Biology subjects

Hou, L.

Publications and source records attributed to Hou, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Loss of age-associated increase in m6A-modified RNA contributes to GABAergic dysregulation in Alzheimer's disease

Dysregulated RNA metabolism is a significant feature of Alzheimers disease (AD), yet how post-transcriptional RNA modifications like N6-methyladenosine (m6A) are altered in AD is unknown. Here, we performed deamination adjacent to RNA modification targets (DART-seq) on human dorsolateral prefrontal cortices to assess changes in m6A with nucleotide resolution. In non-AD brains, m6A sites increased with age, predominantly within the 3'UTR of transcripts encoding tripartite synapse proteins. In contrast, AD brains lost the age-associated m6A site increase and exhibited global hypomethylation of transcripts, including MAPT and APP. Hypomethylated genes involved with GABAergic signaling, glutamate transport, and ubiquitin-mediated proteolysis exhibited reduced expression, connecting m6A to synaptic excitotoxicity and disrupted proteostasis in AD. Site-specific m6A levels were linked with GABRA1 expression and protein levels, but this relationship was abolished in AD. Our findings provide insight into post-transcriptional mechanisms of dysregulated RNA metabolism in AD that are related to aging and GABAergic regulation. HIGHLIGHTSO_LIWith age, the number of m6A sites increases among Control cases (lacking AD pathology) but remains unchanged in AD cases. C_LIO_LITranscripts are globally hypomethylated in AD cases. C_LIO_LIHypomethylation is linked to decreased mRNA expression of transcripts related to synaptic and proteostatic function in AD. C_LIO_LI3UTR-localized m6A sites lack typical association with transcript metabolism of GABRA1 in AD. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/651974v3_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@995c55org.highwire.dtl.DTLVardef@7d0619org.highwire.dtl.DTLVardef@1b6a20org.highwire.dtl.DTLVardef@1d47dce_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions

Whole genome sequencing (WGS) studies have identified hundreds of millions of rare variants (RVs) and have enabled RV association tests (RVATs) of these variants with complex traits and diseases. Analysis of non-coding variants is challenged by the considerable variability in regulatory function which candidate Cis-Regulatory Elements (cCREs) exhibit across cell types. We propose cellSTAAR, which integrates WGS data with single-cell ATAC-seq data to capture variability in chromatin accessibility across cell types via the construction of cell-type-specific functional annotations and variant sets. To reflect the uncertainty in cCRE-gene linking, cellSTAAR also links cCREs to their target genes using an omnibus framework which aggregates results from a variety of popular linking approaches. We applied cellSTAAR on Freeze 8 (N = 60,000) of the NHLBI Trans-Omics for Precision Medicine (TOPMed) consortium data to four lipids phenotypes: LDL cholesterol, a binary variable corresponding to high LDL cholesterol, HDL cholesterol, and triglycerides. We also provide replication results for all four phenotypes using UK Biobank (N = 190,000). Evidence from simulation studies and our real data analysis demonstrates that cellSTAAR boosts power and improves interpretation of RVATs of cCREs.

genetics↗

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↗

bioRxiv2025

Congruent neuronal modulation across competing actions challenges the role of the substantia nigra in action selection

The basal ganglia are involved in the control of movement, but their exact role is unclear. Paradoxically, most of the inhibitory projection neurons in the main output nuclei increase firing around the time of movement; only a small fraction decrease firing. This antagonistic activity pattern could subserve action selection, with the small "decrease" population selectively disinhibiting the desired movement, and the larger "increase" population inhibiting competing movements. The action-selection hypothesis makes an implicit assumption: neurons that decrease firing to disinhibit a specific action should increase firing to inhibit that action when a different action is desired. To test this hypothesis, we recorded projection neurons in the substantia nigra pars reticulata (SNr) of mice trained to alternate between two different types of movements. Many SNr neurons showed a "ramping" pattern of pre-movement firing-rate modulation, with most neurons increasing firing, consistent with previous findings. However, contrary to the action-selection model, the overwhelming majority of SNr neurons exhibited congruent modulation between the competing actions, either increasing or decreasing their firing rates for both actions; only a small fraction of neurons exhibited opposite signs of modulation. Similar results were observed among SNr neurons identified as projecting to the arm or orofacial zones of motor superior colliculus. In addition, brief pauses in SNr firing outside explicit operant tasks were not accompanied by stereotyped movements. Our results are not easily reconciled with simple antagonistic mechanisms for action selection in the basal ganglia output nuclei. We also found that ramping activity in SNr neurons typically began hundreds of ms before self-timed and spontaneous movements, in contrast to previous findings suggesting that basal ganglia output is modulated too late to be involved in movement initiation. Our findings suggest constraints - and raise new questions - about the role of the basal ganglia in movement initiation and action selection.

neuroscience↗

bioRxiv2025

Spinal Cord Ultrasound Stimulation Modulates Corticospinal Excitability

BackgroundLow-intensity focused ultrasound (LIFU) offers superior tissue penetration and enables precise neuromodulation of cortical and subcortical circuits. However, its effects on neural activity in the human spinal cord remain largely unexplored. ObjectiveTo investigate the effects of LIFU on spinal cord neuromodulation under varying conditions of intensity (spatial-peak pulse-average intensity, ISPPA), duty cycle (DC), and pulse repetition frequency (PRF). MethodsThirty-six healthy human volunteers participated in the study. A 500 kHz ultrasound transducer with a focal depth exceeding 100 mm was used to target the C8 spinal cord. Transcranial magnetic stimulation (TMS) was applied to the primary motor cortex (M1) hotspot corresponding to the first dorsal interosseous (FDI) muscle, innervated by the C8 nerve. A 500 ms-duration LIFU was delivered to the C8 spinal cord 400 ms prior to single-pulse TMS over the FDI hotspot. Spinal cord ultrasound stimulation (SCUS) was administered with varying acoustic parameters: intensities (ISPPA: 2.5 and 10 W/cm{superscript 2}), DCs (10% and 30%), and PRFs (500 and 1000 Hz). Changes in corticospinal excitability were assessed by comparing TMS-elicited motor-evoked potentials (MEPs) between active and sham SCUS conditions. ResultsSCUS with an ISPPA of 10 W/cm{superscript 2}, a DC of 30%, and a PRF of 1000 Hz significantly reduced MEP amplitudes compared to sham stimulation. However, at the high intensity (ISPPA of 10 W/cm{superscript 2}), varying the DC between 10% and 30% did not affect MEP amplitudes. Additionally, while a PRF of 1000 Hz decreased MEP amplitudes at 10 W/cm{superscript 2}, a PRF of 500 Hz did not produce significant changes. ConclusionsThe results indicate that ultrasound stimulation of the spinal cord can suppress corticospinal drive to muscles, especially when utilizing high intensity and high PRF parameters. This suggests that ultrasound stimulation may provide a novel method for modulating human spinal neural activity.

neuroscience↗

bioRxiv2024

Discovery and Biosynthesis of Sulfenicin and Its New-to-Nature Acylsulfenic Acid Functional Group

Lifes organic molecules are built with diverse functional groups that enable biology by fine tuning intimate connections through time and space. As such, the discovery of new-to-nature functional groups can expand our understanding of the natural world and motivate new applications in biotechnology and biomedicine. Herein we report the genome-aided discovery of sulfenicin, a novel polyketide-nonribosomal peptide hybrid natural product from a marine Streptomyces bacterium bearing a unique acylsulfenic acid functionality. Through a series of heterologous biosynthesis, functional genetics, and enzymatic reconstitution experiments, we show that this previously described synthetic functional group is biologically assembled by a set of enzymes from both primary and secondary metabolism, including a novel flavin-dependent S-hydroxylase that hydroxylates a thiocarboxylic acids sulfur atom. While the sulfenicin biosynthetic gene cluster is presently without parallel in public databases, acylsulfenic acid-encoding enzymes are widely distributed in bacterial genomes, implying that this labile functional group may similarly have a broad distribution among specialized metabolites.

biochemistry↗

bioRxiv2024

Chromosome-scale assembly and annotation of the wildwheat relative Aegilops comosa

Wild relatives of wheat are valuable sources for enhancing the genetic diversity of common wheat. Aegilops comosa, an annual diploid species with an MM genome constitution, possesses numerous agronomically valuable traits that can be exploited for wheat improvement. In this study, we report a chromosome-level genome assembly of Ae. comosa accession PI 551049, generated using PacBio high-fidelity (HiFi) reads and high-throughput chromosome conformation capture (Hi-C) data. The assembly spans 4.47 Gb, featuring a contig N50 of 23.59 Mb and a scaffold N50 of 619.05 Mb. A total of 39,063 gene models were annotated through a combination of homoeologous proteins, Iso-Seq, and RNA-Seq data. Comparative genome analysis revealed a terminal intrachromosomal translocation in chromosome 2M of Ae. comosa (and Ae. umbellulata) compared to its homoeologous chromosomes in other diploid wheat species. Phylogenetic analysis showed a close relationship between Ae. comosa and Ae. umbellulata. This newly constructed reference genome of Ae. comosa will serve as an important genomic resource for comparative genomic studies and the cloning of agriculturally important genes.

genomics↗

bioRxiv2024

The usual and unusual functions of thioredoxins in the metabolism and stress-response of sulfate-reducing bacteria

Thioredoxins are small, universal, disulfide isomerase proteins with required functions in oxidative stress response and RNA synthesis, among others. However, little is known about how anaerobic organisms maintain their intracellular redox balance or how thioredoxins may function differently under anaerobic metabolism. In this study, we investigated the roles of thioredoxins in sulfate-reducing microorganisms (SRMs). SRMs use sulfate as their primary electron acceptor in respiration to produce sulfide and are found in various environments including marine, freshwater sediments, guts and biofilms on ferrous metals where corrosion occurs. We found SRMs lack common redox maintenance molecules and macromolecules but have many and varied thioredoxins belonging to three types. Then, we probed their functions in the model SRM, Desulfovibrio vulgaris Hildenborough (DvH), by an in vivo disulfide bond capture proteomics experiment in both non-stressed and oxidatively stressed conditions. Our results demonstrated that thioredoxin 1 (Trx1) was essential in DvH and selectively responded to oxidative stress. Our data supported its role in RNA synthesis and energy transduction since Trx1 interacted with DsrC and QmoB. Thioredoxin 3 (Trx3), an atypical thioredoxin, was observed to have roles in sulfur transfer and dissimilatory sulfur metabolism. Next, DvH thioredoxin system protein encoding genes were deleted and single deletion mutant strains were tested for growth phenotypes under a variety of different electron donors, acceptors and toxic metal stresses. It is found that dissimilatory sulfate reduction improves resistance of DvH to metal stress. It appeared the sulfide provided certain protection to DvH from silver and uranium stress. ImportanceWe put forth new functions for thioredoxins and a more robust understanding of sulfate reducing microorganisms physiology. Thioredoxin is of general interest because it has been widely studied for redox homeostasis or cancer therapies dealing with the excess of reactive oxygen species (ROS). Our results indicated that these proteins do have functions in stress response, even in microorganisms that generate large amounts of sulfide. We also identified interaction partners for an atypical thioredoxin, suggesting distinct roles from conserved thioredoxin. Mechanisms of metal stress response were found to be different than direct oxidative stress. Thioredoxin did not appear to be involved in uranium reduction electron transfer pathways, contradicting a hypothesis from the literature.

microbiology↗

bioRxiv2024

Down regulation of Engase in Caenorhabditis elegans may improve its stresses adaptivity

Endo-beta-N-acetylglucosaminidase (ENGASE) is one of the key enzymes involved in the regulation of structure and function of glycoproteins. It is conserved from prokaryotic to eukaryotic cells. Although their activities in vitro and applications have been well studied, the biological function of ENGASE remains to be illustrated. In this study, we analyzed the molecular and physiological function of Engase from Caenorhabditis elegans homolog eng-1(CeEngase). We found that CeEngase knockout or knockdown increased the environmental stresses adaptability, such as heat stress and osmotic stress. Preliminary glycomics analysis showed that the basement membrane proteins of extracellular matrix may be the main targets of CeENGASE. In addition, CeENGASE may selectively prefer to N2H7 glycans on glycoproteins. In conclusion, our data illustrated that the defection and/or down regulation of CeEngase may provide a beneficially adaptation for stresses.

biochemistry↗

bioRxiv2024

Molecular basis of Ad5-nCoV Vaccine-Induced Immunogenicity

In response to coronavirus disease 2019 (COVID-19), numerous vaccines have been developed to protect against SARS-CoV-2 infection. Ad5-nCoV (Convidecia) is a vaccine listed for emergency use by the WHO and has been administrated to millions of people globally. It comprises a series of human adenovirus 5 (Ad5) replication-incompetent vectored vaccines that transduce the spike protein (S) gene of various SARS-CoV-2 strains. Despite promising clinical data demonstrating its safety and effectiveness, the underlying molecular mechanism of its high immunogenicity and incidence of adverse reactions remains less understood. Here we combined cryo-ET, fluorescence microscopy and mass spectrometry to characterize the in situ structures, density and site-specific glycan compositions of the Ad5-nCoV_Wu and Ad5-nCoV_O vaccine-induced S antigens, which encode the unmodified SARS-CoV-2 Wuhan-Hu-1 S gene and optimized Omicron S gene, respectively. We found that the vaccine-induced S are structurally intact, antigenic and densely distributed on the cell membrane. Compared to Ad5-nCoV_Wu induced S, the Ad5-nCoV_O induced S demonstrate significantly better stability and is less likely to induce syncytia among inoculated cells. Our work demonstrated that Ad5-nCoV is a prominent platform for antigen induction and cryo-ET can be a useful technique for vaccine characterization and development.

biophysics↗

bioRxiv2024

Inference of heterogeneous effects in single-cell genetic perturbation screens

Recent single-cell CRISPR screening experiments have combined the advances of genetic editing and single-cell technologies, leading to transcriptome-scale readouts of responses to perturbations at single-cell resolution. An outstanding question is how to efficiently identify heterogeneous causal effects of perturbations using these technologies. Here we present scCAPE, a tool designed to facilitate causal analysis of heterogeneous perturbation effects at the single-cell level. scCAPE disentangles perturbation effects from the inherent cell-state variations and provides nonparametric inferences of perturbation effects at single-cell resolution, permitting a range of downstream tasks including perturbation effect analysis, genetic interaction analysis, perturbation clustering and prioritizing. We benchmarked scCAPE through simulation studies and real datasets to evaluate its performance in characterizing latent confounding factors and accuracy in estimating heterogeneous perturbation effects. The application of scCAPE identified novel heterogeneous genetic interactions among erythroid differentiation drivers. For example, our analysis pinpointed the role of the synergistic interaction between CBL and CNN1 in the S phase.

bioinformatics↗

bioRxiv2024

InstructPLM: Aligning Protein Language Models to Follow Protein Structure Instructions

Large language models are renowned for their efficacy in capturing intricate patterns, including co-evolutionary relationships, and underlying protein languages. However, current methodologies often fall short in illustrating the emergence of genomic insertions, duplications, and insertion/deletions (indels), which account for approximately 14% of human pathogenic mutations. Given that structure dictates function, mutated proteins with similar structures are more likely to persist throughout biological evolution. Motivated by this, we leverage crossmodality alignment and instruct fine-tuning techniques inspired by large language models to align a generative protein language model with protein structure instructions. Specifically, we present a method for generating variable-length and diverse proteins to explore and simulate the complex evolution of life, thereby expanding the repertoire of options for protein engineering. Our proposed protein LM-based approach, InstructPLM, demonstrates significant performance enhancements both in silico and in vitro. On native protein backbones, it achieves a perplexity of 2.68 and a sequence recovery rate of 57.51, surpassing Protein-MPNN by 39.2% and 25.1%, respectively. Furthermore, we validate the efficacy of our model by redesigning PETase and L-MDH. For PETase, all fifteen designed variable-length PETase exhibit depolymerization activity, with eleven surpassing the activity levels of the wild type. Regarding L-MDH, an enzyme lacking an experimentally determined structure, InstructPLM is able to design functional enzymes with an AF2-predicted structure. Code and model weights of InstructPLM are publicly available*.

bioinformatics↗

bioRxiv2024

Co-occurrence of Direct and Indirect Extracellular Electron Transfer Mechanisms during Electroactive Respiration in a Dissimilatory Sulfate Reducing Bacterium

Extracellular electron transfer (EET) propels microbial fuel cell (MFC) technology and contributes to the mobility of redox active minerals and microbial syntrophy in nature. Sulfate-reducing bacteria (SRB), especially the genus Desulfovibrio corrode metal electrodes but are of interest for sulfate-containing MFCs providing wastewater treatment. Although extensive studies on SRB-mediated metal electrode corrosion have been done, there remain knowledge gaps on SRB EET to electrodes. We aimed to determine SRB EET mechanisms towards improving SRB performance in MFC wastewater treatment. Our MFCs with Desulfovibrio vulgaris Hildenborough (DvH), a model SRB, indicated that DvH can harvest and send electrons to the carbon cloth electrode. Electricity production with a maximum power density of [~]0.074 W/m2 was observed when the ratio of lactate (electron and carbon donor) to sulfate (electron acceptor) was 60:20 and 0:10 in the anodic and cathodic chamber, respectively. Patterns in current production compared to variations of electron donor/acceptor ratios in the anode and cathode suggested that attachment of DvH to the electrode and biofilm density were critical for effective electricity generation. Analysis of DvH biofilms at different conditions (planktonic dissimilatory sulfate reduction respiration vs. electroactive respiration) by electron microscopy indicated DvH utilized filaments that resemble nano-pili to attach on electrodes and facilitate EET from cell-to-cell and to the electrode. Proteomics profiling of electroactive respiration proteins indicated DvH adapted to electroactive respiration by presenting more pili-, flagellar-related proteins and histidine kinases on electrodes. To investigate the role of pili and biofilm, we grew two DvH mutants in MFCs under the same conditions. The mutant with a deletion of the major pilus-producing gene yielded less voltage and far less attachment to the electrode, suggesting the importance of pili in EET. The mutant with a deficiency in biofilm formation, however, did not eliminate current production indicating the existence of indirect EET. Untargeted metabolomics profiling showed flavin-based metabolites, potential electron shuttles, were dysregulated between respiration modes. This work revealed the metabolic flexibility of DvH to thrive in less than ideal conditions with solid surfaces as both an electron acceptor (growth on anode) and donor (growth on cathode) by using a combination of direct and indirect EET mechanisms. Understanding DvH EET mechanism could enhance the application of DvH in MFCs treating wastewater. ImportanceWe explored the application of Desulfovibrio vulgaris Hildenborough in microbial fuel cells (MFC) and investigated its potential extracellular electron transfer (EET) mechanism. We also conducted untargeted proteomics and metabolomics profiling, offering insights into how DvH adapts metabolically to different electron donors and acceptors. An understanding of the EET mechanism and metabolic flexibility of DvH holds promise for future uses including bioremediation or enhancing efficacy in MFCs for wastewater treatment applications.

microbiology↗

bioRxiv2024

Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models

The discovery and functional annotation of CRISPR-Cas systems laid the groundwork for the development of novel CRISPR-based gene editing tools. Traditional similarity- search-based Cas discovery strategies, which rely heavily on local sequence alignment and reference Cas homologs, may overlook a significant number of remote homologs with limited sequence similarity; and it can not be applied directly for functional recognition. With the rapid development of protein large language models (LLMs), protein foundation models are expected to help model Cas systems with limited Cas homologs without extensive task-specific training data; however, the full potential of these models for Cas discovery and functional annotation has yet to be determined. To this end, we present a novel, effective and unified AI framework, CHOOSER (Cas HOmlog Observing and SElf-processing scReening), for alignment-free discovery of novel CRISPR-Cas systems with self-processing precursor CRISPR RNA (pre-crRNA) capability utilizing protein foundation models. CHOOSER successfully retrieved 11 novel homologs of Cas{lambda}, the majority of which are predicted to be able to self-process pre-crRNA, nearly doubling the current catalog. One of the candidates, EphcCas{lambda}, was subsequently experimentally validated for its ability to self-process pre-crRNA, target DNA cleavage, and trans-cleavage and was shown to be a promising candidate for use as a CRISPR-Cas-based pathogen detection system. Overall, our study provides an unprecedented perspective and methodology for discovering novel CRISPR-Cas systems with specific functions using foundation models, underscoring the potential for transforming newly identified Cas homologs into genetic editing tools.

bioinformatics↗

bioRxiv2024

Integrated analysis and systematic characterization of the regulatory network for human germline development

Primordial germ cells (PGCs) are the precursors of germline that are specified at embryonic stage. Recent studies reveal that humans employ different mechanisms for PGC specification compared with model organisms such as mice. Moreover, the specific regulatory machinery is still largely unexplored, mainly due to the inaccessible nature of this complex biological process. Here, we collect and integrate multi-omics data, including 581 RNA-seq, 54 ATAC-seq, 45 ChIP-seq, and 69 single-cell RNA-seq samples from different stages of human PGC development to recapitulate the precisely controlled and stepwise process, presenting an atlas in the human PGC database (hPGCdb). With these uniformly processed data and integrated analyses, we characterize the potential key transcription factors and regulatory networks governing human germ cell fate. We validate the important roles of some of the key factors in germ cell development by CRISPRi knockdown. We also identify the soma-germline interaction network and discover the involvement of SDC2 and LAMA4 for PGC development, as well as soma-derived NOTCH2 signaling for germ cell differentiation. Taken together, we have built a database for human PGCs and demonstrate that hPGCdb enables the identification of the missing pieces of mechanisms governing germline development, including both intrinsic and extrinsic regulatory programs.

developmental biology↗

bioRxiv2023

Neutrophil extracellular traps formation is associated with postoperative complications in neonates and infants undergoing congenital cardiac surgery

Pediatric patients with congenital heart diseases (CHD) often undergo surgical repair on cardiopulmonary bypass (CPB). Despite a significant medical and surgical improvement, the mortality of neonates and infants remains high. Damage-associated molecular patterns (DAMPs) are endogenous molecules released from injured/damaged tissues as danger signals. We examined 101 pediatric patients who underwent congenital cardiac surgery on CPB. The mortality rate was 4.0%, and the complication rate was 31.6%. We found that neonates/infants experienced multiple complications most, consistent with the previous knowledge. Neonates and infants in the complication group had received more transfusion intraoperatively than the non-complication arm with lower maximum amplitude (MA) on rewarming CPB thromboelastography (TEG). Despite TEG profiles were comparable at ICU admission between the two groups, the complication arm had higher postoperative chest tube output, requiring more blood transfusion. The complication group showed greater neutrophil extracellular traps (NETs) formation at the end of CPB and postoperatively. Plasma histones and high mobility group box 1 (HMGB1) levels were significantly higher in the complication arm. Both induced NETs in vitro and in vivo. As histones and HMGB1 target Toll-like receptor (TLR)2 and TLR4, their mRNA expression in neutrophils was upregulated in the complication arm. Taken together, NETs play a major role in postoperative complication in pediatric cardiac surgery and would be considered a target for intervention. Key pointsO_LINeonates and infants showed highest postoperative complications with more upregulation of inflammatory transcriptomes of neutrophils. C_LIO_LINeonates and infants with organ dysfunction had more NETs formation with higher plasma histones and HMGB1 levels. C_LI

immunology↗

bioRxiv2023

Unveiling unique microbial nitrogen cycling and novel nitrification drivers in coastal Antarctica

Although microbial nitrogen (N) cycling plays a pivotal role in Antarctic ecosystems, its underlying mechanisms are largely uncharted. In this study, we unravel the biological origin of nitrate via triple oxygen isotopic composition analysis and systematically profile functional N-cycling genes within soil and lake sediment samples from the ice-free areas of East Antarctica. We successfully reconstruct 1,968 metagenome-assembled genomes (MAGs) spanning 29 microbial phyla, enabling the analysis of the presence or absence of 52 diverse metabolic marker genes. Consistent with quantitative data, our metagenomic analyses confirm the active processes of microbial nitrogen fixation, nitrification, and denitrification. We find no detectable anaerobic ammonium oxidation (anammox) processes, underscoring a unique microbial N-cycling dynamic in the region. Notably, we identify the predominance of complete ammonia-oxidizing (comammox) Nitrospira, a recently discovered bacterial guild capable of performing the entire nitrification process within a single organism. Further genomic investigations reveal their adaptive strategies in the Antarctic environment. These strategies likely involve the synthesis of trehalose to counteract cold stress, high substrate affinity to efficiently utilize available resources, and alternative metabolic pathways to adapt to nutrient-scarce conditions. Their significant role in the nitrification process is validated through 13C-DNA-based stable isotope probing (DNA-SIP). This research provides a comprehensive illustration of nitrifications crucial contribution to the nitrogen budget in coastal Antarctica, highlighting comammox Nitrospira clade B as a novel nitrifying agent and shedding new light on the complex biogeochemical processes of nitrogen cycling in coastal Antarctica.

microbiology↗

bioRxiv2023

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.

genetics↗