Biology subjects

Hou, B.

Publications and source records attributed to Hou, B..

12 recordsLinked to original sources

bioRxiv2026

An orthogonal near-infrared optical switch for wireless neuromodulation in freely behaving mice

Modulating neuronal activity with light is a powerful tool for neuroscience research. However, currently available technologies often require invasive fibers for delivery of visible light, causing tissue damage and limiting behavioral studies. Although near-infrared (NIR) neuronal modulation improves tissue penetration depth, sustained NIR illumination during neuromodulation raises significant concerns about photothermal effects. Here, we introduce a dual-wavelength near-infrared switch (Dual-NIR Switch) that uses two transcranial NIR inputs to initiate and terminate neuronal activation, enabling tether-free neuromodulation in freely moving mice. Dual-NIR Switch employs orthogonal dichromatic upconversion nanoparticles that emit blue and green light under 980 nm and 808 nm excitation, respectively, to activate and inactivate the step-function opsin SOUL. Therefore, transient 980 nm NIR illumination initiates neuronal excitation, which will remain excited without further stimulation but will be rapidly terminated on demand by a subsequent 808 nm illumination. Upon transcranial 980 nm and 808 nm NIR illuminations in freely moving mice, we achieve on-demand control of behavioral paradigms across tunable timescales, ranging from seconds to minutes and even extending to sub-hour durations. By eliminating the need for sustained NIR irradiation, Dual-NIR Switch offers an on-demand, duration-tunable neuromodulation tool for both basic neuroscience and potential therapeutic applications in treating brain diseases.

neuroscience↗

bioRxiv2026

TCR signal strength determines Treg instability and discrimination of self versus non-self antigens

Regulatory T cells (Tregs) expressing autoreactive T-cell receptors (TCRs) maintain immune self-tolerance, yet their fate upon antigen encounter remains unclear. Although selected in the thymus for high-affinity self-recognition, the cross-reactive nature of the TCR repertoire allows some Tregs to also recognize foreign antigens with high affinity. Here, we identify cross-reactive destabilization, a process in which high-affinity recognition of foreign antigens erodes Treg stability and redirects lineage fate. Using a thymic-derived Treg (tTreg) TCR capable of recognizing both self and foreign antigens distinct from the self-ligand that mediated its thymic selection, we show that stimulation with high-affinity non-self agonists induces Foxp3 loss and conversion into effector-like ex-Tregs, whereas self-antigen stimulation preserves lineage stability. Treg instability also increases with age and correlates with activation, suggesting that cumulative foreign-antigen exposure drives this process. These findings reveal a signal-strength-dependent model in which strong TCR engagement induces cross-reactive destabilization to balance immune responsiveness and self-tolerance. One Sentence SummaryForeign antigen-driven destabilization of Treg cells balances immunity and tolerance

immunology↗

bioRxiv2025

Themis dominates T cell exhaustion by regulation of TCR and PD-1 signaling

T cell exhaustion is important to protect the host from immunopathology during chronic viral infection, but it also impairs T cell anti-tumor immunity1-5. A fundamental unresolved question is whether and how T cell exhaustion is determined at the onset of TCR signaling6-8. Here we report an unexpected role of Themis, a TCR-proximal signaling molecule9, in T cell exhaustion. Chronic viral infection in mice usually leads to T cell exhaustion and survival of the host. Surprisingly, Themis T-cell conditional knockout mice died from severe CD8+-dependent lung immunopathology in chronic viral infection, showing Themis importance in establishing T cell exhaustion. We found that Themis-deficient CD8+ T cells were hyperactivated at the single-cell level - producing more TNF and IFN{gamma} compared to wild-type counterparts - but defective in population-level expansion. Moreover, TCF-1 and TOX expression were inhibited in Themis-deficient CD8+ T cells, thereby impairing differentiation of exhausted T cell precursors (T-pex) and maintenance of terminally exhausted T cells (T-ex), respectively. Mechanistically, Themis initially promotes TCR signaling to induce PD-1 expression and subsequently mediates PD-1 signaling. In the latter, Themis binds to PD-1 and promotes PD-1 phosphorylation and its recruitment of SHP2, thereby acting as a negative regulator to inhibit T cell effector functions. Without Themis, the orderly regulation of TCR and PD-1 signaling, and therefore exhaustion, is disrupted. Thus, our results unequivocally demonstrate that Themis-mediated early TCR signaling plays a decisive role in T cell exhaustion and provide a novel mechanism of PD-1 signaling through Themis.

immunology↗

bioRxiv2023

Activated PI3Kδ specifically perturbs mouse Treg homeostasis and function leading to immune dysregulation

Foxp3+ regulatory T cells (Treg) are required for maintaining immune tolerance and preventing systemic autoimmunity. PI3K{delta} is required for normal Treg development and function. However, the impacts of dysregulated PI3K{delta} signaling on Treg function remain incompletely understood. Here, we used a conditional mouse model of activated PI3K{delta} syndrome (APDS) to investigate the role of altered PI3K{delta} signaling specifically within the Treg compartment. Aged mice expressing a PIK3CD gain-of-function mutation (aPIK3CD) specifically within the Treg compartment exhibited weight loss and evidence for chronic inflammation as demonstrated by increased memory/effector CD4+ and CD8+ T cells with enhanced IFN-{gamma} secretion, spontaneous germinal center responses and production of broad-spectrum autoantibodies. Intriguingly, aPIK3CD facilitated Treg precursor development within the thymus and an increase in peripheral Treg numbers. Peripheral Treg, however, exhibited an altered phenotype including increased PD1 expression and reduced competitive fitness. Consistent with these findings, Treg specific-aPIK3CD mice mounted an elevated humoral response following immunization with a T-cell dependent antigen, that correlated with a decrease in follicular Treg. Taken together, these findings demonstrate that an optimal threshold of PI3K{delta} activity is critical for Treg homeostasis and function, suggesting that PI3K{delta} signaling in Treg might be therapeutically targeted to either augment or inhibit immune responses.

immunology↗

bioRxiv2023

The microbial community of rust layer biofilm was driven by seawater microbial community

Microbiologically influenced corrosion (MIC) accounts for approximately 20% of the total corrosion-related losses worldwide, causing significant economic damage each year, particularly in Marine environments. However, there are still no truly effective and eco-friendly protection solutions against MIC, among which the incomplete understanding of the microbial biofilm development on metallic surface is a key limitation. Using 16S rRNA and ITS sequencing, we studied bacterial and fungal communities in rust layer biofilm and seawater. The results showed that Proteobacteria, Cyanobacteria and Bacteroidota were the dominant bacterial phyla, and Ascomycota and Basidiomycota were the dominant fungal phyla both in the rust layer biofilm and seawater. Bacteria like Erythrobacter and Aquimarina, as well as fungi like Aspergillus and Acremonium were were notable microorganisms in the rust layer biofilm. Source analysis revealed differences between biofilm and seawater communities, with 23.08% bacterial and 21.48% fungal communities originating from seawater. Stochastic processes governed biofilm and seawater microbial communities, and network analysis showed coexistence and interaction among bacteria and fungi. IMPORTANCEThe composition and source analysis of bacterial and fungal communities in the rust layer and seawater were studied, and the interaction of bacteria and fungi in the rust layer was discussed for the first time. Based on these findings, we provided a framework to explain the observed characteristics of microbial communities in rust layer biofilm and presented key evidence supporting the relationship between different microbial structures and interactions with metal corrosion. These findings, from the perspective of microbial ecology, provide a theoretical foundation for studying microbial corrosion in marine environments.

microbiology↗

bioRxiv2023

Phenotypic plasticity of antibiotic resistance, metabolism byproduct utilization and the evolution of mutually beneficial cooperation in Escherichia coli

Although tag-based donation and recognition have well explained how the cooperative individuals are positively assorted if the cooperative individuals possess some signals and are also able to detect such signals, an additional mechanism is required to explain why some individuals pay the costs of evolving such a tag that may not be rewarded subsequently, and how such tag-based cooperative individuals will meet other similar individuals with a very low mutation rate. Here, we show that many and even all Escherichia coli bacteria cells in the increased antibiotic concentration will plastically evolve to be antibiotic resistant individuals who could protect antibiotic sensitive strain from the attack of antibiotics, and the antibiotic resistant strain could reversibly evolve to be antibiotic sensitive in non-antibiotic supplement medium but in a harsher environment with low glucose. A further experiment showed that antibiotic-sensitive E. coli strain could in turn help reduce the concentration of indole produced by the resistant strain. This metabolic product is harmful to the growth of the antibiotic-resistant strain but benefits the antibiotic-sensitive strain by helping turn on the multi-drug exporter to discharge the antibiotic. The utilization of metabolism byproduct indole produced by antibiotic-resistant cells benefits antibiotic-sensitive cells, while the indole-absorbing service of antibiotic sensitive cells unconsciously help in nullifying the indole side effect on antibiotic resistant strain, and a mutual benefit cooperation could therefore evolve.

ecology↗

bioRxiv2021

LmbU directly regulates SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780, which are located outside the lmb cluster and inhibit lincomycin biosynthesis in Streptomyces lincolnensis

The productions of antibiotics are usually regulated by cluster-situated regulators (CSRs), which can directly regulate the genes within the corresponding biosynthetic gene cluster (BGC). However, few studies have looked into the regulation of CSRs on the targets outside the BGC. Here, we screened the targets of LmbU in the whole genome of S. lincolnensis, and found 14 candidate targets, among of which, 8 targets can bind to LmbU by EMSAs. Reporter assays in vivo revealed that LmbU repressed transcription of SLINC_RS02575 and SLINC_RS05540, while activated transcription of SLINC_RS42780. In addition, disruptions of SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780 promoted the production of lincomycin, and qRT-PCR showed that SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780 inhibited transcription of the lmb genes, indicating that all the three regulators can negatively regulate lincomycin biosynthesis. Whats more, the homologues of LmbU and its targets SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780 are widely found in actinomycetes, while the distributions of DNA-binding sites (DBS) of LmbU are diverse, indicating the regulatory mechanisms of LmbU homologues in various strains are different and complicated. IMPORTANCELincomycin is widely used in clinic treatment and animal husbandry. Our previous study firstly demonstrated that LmbU, a novel transcriptional regulator family, functions as a CSR and positively regulates lincomycin biosynthesis. Here, we revealed that LmbU may act as a pleiotropic transcriptional regulator, and directly regulates SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780 which are located outside the lmb cluster and negatively regulate lincomycin biosynthesis. Interestingly, the homologues of LmbU and its targets are widely found in actinomycetes, indicating the regulatory patterns of LmbU to the targets may exist in a variety of strains. Collectively, our findings elucidated the molecular mechanism with which LmbU regulates the target genes outside the lmb culster, and draw a network diagram of LmbU regulation on lincomycin biosynthesis. This lays a solid foundation for the realization of high-yield of lincomycin in industry, and provides the theoretical basis for the functional research of LmbU family proteins.

molecular biology↗

bioRxiv2020

Knockdown of LC3 increases mitochondria-to-micronucleus transition

Nuclear-localized mitochondria were discovered over sixty years ago1; however, the function of these organelles in the initiation of nuclear formation and development remains unknown. Here, we showed that mitochondria fragmented into dense particles to initiate and develop a nucleus, and multiple nuclei were separately and simultaneously formed by fragmented mitochondria in a single cell. The combination of nuclei individually constructed by the mitochondrial assembly of dense particles for nuclear transition partitioned the cytoplasm to form an intranuclear inclusion (INC), whose formation was not related to herniation or invagination of the cytoplasm. During nuclear conversion of itself and neighbouring organelles, the mitochondrion was incorporated into the nucleus to become a nuclear mitochondrion. Knockdown of microtubule-associated protein light chain 3 (LC3), a key autophagic protein, increased free micronuclei by delaying nuclear fusion and enhancing the mitochondria-to-micronuclei transition.

cell biology↗

bioRxiv2020

Mitochondria fragment and reassemble to initiate the formation and development of the nucleus

The function of nuclear-localized mitochondria remains unknown. We found that mitochondria assembled dense particles to fragment and disperse into the particles, which reassembled to initiate nuclear formation and development. Individually-formed nuclei in one single cell were joined together by mitochondrial fragmentation concurrently partitioning cytoplasm to form an intranuclear inclusion (INC), whose creation was not related to herniation or invagination of the cytoplasm. Along with the nuclear transition of a mitochondrion and its neighboring counterparts, the organelle included itself in the nucleus to become nuclear mitochondrion through peripherally assembling of dense particles. New medium reversed the nuclear formation of the organelles to recovery and re-establishment via the return of the particles, which consisted of dense microvesicles (MIVs).

cell biology↗

bioRxiv2020

Cross-Protection Against Zika Virus Infection Conferred by a Live Attenuated Japanese Encephalitis SA14-14-2 Vaccine

Zika virus (ZIKV) and Japanese encephalitis virus (JEV) are closely related mosquito-borne flaviviruses. Japanese encephalitis (JE) vaccine SA14-14-2 has been in the Chinese national Expanded Program on Immunization since 2007. The recent recognition of severe disease syndromes associated with ZIKV, and the identification of ZIKV from mosquitoes in China, prompts an urgent need to investigate the potential interaction between the two. In this study, we showed that SA14-14-2 is protective against ZIKV infection in mice. JE vaccine SA14-14-2 triggered both Th1 and Th2 cross-reactive immune responses to ZIKV; however, it was cellular immunity that predominantly mediated cross-protection against ZIKV infection. Passive transfer of immune sera did not result in significant cross-protection, but did mediate antibody dependent enhancement in vitro, though this did not have an adverse impact on survival. This study suggests that SA14-14-2 vaccine can protect against ZIKV through a cross-reactive T cell response. This is vital information in terms of ZIKV prevention or precaution in those ZIKV-affected regions where JEV circulates or SA14-14-2 is in widespread use, and opens a promising avenue into developing a novel bivalent vaccine against both ZIKV and JEV. ImportanceJapanese encephalitis is a controllable disease in many countries in Asia, especially in China, where many people have Japanese encephalitis virus (JEV) immunity due to extensive JEV vaccination campaigns or natural exposure. Live-attenuated SA14-14-2 strain is a safe and effective vaccine recommended by the World Health Organization and has been vaccinated more than 600 million doses since 1989. As the prevalence of Zika virus (ZIKV) and rising risk in above regions, the cross-reactive immune response between these two antigenically closely related flaviviruses, JEV and ZIKV, should also be fully recognized, which is presumed to be based on those ambiguous cross-reactive immunity between dengue virus and ZIKV. In this study, we found that JEV SA14-14-2 vaccine conferred cross-protection against ZIKV challenge in mice, which is mainly due to cellular immunity rather than neutralizing antibody response. However, specific protective components or cooperation between components warrant to be explored in subsequent experiments. In conclusion, this study can provide important evidence for those who live in JEV-endemic areas and are at risk for ZIKV infection.

microbiology↗

bioRxiv2019

Controlling emulsification for organic solvent-based tissue clearing

Organic solvent-based tissue clearing techniques are hampered by the quenching of fluorescent proteins, partially due to routine complete dehydration. Unexpectedly, we discovered that complete dehydration is unnecessary for organic solvents to clear tissues and that the hidden purpose has been to prevent emulsification. After controlling emulsification of organic solvent-cleared but incompletely dehydrated mouse brain, we achieved sufficient tissue transparency that allowed light-sheet imaging while well-preserving the fluorescence of fluorescent proteins.

neuroscience↗

bioRxiv2019

An Array of 60,000 Antibodies for Proteome-Scale Antibody Generation and Target Discovery

Antibodies are essential for elucidating the roles of genes decoded by genome sequencing. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed the Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 mAbs against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic feature of an antibody. Distinctive combinations of 10,000-20,000 mAbs were found to target specific proteomes by array screening. Phenotype-specific mAb-target pairs were discovered for maize and zebrafish samples. Immunofluorescence and flow cytometry mAbs for human membrane proteins and ChIP-seq mAbs for transcription factors were identified from respective proteome-binding PETAL mAbs. Differential screening of cell surface proteomes of tumor and normal tissues discovered internalizing tumor antigens for antibody-drug conjugates. By discovering high affinity mAbs at a fraction of current time and cost, PETAL enables proteome-scale antibody generation and target discovery.

systems biology↗