Biology subjects

Bian, K.

Publications and source records attributed to Bian, K..

8 recordsLinked to original sources

bioRxiv2026

Genome-resolved and kinetic evidence for low-DO comammox-anammox synergy and acetate-stimulated nitrate reduction in IFAS biofilms

Mainstream anammox implementation for nitrogen removal is constrained by unstable nitrite supply and organic carbon requirements for nitrate byproduct removal. This study evaluated integrated fixed-film activated sludge (IFAS) biofilms to enhance anammox activity by coupling low-oxygen ammonium oxidation with volatile fatty acid (VFA)-driven nitrate reduction. Nanopore long-read metagenomic assembly recovered a high-quality, circular single-contig Candidatus Brocadia sapporoensis metagenome-assembled genome (MAG) from full-scale IFAS biofilms. This MAG encodes complete anammox metabolism, dissimilatory nitrate reduction to ammonium (DNRA) and acetate/propionate carbon transformation pathways. Metatranscriptomics showed that low dissolved oxygen (DO) upregulated Ca. B. sapporoensis genes involved in anammox, nitrate reduction, and carbon metabolism. Microaerobic assays established a DO level of 0.7 mg/L as optimal for sustaining near-maximal ammonium oxidation alongside anammox-driven total inorganic nitrogen (TIN) loss. Anoxic tests conducted in secondary effluent indicated that external acetate amendment promoted greater partial nitrate reduction and TIN loss than additional propionate amendment. Integrating this dissolved oxygen concentration with external acetate amendment in a two-stage microaerobic-anoxic system successfully achieved sequential ammonium oxidation, partial nitrate reduction, and anammox-mediated TIN removal. Stage-specific expression suggested Ca. B. sapporoensis could contribute to nitrite self-supplementation via nxrAB-mediated nitrate reduction. Overall, microaerobic ammonium oxidation and Ca. B. sapporoensis-driven partial nitrate reduction jointly sustain mainstream anammox activity. Furthermore, this study demonstrates that successful metabolic synergy depends fundamentally upon precise dissolved oxygen control and effective external acetate amendment.

microbiology↗

bioRxiv2026

High-accuracy hierarchical rRNA operon profiling resolves genomovar-level taxonomy and microdiversity using Nanopore sequencing.

Genomovar-level and intragenomic diversity cannot be resolved by conventional amplicon sequencing due to the limitation of fragment lengths and read accuracy, while the application of metagenomic profiling to a large number of samples can be resource intensive. Here, we report UltraRes-rrn, an integrated wet-lab and computational workflow for high-accuracy rrn (i.e., 16S- ITS-23S rRNA) operon profiling using Nanopore sequencing. By integrating ultra-long DNA recovery, long-read amplicon sequencing, and unique molecular identifiers (UMI)-based consensus correction, UltraRes-rrn obtains full-length 16S-ITS-23S rRNA operon consensus sequences with mean accuracies exceeding 99.98%. To achieve higher resolution, we propose a hierarchical rRNA operon profiling strategy in which concatenated 16S+23S rRNA genes (16S23S) serve as a primary and the internal transcribed spacer (ITS) provides a secondary marker. The 16S23S marker achieved discrimination at the genomovar level compared to either 16S or 23S rRNA genes alone, which mitigates the ITS-driven over-splitting observed with the full-length rrn operon and allows for larger proportion of data being classified at higher confidence thresholds. Further, ITS variation was strongly structured by tRNA occurrence patterns, suggesting that ITS can capture taxon microdiversity missed by either 16S or 23S rRNA gene sequences alone. The UltraRes-rrn workflow was applied to full-scale nitrogen removal reactors, revealing intraspecies diversity variation driven by different carbon regimes, which would not have been possible with a shorter gene sequence. In summary, UltraRes-rrn enables cost-effective community profiling at genomovar-level resolution in complex ecosystems.

microbiology↗

bioRxiv2026

Dissociable frequency regimes in human temporal cortex integrate facial and acoustic cues during natural speech

Face-to-face communication relies on the seamless integration of visual and acoustic cues, yet the spatiotemporal principles governing how the human brain dynamically represents and combines these multisensory streams remain largely unresolved. To address this, we recorded high-density electrocorticography (ECoG) from eight participants perceiving matched audiovisual, audio-only, and video-only continuous natural Mandarin speech. Using time-frequency-resolved encoding models, we reveal complementary, frequency-dependent integration regimes across the temporal lobe. We show that the superior temporal gyrus (STG) implements a feature-selective, auditory-dominant strategy, utilizing visual input to selectively strengthen low-frequency representations of lip-reading kinematics. Conversely, the middle temporal gyrus (MTG) acts as a higher-order multisensory hub, employing a frequency-selective strategy to broadly integrate diverse facial and articulatory features. Crucially, we demonstrate that access to visual information during perception significantly improves the acoustic and lexical accuracy of neural speech decoding and re-synthesis, with the MTG driving the largest gains in linguistic intelligibility. These findings uncover the dissociable neural architectures supporting robust multisensory perception, providing critical mechanistic insights for the development of next-generation, multimodal brain-computer interfaces.

neuroscience↗

bioRxiv2025

Quantitative metagenomics using a portable protocol.

A field-deployable DNA sequencing approach for quantitative microbial community profiling can enable rapid responses for a range of applications in the water sector - from process control to wastewater surveillance. Current quantitative approaches have complex instrumentation requirements and long turnaround time for DNA recovery and absolute quantitation. In this study, we report a field-deployable rapid detection and absolute quantitation (rD+rQ) workflow that leverages the real-time sequencing capabilities of Nanopore sequencing for quantitative metagenomics. This workflow integrates a high-molecular-weight DNA recovery protocol for diverse environmental matrices of relevance to the water sector and multiplexed Nanopore sequencing with barcoded spike-in-based calibration (BSINC). BSINC using multi-species genomic spike-in controls exhibits significantly higher calibration accuracy compared to conventional approaches that utilize either single DNA fragment or single organism spike in controls. Dynamic detection and quantitation limits were established based on coverage fraction of sequenced genomes and the coefficient of variation of genome copy numbers across replicates to enhance the accuracy and precision of microbial quantitation. The rD+rQ workflow achieves species-level identification and absolute quantitative results comparable to digital PCR in environmental samples. This portable laboratory and easy-to-use rD+rQ workflow should facilitate rapid decision-making for the water industry.

microbiology↗

bioRxiv2024

Metatranscriptomic analysis reveals synergistic activities of comammox and anammox bacteria in full-scale attached growth nitrogen removal system.

0-Leveraging comammox Nitrospira and anammox bacteria for shortcut nitrogen removal can drastically lower the carbon footprint of wastewater treatment facilities by decreasing aeration energy, carbon, alkalinity, and tank volume requirements while also potentially reducing nitrous oxide emissions. However, their co-occurrence as dominant nitrifying bacteria is rarely reported in full-scale wastewater treatment. As a result, there is poor understanding of how operational parameters, in particular dissolved oxygen, impact their activity and synergistic behavior. Here, we report the impact of dissolved oxygen concentration (DO = 2, 4, 6 mg/L) on the microbial communitys transcriptomic expression in a full-scale integrated fixed film activated sludge (IFAS) municipal wastewater treatment facility predominantly performed by comammox Nitrospira and anammox bacterial populations. 16S rRNA transcript compositions revealed anammox bacteria and Nitrospira were significantly more active in IFAS biofilms compared to suspended sludge biomass. In IFAS biofilms, anammox bacteria significantly increased hzo expression at lower dissolved oxygen concentrations and this increase was highly correlated with the amoA expression levels of comammox bacteria. Interestingly, the genes involved in nitrite oxidation by comammox bacteria were significantly more upregulated relative to the genes involved in ammonia oxidation with decreasing dissolved oxygen concentrations. Ultimately, our findings suggest that comammox Nitrospira supply anammox bacteria with nitrite via ammonia oxidation and that this synergistic behavior is dependent on dissolved oxygen concentrations. SynopsisComammox bacteria differentially regulate ammonia and nitrite oxidation in response to dissolved oxygen concentration suggesting dissolved oxygen dependence of their synergistic nitrogen removal with anammox bacteria in IFAS biofilms.

microbiology↗

bioRxiv2023

Mechanism of ozone alleviation of malignant ascites in hepatocellular carcinoma through inhibition of NETs

Malignant ascites in hepatocellular carcinoma is usually a sign of advanced disease and poor prognosis and is also thought to be associated with chronic inflammation mediated by neutrophil extracellular trap networks (NETs). Whereas ozone, a strong oxidant, has significant antibacterial and anti-inflammatory effects, its effectiveness in treating malignant liver ascites is unclear.cOzone showed significant anti-peritoneal fluid production properties in H22 tumor-bearing mice, and ozone reduced peritoneal fluid production by activating AMPK and up-regulating SR-A phagocytosis damage-associated molecular patterns (DAMPs) to reduce the production of NETs. This suggests that ozone could be used as a new drug for the treatment of malignant ascites in hepatocellular carcinoma.

cancer biology↗

bioRxiv2020

Developing Commotio Cordis Injury Metrics by Correlating Chest Force and Rib Deformation to Left Ventricle Strain and Pressure

Commotio cordis is a sudden death mechanism that occurs when the heart is impacted during the repolarization phase of the cardiac cycle. This study aimed to investigate commotio cordis injury metrics by correlating chest force and rib deformation to left ventricle (LV) strain and pressure. We simulated 128 chest impacts using a simulation matrix which included two initial velocities, 16 impact locations spread across the transverse and sagittal plane, and four baseball stiffness levels. Results showed that an initial velocity of 17.88 m/s and an impact location over the LV was the most damaging setting across all possible settings, causing the most considerable LV strain and pressure increases. The impact force metric did not correlate with LV strain and pressure, while rib deformations located over the LV were strongly correlated to LV strain. This leads us to the recommendation of exploring new injury metrics such as the rib deformations we have highlighted for future commotio cordis safety regulations.

bioengineering↗

bioRxiv2018

HDAC11 Deficiency Prevents High-Fat Diet-Induced Obesity and Metabolic Syndrome

Significance StatementObesity is a serious and widespread health problem which has become a growing concern in many societies. Most currently available weight-loss medications do not work for everyone, and the effects decline over time. Thus, there is an urgent need to identify new molecular targets to improve drug development for the treatment of obesity and obesity-related diseases. In this study, we discovered that the histone deacetylase 11 (HDAC11) enzyme is a key regulator of metabolism and obesity, and the absence of HDAC11 prevents obesity in mice. Our findings will facilitate the development of novel therapeutics to treat obesity by targeting HDAC11.\n\nAbstractObesity and its associated metabolic syndromes are the consequence of susceptible genes and obesogenic environments. We report here that histone deacetylase 11 (HDAC11) plays a critical role in the development of obesity and in metabolic homeostasis. HDAC11 knockout mice display resistance to high-fat diet-induced obesity and associated syndromes by enhancing glucose tolerance and insulin sensitivity, attenuating hypercholesterolemia and hyperinsulinemia, and blocking hepatosteatosis and liver damage. Mechanistically, HDAC11 deficiency boosts energy expenditure through promoting thermogenic capacity, which attributes to the elevation of uncoupling protein 1 (UCP1) expression and activity in brown adipose tissue. Moreover, loss of HDAC11 stimulates mitochondrial oxidation, elevates plasma adiponectin, and activates the adiponectin-AdipoR-AMPK pathway in the liver, which may contribute to a reversal in hepatosteatosis. These findings establish HDAC11 as a key regulator of metabolism and indicate that HDAC11 inhibitors may hold promise for treating overweight and obesity-related diseases.

molecular biology↗