Biology subjects

Zhang, J.-H.

Publications and source records attributed to Zhang, J.-H..

4 recordsLinked to original sources

bioRxiv2026

Extending Kilosort for 3D Neural Probes

Kilosort 2.0 is a widely adopted spike sorting algorithm recognized for its efficiency and accuracy on planar electrode arrays, such as Neuropixels. To adapt its robust architecture to emerging three-dimensional (3D) neural probes, we present Kilosort 2.0-3D, a modified version that leverages 3D spatial information. Our modification specifically redefines the spatial processing components of Kilosort 2.0 to operate in 3D space while leaving the core template-matching process unchanged. By using synthetic extracellular recording data with ground-truth neuron positions and firing times, we demonstrate that Kilosort 2.0-3D effectively resolves spatial ambiguities and unit misclassifications inherent in 2D spatial assumptions. Our results show that Kilosort 2.0-3D achieves rotational invariance and maintains full backward compatibility with planar arrays. This work establishes a validated, scalable tool for spike sorting of high-density 3D neural electrophysiology data.

neuroscience↗

bioRxiv2025

Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening

We profiled developmental-series transcriptome, methylome, and metabolome profiling to reveal extensive epigenetic reprogramming during black raspberry (Rubus occidentalis) fruit ripening. Fruit tissues exhibit globally higher DNA methylation than leaves, particularly in CHG and CHH contexts. Local methylation in all cytosine contexts progressively decreases in promoter regions during ripening, whereas CHG and CHH methylation increase in transposon-rich regions. Two primary methylation transitions--promoter hypomethylation and CHH hypermethylation--govern transcriptional shifts in genes involved in ripening processes. Methyl-binding transcription factors with activation potential likely promote CHH hypermethylation-linked transcriptional activation. Multi-omics integration revealed coordinated anthocyanin accumulation parallels expression of biosynthetic and regulatory genes within coherent networks. Elevated non-CG methylation in heterochromatin coincides with increased transcription of histone variants mediating chromatin compaction, suggesting chromatin remodelers fine-tune accessibility for methyltransferases. Our study highlights both genome-wide and locus-specific epigenetic reprogramming and demonstrates a coordinated interplay between DNA methylation and transcriptional regulation during black raspberry fruit ripening.

genomics↗

bioRxiv2025

Real-time spike sorting with 3D neural probe and triangulation localization

A key challenge in correlating neuronal activity with brain function is the limited sampling probability of neuronal activity in real time. It is crucial to increase the sampling probability substantially and in real time. We hypothesized that 3-dimensional (3D) neural probes offer faster and stronger prospects for cell yield than 2D electrode arrays. We simulated a 1000-neuron neuronal network, mimicking the granular layer of the barrel cortical column, recorded signals from inserted 384 electrodes (organized in 3D or 2D), and sorted units using Kilosrt or triangulation localization. We demonstrated that 3D electrode arrays converge more space for triangulation spike sorting than 2D probes do. 3D neural probes, together with triangulation, could isolate up to 80% of the simulated 1000 neurons (as ground truth) and have a cell yield of up to 5, which is, to the best of our knowledge, significantly higher than standard 2D electrodes with Kilosort or triangulation. With a signal-to-noise ratio (SNR) of 10, which is close to the real world, the simulation data suggest that 3D electrode arrays in a face-centric cubic (FCC) arrangement provide a better cell yield. However, larger background noise (e.g. an SNR of 1, which can be improved with lower electrode impedance) has a stronger impact on the triangulation spike sorting. Since only the peak value of spikes are required for triangulation localization, the computing loading is much less than spike waveform-based spike sorting approach. Thus, combining 3D electrode arrays with triangulation localization is ideal for real-time spike sorting. Thus, we demonstrated that adding one more dimension in designing neural probes can dramatically increase cell yield and speed up isolating neuronal unit activity. We, for the first time, provide a tool for utilizing computer simulations to optimize the design of neural electrode arrays before time-consuming probe fabrication.

neuroscience↗

bioRxiv2018

Hydrogen sulfide promotes nodulation and nitrogen fixation in soybean-rhizobia symbiotic system

The rhizobium-legume symbiotic system is crucial for nitrogen cycle balance in agriculture. Hydrogen sulfide (H2S), a gaseous signaling molecule, may regulate various physiological processes in plants. However, whether H2S has regulatory effect in this symbiotic system remains unknown. Herein, we investigated the possible role of H2S in the symbiosis between soybean (Glycine max) and rhizobium (Sinorhizobium fredii). Our results demonstrated that exogenous H2S donor (sodium hydrosulfide, NaHS) treatment promoted soybean growth, nodulation and nitrogenase (Nase) activity. Western blotting analysis revealed that the abundance of nitrogenase component nifH was increased by NaHS treatment in nodules. Quantitative real-time PCR data showed that NaHS treatment up-regulated the expressions of symbiosis-related genes nodC and nodD of S. fredii. Besides, expression of soybean nodulation marker genes including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN), nodulation signaling pathway2b (GmNSP2b) and nodulation inception genes (GmNIN1a, GmNIN2a and GmNIN2b) were up-regulated. Moreover, the expressions of glutamate synthase (GmGS), nitrite reductase (GmNiR), ammonia transporter (GmSAT1), and nifH involved in nitrogen metabolism were up-regulated in NaHS-treated soybean roots and nodules. Together, our results suggested that H2S may act as a positive signaling molecule in soybean-rhizobia symbiotic system and enhance their nitrogen fixation ability.\n\nHighlightWe demonstrated for the first time that H2S as a signaling molecule may promote the establishment of symbiotic relationship and nitrogen fixation ability in the soybean-rhizobia symbiotic system.

plant biology↗