia, S.

Publications and source records attributed to Kalia, S..

7 recordsLinked to original sources

bioRxiv2026

Integration of QTL Mapping, Transcriptomics, and Genome Resequencing Identifies Yield-Associated Genes for Salt Stress in Rice

Salinity and sodicity stresses adversely affect rice growth and yield. To overcome yield losses, suitable tolerant rice cultivars can be developed through a marker-assisted breeding (MAB) program. In the present study, genomic regions associated with sodicity stress tolerance at the reproductive stage were identified using a high-density 50kSNP array in a recombinant inbred line (RIL) population derived from the contrasting rice genotypes CSR11 and MI48. A total of 50 QTLs were detected for various yield-related traits; further, 19 QTLs with [≥]15% of phenotypic variance were selected for integrated (omics) analysis. RNA sequencing of leaves and panicles at the reproductive stage under sodic stress conditions was employed to find differentially expressed genes. A total of 1368 and 1410 SNPs; 104 and 144 indels were found for MI48 and CSR11, respectively, within the QTL regions from resequencing. At chromosomes 1 and 6, colocalized QTLs (qPH1-1/qGP1-1 and qGP6-2/qSSI6-2) were discovered. Differentially expressed genes (DEGs) were mapped over the QTL regions selected, and SNP variations and indels were screened for colocalized QTLs. Potential candidate genes, namely Os-pGlcT1 (Os01g0133400), OsHKT2;1 (Os06g0701600) and OsHKT2;4 (Os06g0701700), OsANTH12 (Os06g0699800), and OsPTR2 (Os06g0706400), were identified as being responsible for glucose transport, ion homeostasis, pollen germination, and nitrogen use efficiency, respectively, under salt stress. Finally, our study provides important insights into the genes and potential mechanisms affecting grain yield under sodic stress in rice, which will contribute to the development of molecular markers for rice breeding programs.

plant biology↗

bioRxiv2025

Identification of donor landraces for early vegetative stage salinity tolerance in wheat by employing multivariate selection indices

Soil salinity (EC of [≥]4 dS m-1) is a major abiotic stress leading to decreased crop production due to osmotic, ionic, and cellular ionic imbalance balance. The current study aims to identify salinity-tolerant wheat landraces by investigating morpho-physiological traits. Three hundred fifty wheat landraces and check lines were evaluated for salt stress (15 dS m-1) tolerance in a hydroponic set-up. The clustering analysis categorized 350 genotypes into four control and 15 dS m-1 conditions clusters. Across the multi-trait genotype-ideotype distance index (MGIDI), Smith Hazel Index (SHI), and Stress Susceptibility Index (SSI), seven genotypes were consistently identified as tolerant among the top 150. In comparison, 12 genotypes were consistently classified as least tolerant. These identified tolerant landraces serves as important resources and novel salt tolerance donors for wheat. The tolerant*sensitive, tolerant* tolerant check, crosses can be used for generating RIL populations to delineate genetic basis of salt tolerance of newly identified lines.

physiology↗

bioRxiv2023

Uncovering network mechanism underlying thalamic Deep Brain Stimulation using a novel firing rate model

Thalamic ventral intermediate nucleus (Vim) is the primary surgical target of deep brain stimulation (DBS) for reducing symptoms of essential tremor. High-frequency Vim-DBS ([≥]100Hz) has been clinically effective, generating two experimentally-observed features in Vim spiking activity: 1) a large transient excitatory response (lasting <1s), followed by 2) a suppressed steady-state consisting of oscillations. Yet, mechanisms underlying these observations have not been fully understood by previous studies. In this work, we developed a network rate model and a novel parameter optimization method that accurately fit in-vivo single-unit recordings of Vim in human patients with essential tremor receiving a wide range of DBS frequencies (5[~]200Hz). Our model incorporates both the DBS-induced synaptic plasticity of Vim neurons, and the recurrent connections among excitatory and inhibitory neurons in Vim-network. We hypothesized that besides inducing synaptic depression, the therapeutic mechanism of high-frequency Vim-DBS could be to engage more inhibitory neurons in stabilizing the underlying circuits. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/570924v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e78cbcorg.highwire.dtl.DTLVardef@c8bde1org.highwire.dtl.DTLVardef@12a3bb3org.highwire.dtl.DTLVardef@1b5a0dd_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Haplo-pheno association for OsNRT1.1 paralog in rice reveals superior haplogroup with high nitrate uptake efficiency

Haplotype-based breeding approaches hold promise for enhancing crop improvement strategies, allowing for targeted selection of superior genetic combinations to develop high-yielding and resilient varieties. The current study aimed at identification of NRT1.1 nitrate transporter haplotype that could serve as "donors" in haplotype-based breeding. We phenotyped 272 rice accessions in hydroponics with sufficient and low nitrogen (N) for nitrate uptake efficiency. By employing principal component and hierarchical cluster analysis, the accessions were grouped into N efficient, intermediate, and inefficient clusters. Haplotype analysis unveiled the presence of two haplogroups for OsNRT1.1A, three for OsNRT1.1B, and five for OsNRT1.1C. Through haplo-pheno association, the comparison of mean trait values revealed H2 and H3 as the superior haplotypes (SH) for OsNRT1.1A and OsNRT1.1B, respectively. In the case of OsNRT1.1C, H3 and H1 emerged as SH within the N-efficient cluster. Conversely, the inferior haplotypes (IH) consisted of H1 in OsNRT1.1A, H3 in OsNRT1.1B, and H3 and H2 in OsNRT1.1C within the N-inefficient cluster. However, relative expression of OsNRT1.1 (with specific paralogs) in contrasting rice accessions revealed that a few of the inferior accession exhibited higher expression levels in the root but lower in the shoot, which might have contributed to their N-inefficiency. Furthermore, amino acid change at position 403 (Isoleucine to Valine) in inferior accessions influences the active site OsNRT1.1C protein causing N-inefficiency. Ours is the first report on haplotype analysis of NRT1.1 gene demonstrating its genetic diversity, as well as its association with phenotype will have potential implications for improving nitrate uptake efficiency.

plant biology↗

bioRxiv2022

Modelling Instantaneous Firing Rate of DBS Target Neuronal Ensembles in Basal Ganglia and Thalamus

ObjectiveDeep Brain Stimulation (DBS) is an effective treatment for movement disorders, including Parkinsons disease and essential tremor. However, the underlying mechanisms of DBS remain elusive. Despite the capability of existing models in interpreting experimental data qualitatively, there are very few unified computational models that quantitatively capture the dynamics of the neuronal activity of varying stimulated nuclei--including subthalamic nucleus (STN), substantia nigra pars reticulata (SNr) and ventral intermediate nucleus (Vim)--across different DBS frequencies. Materials and MethodsBoth synthetic and experimental data were utilized in the model fitting; the synthetic data were generated by an established spiking neuron model that was reported in our previous work 1, and the experimental data were provided using single-unit microelectrode recordings (MER) during DBS (microelectrode stimulation). Based on these data, we developed a novel mathematical model to represent the firing rate of neurons receiving DBS, including neurons in STN, SNr and Vim--across different DBS frequencies. In our model, the DBS pulses were filtered through a synapse model and a nonlinear transfer function to formulate the firing rate variability. For each DBS-targeted nucleus, we fitted a single set of optimal model parameters consistent across varying DBS frequencies. ResultsOur model accurately reproduced the firing rates observed and calculated from both synthetic and experimental data. The optimal model parameters were consistent across different DBS frequencies. ConclusionThe result of our model fitting were in agreement with experimental single-unit microelectrode recording data during DBS. Reproducing neuronal firing rates of different nuclei of the basal ganglia and thalamus during DBS can be helpful to further understand the mechanisms of DBS, and to potentially optimize stimulation parameters based on their actual effects on neuronal activity.

neuroscience↗

bioRxiv2021

Persistent synaptic inhibition of the subthalamic nucleus by high frequency stimulation

BackgroundDeep brain stimulation (DBS) provides symptomatic relief in a growing number of neurological indications, but local synaptic dynamics in response to electrical stimulation that may relate to its mechanism of action have not been fully characterized. ObjectiveThe objectives of this study were to (1) study local synaptic dynamics during high frequency extracellular stimulation of the subthalamic nucleus (STN), and (2) compare STN synaptic dynamics with those of the neighboring substantia nigra pars reticulata (SNr). MethodsTwo microelectrodes were advanced into the STN and SNr of patients undergoing DBS surgery for PD. Neuronal firing and evoked field potentials (fEPs) were recorded with one microelectrode during stimulation from an adjacent microelectrode. ResultsExcitatory and inhibitory fEPs could be discerned within the STN and their amplitudes predicted bidirectional effects on neuronal firing (p = .007). There were no differences between STN and SNr inhibitory fEP dynamics at low stimulation frequencies (p > .999). However, inhibitory neuronal responses were sustained over time in STN during high frequency stimulation, but not SNr (p < .001) where depression of inhibitory input was coupled with a return of neuronal firing (p = .003). InterpretationPersistent inhibitory input to the STN suggests a local synaptic mechanism for the suppression of subthalamic firing during high frequency stimulation. Moreover, differences in the resiliency versus vulnerability of inhibitory inputs to the STN and SNr suggest a projection source- and frequency-specificity for this mechanism. The feasibility of targeting electrophysiologically-identified neural structures may provide insight into how DBS achieves frequency-specific modulation of neuronal projections.

neuroscience↗

bioRxiv2021

Cognitive boundary signals in the human medial temporal lobe shape episodic memory representation

While experience unfolds continuously, memories are organized as a set of discrete events that bind together the "where", "when", and "what" of episodic memory. This segmentation of continuous experience is thought to be facilitated by the detection of salient environmental or cognitive events. However, the underlying neural mechanisms and how such segmentation shapes episodic memory representations remain unclear. We recorded from single neurons in the human medial temporal lobe while subjects watched videos with different types of embedded boundaries and were subsequently evaluated for memories of the video contents. Here we show neurons that signal the presence of cognitive boundaries between subevents from the same episode and neurons that detect the abstract separation between different episodes. The firing rate and spike timing of these boundary-responsive neurons were predictive of later memory retrieval accuracy. At the population level, abrupt neural state changes following boundaries predicted enhanced memory strength but impaired order memory, capturing the behavioral tradeoff subjects exhibited when recalling episodic content versus temporal order. Successful retrieval was associated with reinstatement of the neural state present following boundaries, indicating that boundaries structure memory search. These findings reveal a neuronal substrate for detecting cognitive boundaries and show that cognitive boundary signals facilitate the mnemonic organization of continuous experience as a set of discrete episodic events.

neuroscience↗