Biology subjects

Xing, D.

Publications and source records attributed to Xing, D..

At least 19 recordsLinked to original sources

bioRxiv2026

A sampling-theory framework for richness-uniqueness relationships

Ecological uniqueness, commonly quantified by local contribution to beta diversity (LCBD), is important for understanding and conserving biodiversity. Its widely documented negative relationship with species richness has led to the view that species-poor communities may be disproportionately important for regional diversity. Here, we derive neutral expectations for richness-uniqueness relationships and show that negative slopes can arise from neutral assembly rather than necessarily reflecting an ecological signal of uniqueness. Neutral simulations validate the analytical expectations across abundance- and incidence-based LCBD formulations. Applying the framework to the Barro Colorado Island tropical forest and North American Breeding Bird Survey, we show that accounting for neutral sampling expectations substantially changes the ranking and spatial distribution of ecologically unique sites. By separating neutral sampling expectations from excess uniqueness, our framework provides a principled basis for interpreting ecological uniqueness and informing biodiversity conservation.

ecology↗

bioRxiv2026

Shank3 mutation disrupts affective touch encoding in the dorsal medial prefrontal cortex of Beagle dogs

Individuals with autism spectrum disorder (ASD) often show aversion to affective touch (AT). However, the neural mechanism of this abnormality in cortices remains poorly understood probably due to the lack of effective animal models. Here, we used a canine model to address this issue by leveraging the intimate dog-human interactions. In a newly-designed heterospecific AT paradigm, we found that dogs carrying mutations in Shank3, a high-risk gene for ASD, avoided human AT. In vivo single-unit recording analysis showed that AT-evoked oscillations in the dorsal medial prefrontal cortex (dmPFC) were significantly altered in Shank3 mutant dogs. Shank3 mutation also reduced the number of neurons encoding AT in the dmPFC. Importantly, the aversion to AT and altered neural processing in Shank3 mutants were largely rescued by a GABAA receptor antagonist pentylenetetrazole. Together, these findings provide neural mechanisms for abnormal AT processing in ASD and suggest potential biomarkers for therapeutic strategies.

neuroscience↗

bioRxiv2026

The Capillary endothelial cell-governed niche sustains angiogenesis in proliferating infantile hemangioma via multilayer stromal support

Infantile hemangioma (IH), the most common benign vascular tumor in infants, is characterized by the aberrant proliferation of hemangioma endothelial cells (HemECs) and excessive angiogenesis. However, it is unclear how the tumor microenvironment sustains these active angiogenic signals. We performed single-cell RNA sequencing and spatial transcriptomic to profile 30 samples from proliferating IH, involuting IH, and normal skin. The results indicated that HemECs comprised distinct subpopulations. Among them, capillary endothelial cells (Cap.ECs) had an immature phenotype and functioned as the core drivers of IH. The endothelial-to-mesenchymal transition endothelial cells (endoMT-ECs) secreted collagen and engaged in CD44-mediated crosstalk with Cap.ECs to construct the angiogenesis-active niche in the tumor microenvironment (TME) of proliferating IH. Blockade of CD44-mediated intercellular communication effectively suppresses the angiogenesis of HemECs and promotes tumor regression. Beyond the endothelial layer, pericytes tightly enveloped Cap.ECs, with SERPINE2+ subtypes sustaining their angiogenic activity via ANGPT signaling. Pseudotime trajectory analysis revealed that the mesenchymal stem cells (MSCs)-enriched niche serves as a progenitor pool for Cap.ECs in proliferating IH. Our findings thus revealed that IH progression relies on CD44-mediated endoMT-EC-Cap.EC crosstalk and on both pericyte and MSC niches to sustain angiogenesis. HIGHLIGHTSO_LICapillary endothelial cells drive infantile hemangioma progression, with pericytes tightly ensheathing them. C_LIO_LICD44-mediated capillary and endoMT-derived endothelial cells crosstalk construct the angiogenic-active niche in the tumor microenvironment of proliferating infantile hemangioma. C_LIO_LIThe MSC-enriched niche provides a progenitor pool for the capillary endothelial cells in proliferating infantile hemangioma. C_LI

cancer biology↗

bioRxiv2026

Hippocampal-cortical coupling dynamics drive system consolidation of remote memory

System consolidation transforms temporary hippocampal representation of memory into long-term storage in cortex. The underlying neural substrate, however, remains enigmatic. Here, we tracked the spatiotemporal evolution of hippocampus (HPC)-cortex local field potentials and single-neuron spikes in behaving animals during fear memory formation. During learning, HPC fast gamma exhibited a progressive phase shift relative to PFC theta oscillations, with gamma power aligning to progressively later phases of the PFC theta cycle. Strikingly, a related phase-shifted coupling pattern re-emerged during subsequent consolidation in association with hippocampal sharp-wave ripples and transient PFC spindle events during NREM sleep. Across this process, interregional interactions evolved from HPC-driven cortical gamma coherence at recent stages to PFC-mediated cortical low-frequency coherence at remote stages. Using closed-loop optogenetic perturbations, we demonstrated a stepwise causal chain of coupling events underlying remote memory formation. Our study revealed HPC-PFC coupling phase shift as a feasible substrate mediating recent-to-remote transformation of memory.

neuroscience↗

bioRxiv2026

CD248 activates TGF-β receptor I to promote vascular remodeling in pulmonary arterial hypertension

I.BackgroundPulmonary arterial hypertension (PAH) is a debilitating cardiopulmonary disease characterized by progressive remodeling of the pulmonary vasculature. Pathologic transforming growth factor-{beta} (TGF-{beta}) signaling is an essential driver of vascular remodeling in PAH. While global inhibitors of TGF-{beta} exist, their clinical application is limited by systemic adverse effects. Therefore, a critically unmet need in PAH is to identify pulmonary vascular-specific regulators of the TGF-{beta} axis, which would selectively enhance clinical efficacy while minimizing adverse effects. As the clinical care of PAH largely promotes vasodilation, and only one FDA-approved agent targets vascular remodeling, this study aimed to identify selective, therapeutically targetable regulators of the TGF-{beta} axis in the PAH pulmonary vasculature. MethodsCD248 was identified via liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics in human lungs. CD248 levels were assessed across human, rat, and mouse lung tissues using western blotting, RTqPCR, and/or immunofluorescence techniques. CD248-null (CD248-/-) mice were used to study the contribution of CD248 to hypoxia-sugen (H/S)-induced PAH. The mechanistic role of CD248 in PAH vascular remodeling and TGF-{beta} signaling was assessed by genetic (siRNA knockdown; overexpression) and pharmacologic (Ontuxizumab) manipulation of primary human pulmonary vascular cells. ResultsLC-MS/MS proteomics coupled with pathway enrichment analysis of human lung tissue identified CD248 as a putative mediator of vascular remodeling that is elevated in PAH lungs. CD248 was elevated in PAH pulmonary artery smooth muscle cells (PASMCs) across human, rat, and mouse lung tissue. CD248-/- mice were protected from H/S-induced elevations in right ventricular (RV) systolic pressure (RVSP), RV hypertrophy, and pulmonary artery muscularization. CD248 knock-down reduced cell proliferation and migration of primary PAH PASMCs. CD248 was essential for phospho-activation of TGF-{beta} receptor I (T{beta}RI) at S165 and canonical phosphorylation of SMAD3 at S423/425. CD248 loss blunted TGF-{beta}-induced gene expression (FN1, Col11, -SMA) and activated expression of the vasoprotective matrix metalloprotease, MMP-8. Mechanistically, CD248 interacted with and enhanced de novo phosphorylation and stability of T{beta}RI, blocking its ubiquitin-mediated proteasomal degradation. Ontuxizumab promoted T{beta}RI instability and attenuated the production of FN1, Col11, and -SMA in primary PAH PASMCs. ConclusionsThis work identifies CD248 as a previously unrecognized co-activator of T{beta}RI in PAH. As CD248 is largely quiescent in most adult tissues yet pathologically upregulated in the PAH pulmonary vasculature, this study supports the potential of anti-CD248 therapy as a novel pulmonary vascular-specific alternative to systemic TGF-{beta} inhibition.

molecular biology↗

bioRxiv2026

Coupling abundance and spatial distribution for an unbiased and tractable beta diversity framework

While fundamental for understanding community assembly, dominant beta diversity metrics suffer from severe sample-size dependence and lack tractable generative predictions. Here, we generalize Whittakers multiplicative index into a novel abundance-weighted framework. By proving this index strictly equals the expectation of the Good-Turing sample coverage deficit, we unify species abundance and spatial occupancy into a single, design-unbiased parameter. Furthermore, deriving exact neutral expectations provides process-based baselines to dissect beta diversitys internal structure via additive decomposition into species (SCBD) and local (LCBD) contributions. Application to two large-scale forest plots empirically validates its strict sampling invariance and reveals non-neutral signatures. Crucially, our SCBD diagnostic reveals a striking ecological phase transition: rare-to-intermediate species are more spatially scattered than neutral drift predicts until reaching an aggregation onset threshold, beyond which dominant species exhibit supra-neutral aggregation, reflecting competition-colonization trade-offs. Concurrently, LCBD diagnostics successfully isolate the spatial footprints of environmental filtering from pervasive neutral noise. By avoiding the conflation of statistical estimation bias from genuine biological scaling and anchoring metrics in tractable models, this framework provides a rigorous toolkit that transforms our empirical understanding of spatial coexistence.

ecology↗

bioRxiv2025

Beyond Inheritance: De novo Fast Motion Computation in Primate Visual Cortex

Objects move through space and time, generating sequential visuotopic activations in all sighted animals leading to motion perception of velocity defined by direction and speed. Humans can effortlessly see motion with speeds ranging from 0.25 to 500{degrees}/s. However, direction-selective neurons in the primary visual cortex (V1)--from which all subsequent processing is presumed to derive-- only encode directionality at low speeds. To resolve this paradox, we recorded neuronal responses to moving dots, gratings, and movies across the LGN, V1, MT and MST of the macaque motion pathway. Regardless of cell type and motion stimuli, V1 neurons lost direction selectivity at [~]29{degrees}/s while MT and MST neurons maintained it up to [~]82{degrees}/s and [~]183{degrees}/s, respectively. A cascaded spatiotemporal integration model reveals that at each cortex direction-selective neurons can generate velocity selectivity de novo, by integrating sequential visuotopic activations from preceding areas, irrespective of speed and directionality. By computing velocity anew, the primate brain effectively uses the cortical hierarchy itself to shift gears to efficiently encode slow and fast motion. Thus, five visual areas from the retina into the brains processing hierarchy, external spatiotemporal information is being computed afresh, offering insights for motion processing in other species, modalities and machine vision.

neuroscience↗

bioRxiv2025

Regional Vulnerability of Cardiac Chambers to Radiotherapy: A Multi-Omics Perspective

The heart is highly vulnerable to radiotherapy (RT)-induced injury, leading to molecular and structural remodeling collectively termed radiation-induced cardiac toxicity (RICT). Although several biological pathways have been implicated, the regional, cardiac-specific molecular responses to radiation exposure remain incompletely understood. Here, a multi-omics approach was adopted to longitudinally characterise the unique responses to radiation of the heart base (including ventricular base and right atrium), or the heart apex. Ventricular base irradiation induced a cardiomyopathy phenotype, with pronounced molecular perturbations in metabolism and electrical conduction, while changes related to tissue structure were predominant following apex-directed RT. In the right atrium, irradiation drives fibrotic tissue remodelling, leading to an increased propensity for atrial fibrillation, underpinned by changes in sarcomere organisation. This study represents a comprehensive characterisation of differential spatiotemporal radiation effects in the heart and highlights biological and functional pathways that are potentially clinically actionable for cardiac radioprotection and monitoring.

cell biology↗

bioRxiv2025

First Whole-Genome Chikungunya Virus Sequence Detected in Mosquitoes during the 2025 Foshan Outbreak: Evidence of Field Vector Infection and Transmission Potential in China

BackgroundSince July 2025, an outbreak of mosquito-borne chikungunya fever occurred in Foshan City, Guangdong Province, China. This was the second outbreak in China following the one that occurred in Dongguan City, Guangdong Province, in 2010. Moreover, the intensity of this outbreak was significantly greater than that of the previous one. Updates to 23 August, more than 10,000 human cases had been reported. Here, we present the first full genome sequence of the chikungunya virus (CHIKV) derived from field-trapped mosquitoes during the outbreak. MethodsAdult Aedes albopictus were BG-trap captured from residences and parklands in three hotspot towns with high density of confirmed human cases. Mosquitoes were morphologically identified and pooled by species, sex and environment types. RNA was extracted, screened by CHIKV RT-qPCR, then positive pools underwent sanger and whole-genome sequencing for complete sequences. Lineage and mutational profiles were inferred by maximum likelihood phylogenetic and comparison against human and mosquito genomes. The distribution of amino acid site mutations in different protein coding regions was also analyzed. ResultThrough 11 days of collection using 10 BG-traps, 2,803 mosquitoes were captured. 1569 (55.97%) female Ae. albopictus were divided into 77 pools and 9.09% (7/77) of the pools tested positive for CHIKV. The local Ae. albopictus minimum infection rate (MIR, per 1000 females) was 4.46, while the MIR for residences in Lecong Town was the highest at 9.17. The MIR for parklands was slight higher than for residences (4.60 vs. 4.30). All the 5 Ae. albopictus-derived complete CHIKV genome clustered within ECSA-Indian Ocean lineage genotype, closely related to human-derived genomes on 2025 Reunion Island. Amino-acid mutations E1-A226V/E2-L210Q were detected in the strains, which enhanced adaptability to Ae. albopictus and increased the transmission capacity. Novel mutation observed on E1 and E2 were totally consist to the patient-derived CHIKV in 2025 Reunion Island. ConclusionsIt was the first mosquito-derived CHIKV whole-genome during the 2025 Foshan outbreak, filling a critical gap between human case and entomological surveillance. Ae. albopictus was confirmed as the primary vector during the outbreak. The current outbreak CHIKV strain with particular amino-acid mutations had adapted to Ae. albopictus transmission. Compared to previous Chikungunya outbreaks over the past decade, the Foshan outbreak occurred earlier (early July), in a larger urban area (with a population of over 9.5 million), and with abundant breeding sites for the vector mosquito Ae. albopictus. However, the outbreak was quickly brought under control, with daily case numbers consistently decreasing, which is closely linked to the strong vector control measures implemented by the Chinese government in the early stages of the outbreak. Moreover, this event once again underscores the necessity of early monitoring of vector mosquitoes and the importance of implementing highly effective vector intervention measures as soon as possible after an outbreak occurs.

microbiology↗

bioRxiv2025

scDIAGRAM: Detecting Chromatin Compartments from Individual Single-Cell Hi-C Matrix without Imputation or Reference Features

Single-cell Hi-C (scHi-C) provides unprecedented insight into 3D genome organization, but its sparse and noisy data pose challenges in accurately detecting A/B compartments, which are crucial for understanding chromatin structure and gene regulation. We presented scDIAGRAM, a data-driven method for annotating A/B compartments in single cells using direct statistical modeling and graph community detection. Unlike existing approaches, scDIAGRAM operates without relying on external information, such as the CpG density or imputation techniques, and preserves cell-to-cell heterogeneity. Accuracy and robustness of scDIAGRAM were illustrated through simulated scHi-C datasets and a human cell line. We applied scDIAGRAM to real scHi-C datasets from the mouse brain cortex, mouse embryonic development, and human acute myeloid leukemia (AML), demonstrating its ability to capture compartmental shifts associated with transcriptional variation. This robust framework offers new insights into the functional roles of chromatin compartments at single-cell resolution across various biological contexts.

bioinformatics↗

bioRxiv2025

HSV-1 orchestrates host RAP80 ubiquitination by ICP0 and UL36USP to promote viral survival

Herpes simplex virus 1 (HSV-1) is a widespread human pathogen that establishes lifelong infections, ubiquitination is crucial for HSV - 1 to interact with the host and regulate its life activities. But the mechanisms of how HSV-1 dynamically modulates host proteins at different infection stages to promote its own survival remains challenging. Here we identified DNA damage response protein RAP80 as a critical target of HSV-1 ubiquitination enzymes ICP0 and UL36USP throughout HSV-1s infection cycle. In early stages, RAP80 inhibits HSV-1 transcription by directly binding to the viral genome, blocking viral protein ICP4 binding to transcription factors. This interaction is regulated by phase separation via an intricate interplay between RAP80 and ICP0/ICP4. As infection progresses, the viral E3 ligase ICP0 degrades RAP80, dissolving phase separation, and allowing the formation of a mature viral replication compartment. In late infection stages, RAP80 is deubiquitinated by the viral deubiquitinase UL36USP, which restores cellular homeostasis and promotes HSV-1 survival. This process involves modulating the R-loop-cGAS-apoptosis pathway. These findings underscore the dynamic interplay between viral and host factors and the complex mechanisms used by HSV-1 to subvert host defenses, offering practical implications for the future development of antiviral strategies.

molecular biology↗

bioRxiv2024

Hypoxia exposure fine-tunes mitochondrial function in sea turtle cells

Sea turtles experience extreme fluctuations in oxygen availability derived from extended breath-hold diving, yet the cellular adjustments that underlie hypoxia tolerance in these animals remain poorly understood. Here, we used metabolite profiling, extracellular flux assays, and microscopic analyses of the mitochondrial reticulum to study how primary cells derived from sea turtles and lizards cope with extended hypoxia exposure. Cells from both species proliferate in primary culture, stain positive for fibroblast markers, are metabolically active, and stabilize HIF1- when exposed to chemical or environmental hypoxia. In contrast to lizard cells, sea turtle cells exhibit a faster and more robust response to 1 or 24-hour hypoxia exposure (0.1% O2), upregulating antioxidant pathways and optimizing oxygen use rather than relying on glycolytic metabolism. Similarly, the mitochondrial reticulum is maintained without apparent fragmentation during hypoxia exposure in sea turtle cells. Consistent with these observations, mitochondrial function readily recovers in sea turtle but not lizard cells upon reoxygenation. These findings show that sea turtle cells undergo intrinsic metabolic adjustments to cope with extreme oxygen fluctuations, aligning with the remarkable hypoxic tolerance exhibited by these animals, which can endure up to 7 hours of breath-holding underwater.

physiology↗

bioRxiv2022

Spatial transcriptomic profiling of coronary endothelial cells in SARS-CoV-2 myocarditis

ObjectivesOur objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. BackgroundSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has well-established links to thrombotic and cardiovascular events. Endothelial cell infection was initially proposed to initiate vascular events; however, this paradigm has sparked growing controversy. The significance of myocardial infection also remains unclear. MethodsAutopsy-derived cardiac tissue from control (n = 4) and COVID-19 (n = 8) patients underwent spatial transcriptomic profiling to assess differential expression patterns in myocardial and coronary vascular tissue. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. In so doing, we examined the paracrine effect of SARS-CoV-2 infection in cardiac tissue. ResultsWe observed heterogeneous myocardial infection that tended to colocalize with CD31 positive cells within coronary capillaries. Despite these differences, COVID-19 patients displayed a uniform and unique myocardial transcriptional profile independent of local viral burden. Segmentation of tissues directly infected with SARS-CoV-2 showed unique, pro-inflammatory expression profiles including upregulated mediators of viral antigen presentation and immune regulation. Infected cell types appeared to primarily be capillary endothelial cells as differentially expressed genes included endothelial cell markers. However, there was limited differential expression within the endothelium of larger coronary vessels. ConclusionsOur results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. However, similar patterns were not observed in larger vessels, diminishing endotheliitis and endothelial activation as key drivers of cardiovascular events during COVID-19. Condensed AbstractSARS-CoV-2 is linked to thrombotic and cardiovascular events; however, the mechanism remains uncertain. Our objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. Autopsy-derived coronary arterial and cardiac tissues from control and COVID-19 patients underwent spatial transcriptomic profiling. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. We observed unique, pro-inflammatory expression profiles among all COVID-19 patients. While heterogeneous viral expression was noted within the tissue, SARS-CoV-2 tended to colocalize with CD31 positive cells within coronary capillaries and was associated with unique expression profiles. Similar patterns were not observed in larger coronary vessels. Our results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. Such results diminish coronary arterial endotheliitis and endothelial activation as key drivers of cardiovascular events during COVID-19 infection. LIST OF HIGHLIGHTSO_LISARS-CoV-2 has variable expression patterns within the myocardium of COVID-19 patients C_LIO_LISARS-CoV-2 infection induces a unique myocardial transcriptional programming independent of local viral burden C_LIO_LISARS-CoV-2 myocarditis is predominantly associated with capillaritis, and tissues directly infected with SARS-CoV-2 have unique, pro-inflammatory expression profiles C_LIO_LIDiffuse endothelial activation of larger coronary vessels was absent, diminishing large artery endotheliitis as a significant contributor to cardiovascular events during COVID-19 infection. C_LI

pathology↗

bioRxiv2022

Engineering of NEMO as calcium indicators with ultra-high dynamics and sensitivity

Genetically-encoded calcium indicators (GECI) are indispensable tools for real-time monitoring of intracellular calcium signals and cellular activities in living organisms. Current GECIs face the challenge of sub-optimal peak signal-to-baseline-ratio (SBR) with limited resolution for reporting subtle calcium transients. We report herein the development of a suite of calcium sensors, designated NEMO, with fast kinetics and wide dynamic ranges (>100-fold). NEMO indicators report Ca2+ transients with peak SBRs ~20-fold larger than the top-of-the-range GCaMP series. NEMO sensors further enable the quantification of absolution calcium concentration with ratiometric or photochromic imaging. Compared to GCaMPs, NEMOs could detect single action potentials in neurons with a peak SBR two times higher and a median peak SBR four times larger in vivo, thereby outperforming most existing state-of-the-art GECIs. Given their high sensitivity and resolution to report intracellular Ca2+ signals, NEMO sensors may find broad applications in monitoring neuronal activities and other Ca2+-modulated physiological processes in both mammals and plants.

synthetic biology↗

bioRxiv2022

A high potent synthetic nanobody with broad-spectrum activity neutralizes SARS-Cov-2 virus and Omicron variant through a unique binding mode

The major challenge to control COVID pandemic is the rapid mutation rate of the SARS-Cov-2 virus, leading to the escape of the protection of vaccines and most of the neutralizing antibodies to date. Thus, it is essential to develop neutralizing antibodies with broad-spectrum activity targeting multiple SARS-Cov-2 variants. Here, we reported a synthetic nanobody (named C5G2) obtianed by phage display and subsequent antibody engineering. C5G2 has a single digit nanomolar binding affinity to RBD domain and inhibits its binding to ACE2 with an IC50 of 3.7 nM. Pseudovirus assay indicated that the monovalent C5G2 could protect the cells from the infection of SARS-Cov-2 wild type virus and most of the virus of concern, i.e. Alpha, Beta, Gamma and Omicron variants. Strikingly, C5G2 has the highest potency against Omicron among all the variants with the IC50 of 4.9ng/mL. The Cryo-EM structure of C5G2 in complex with the Spike trimer showed that C5G2 bind to RBD mainly through its CDR3 at a conserved region that not overlapping with the ACE2 binding surface. Additionally, C5G2 bind simultaneously to the neighboring NTD domain of spike trimer through the same CDR3 loop, which may further increase its potency against the virus infection. Third, the steric hindrance caused by FR2 of C5G2 could inhibit the binding of ACE2 to RBD as well. Thus, this triple-function nanobody may be served as an effective drug for the prophylaxis and therapy against Omicron as well as future variants.

biochemistry↗

bioRxiv2022

Emergence of distinct neural subspaces in motor cortical dynamics during volitional adjustments of ongoing locomotion

3The brain is capable of simultaneously carrying out multiple functions, such as making different types of movements at the same time. One example is how we are able to both carry out stereotyped walking or running movements, while concurrently performing precise, target-directed movements such as kicking a ball in a soccer match. Recently, research has shown that different computations within the same population of neurons can be carried out without disrupting each other by confining the processes into separate subspaces. Whether this strategy is used to precisely control our limbs while maintaining locomotion is still an open question. Here, we recorded the activity of primary motor cortex in nonhuman primates during obstacle avoidance on a treadmill. We found that the same neural population was active during both basic unobstructed locomotion and volitional obstacle avoidance movements. Additionally, we identified the neural modes spanning the subspace of the low-dimensional dynamics in M1 using both supervised and unsupervised techniques. We found that motor cortex employs a subspace that consistently maintains the same cyclic activity throughout obstacle stepping, despite large changes in the movement itself. All the variance corresponding to the large change in movement during the obstacle avoidance is confined to its own distinct subspace. Our findings suggest that M1 utilizes different activity subspaces to coordinate the maintenance of ongoing locomotor-related neural dynamics and fast volitional gait adjustments during complex locomotion. 4 Significance StatementOur ability to modulate our ongoing walking gait with precise, voluntary adjustments is what allows us to navigate complex terrains. Locomotion and precise, goal-directed movements, such as reaching are two distinct movement modalities and have been shown to have differing requirements of motor cortical input. It is unknown how these two movements are represented in M1 low dimensional dynamics when both are carried out at the same time, such as during obstacle avoidance. We developed a novel obstacle avoidance paradigm in freely-moving non-human primates and discovered that the strategy employed by motor cortex is to confine the rhythmic locomotion-related dynamics and the voluntary, gait-adjustment movement into separate subspaces.

neuroscience↗

bioRxiv2022

Bacterial threat assessment of bacteriophage infection is mediated by intracellular polyamine accumulation and Gac/Rsm signaling

When eukaryotic cells are killed by pathogenic microorganisms, damage-associated and pathogen-associated signals are generated that alert other cells of nearby danger. Bacteria can detect the death of their kin; however, how bacteria make threat assessments of cellular injury is largely unexplored. Here we show that polyamines released by lysed bacteria serve as damage-associated molecules in Pseudomonas aeruginosa. In response to exogenous polyamines, Gac/Rsm and cyclic-di-GMP signaling is activated and intracellular polyamine levels increase. In the absence of a threat, polyamines are catabolized, and intracellular polyamines return to basal levels, but cells infected by bacteriophage increase and maintain intracellular polyamine levels, which inhibits phage replication. Phage species not inhibited by polyamines did not trigger polyamine accumulation by P. aeruginosa, suggesting polyamine accumulation and metabolism are targets in the phage-host arms-race. Our results suggest that like eukaryotic cells, bacteria can differentiate damage-associated and pathogen-associated signals to make threat assessments of cellular injury. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/486733v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1f69334org.highwire.dtl.DTLVardef@13a4422org.highwire.dtl.DTLVardef@4f3edeorg.highwire.dtl.DTLVardef@a86c43_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

CsMYB4a from Camellia sinensis Regulates the Auxin Signaling Pathway by Interacting with CsIAA4

Members of the R2R3-MYB4 subgroup are well-known negative regulatory transcription factors of phenylpropane and lignin pathways. In this study, we found that transgenic tobacco plants overexpressing a R2R3-MYB4 subgroup gene from Camellia sinensis (CsMYB4a) showed inhibited growth that was not regulated by phenylpropane and lignin pathways, and these plants exhibited altered sensitivity to synthetic auxin 1-naphthaleneacetic acid (-NAA) treatment. An auxin/indole-3-acetic acid 4 (AUX/IAA4) gene from Camellia sinensis (CsIAA4) participating in the regulation of the auxin signal transduction pathway was screened from the yeast two-hybrid library with CsMYB4a as the bait protein, and tobacco plants overexpressing this gene showed a series of auxin-deficiency phenotypes, such as dwarfism, small leaves, reduced lateral roots, and a shorter primary root. CsIAA4 transgenic tobacco plants were less sensitive to exogenous -NAA than control plants, which was consistent with the findings for CsMYB4a transgenic tobacco plants. The knockout of the endogenous NtIAA4 gene (a CsIAA4 homologous gene) in tobacco plants alleviated growth inhibition in CsMYB4a transgenic tobacco plants. Furthermore, protein-protein interaction experiments proved that domain II of CsIAA4 is the key motif for the interaction between CsIAA4 and CsMYB4a and that the degradation of CsIAA4 is prevented when CsMYB4a interacts with CsIAA4. In summary, our results suggest that CsMYB4a is a multifunctional transcription factor that regulates the auxin signaling pathway, phenylpropane and lignin pathways. This study provides new insights into the multiple functions of R2R3-MYB4 subgroup members as a group of well-known negative regulatory transcription factors. One-sentence summaryCsMYB4a act as multifunctional transcription factor that regulates the auxin signaling pathway, phenylpropane and lignin pathways.

physiology↗