Biology subjects

Chen, P.

Publications and source records attributed to Chen, P..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Exploring Genomic Large Language Models: Bridging the Gap between Natural Language and Gene Sequences

MotivationWith the rapid development of genomic sequencing technologies and accumulation of sequencing data, there is an increasing demand for analysis tools that are more user-friendly for non-programmer users. In support of this initiative, we developed an all-in-one tool called GenomicLLM that can understand simple grammar in the question input and perform different types of analyses and tasks accordingly. ReaultsWe trained the GenomicLLM model using three large open-access datasets, namely GenomicLLM_GRCh38, Genome Understanding Evaluation and GenomicBenchmarks, and developed a hybrid tokenization approach to allow better comprehension from mixed corpora that include sequence and non-sequence inputs. GenomicLLM can carry out a wider range of tasks. In the classification tasks that are also available in the state-of-the-art DNABERT-2 and HyenaDNA, GenomicLLM has comparable performance. Moreover, GenomicLLM can also carry out other regression and generation tasks that are not accomplishable by these tools. In summary, we demonstrated here a successful large language model with a mixture of gene sequences and natural language corpus that enables a wider range of applications. Availability and implementationCodes and data can be accessed at https://github.com/Huatsing-Lau/GenomicLLM and https://zenodo.org/records/10695802

bioinformatics↗

bioRxiv2024

Gentle rhodamines for live-cell fluorescence microscopy

Rhodamines have been continuously optimized in brightness, biocompatibility, and colors to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglected, hampering their use in time-lapse imaging. Here we introduce cyclooctatetraene (COT) conjugated rhodamines that span the visible spectrum and exhibit significantly reduced phototoxicity. We identified a general strategy for the generation of Gentle Rhodamines, which preserved their outstanding spectroscopic properties and cell permeability while showing an efficient reduction of singlet-oxygen formation and diminished cellular photodamage. Paradoxically, their photobleaching kinetics do not go hand in hand with reduced phototoxicity. By combining COT-conjugated spirocyclization motifs with targeting moieties, these gentle rhodamines compose a toolkit for time-lapse imaging of mitochondria, DNA, and actin and synergize with covalent and exchangeable HaloTag labeling of cellular proteins with less photodamage than their commonly used precursors. Taken together, the Gentle Rhodamines generally offer alleviated phototoxicity and allow advanced video recording applications, including voltage imaging.

cell biology↗

bioRxiv2024

DeepResBat: deep residual batch harmonization accounting for covariate distribution differences

Pooling MRI data from multiple datasets requires harmonization to reduce undesired inter-site variabilities, while preserving effects of biological variables (or covariates). The popular harmonization approach ComBat uses a mixed effect regression framework that explicitly accounts for covariate distribution differences across datasets. There is also significant interest in developing harmonization approaches based on deep neural networks (DNNs), such as conditional variational autoencoder (cVAE). However, current DNN approaches do not explicitly account for covariate distribution differences across datasets. Here, we provide mathematical results, suggesting that not accounting for covariates can lead to suboptimal harmonization. We propose two DNN-based covariate-aware harmonization approaches: covariate VAE (coVAE) and DeepResBat. The coVAE approach is a natural extension of cVAE by concatenating covariates and site information with site- and covariate-invariant latent representations. DeepResBat adopts a residual framework inspired by ComBat. DeepResBat first removes the effects of covariates with nonlinear regression trees, followed by eliminating site differences with cVAE. Finally, covariate effects are added back to the harmonized residuals. Using three datasets from three continents with a total of 2787 participants and 10085 anatomical T1 scans, we find that DeepResBat and coVAE outperformed ComBat, CovBat and cVAE in terms of removing dataset differences, while enhancing biological effects of interest. However, coVAE hallucinates spurious associations between anatomical MRI and covariates even when no association exists. Future studies proposing DNN-based harmonization approaches should be aware of this false positive pitfall. Overall, our results suggest that DeepResBat is an effective deep learning alternative to ComBat. Code for DeepResBat can be found here: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/harmonization/An2024_DeepResBat.

neuroscience↗

bioRxiv2024

Tcf12 controls dynamic calvarial bone growth and motor learning in mice

Heterozygous loss-of-function mutations of TCF12 and TWIST1 can each cause craniosynostosis and neurodevelopmental delay in humans. Twist1-Tcf12 interaction plays an important role in regulating suture development. Although the molecular and cellular mechanisms underlying craniosynostosis and neurocognitive dysfunctions in Twist1+/- mice have been studied, less information on the role of Tcf12 in these defects is available. To investigate the functional mechanism of Tcf12 in regulating skull and brain development, we analyzed the skull shape of Wnt1-Cre;Mesp1-Cre;Tcf12fl/fl mice and found that, despite mild coronal synostosis, their skull shape appears to be similar to that of controls. We also found evidence of impaired motor learning ability in Tcf12 mutant mice. Furthermore, loss of Tcf12 in neural crest lineage leads to upregulated Runx2 expression in the calvarial mesenchyme and posterior expansion of the frontal bone in Wnt1-Cre;Tcf12fl/fl mice. Mechanistically, we show that Lmx1b is a direct downstream target of Tcf12 for the regulation of osteogenic differentiation in the calvarial mesenchyme during embryonic development. Importantly, overexpression of Lmx1b inhibits osteogenic differentiation in the calvarial mesenchyme of Wnt1-Cre;Tcf12fl/fl mice, indicating Tcf12s regulation of Lmx1b expression is crucial for controlling osteogenesis during calvarial bone development. Our study suggests that Tcf12 expression in the brain is crucial for motor learning. Moreover, this study establishes a new molecular mechanism underlying regulation of calvarial bone formation. Author SummaryCraniosynostosis is characterized by premature fusion of cranial sutures and associated with abnormal skull growth, delayed brain development, and often impaired brain functions. Loss-of-function mutation of TCF12 can cause coronal synostosis and neurodevelopmental delay in humans. In developing mouse sutures, Tcf12 is essential for maintaining the boundary between sutural and osteogenic cells. However, roles of Tcf12 in skull formation and brain development have not been fully investigated. In this study, we show that loss of Tcf12 leads to brain abnormalities even in the absence of coronal synostosis and that frontal bone expansion results from upregulated osteogenic differentiation in the calvarial mesenchyme in mice. Furthermore, we identify Lmx1b as a downstream target of Tcf12 for the regulation of osteogenic differentiation in the calvarial mesenchyme during frontal bone development. Our findings highlight the role of Tcf12 in the development of calvarial bones and provide new insight into molecular mechanisms for regulation of calvarial bone formation.

developmental biology↗

bioRxiv2024

Translating phenotypic prediction models from big to small anatomical MRI data using meta-matching

Individualized phenotypic prediction based on structural MRI is an important goal in neuroscience. Prediction performance increases with larger samples, but small-scale datasets with fewer than 200 participants are often unavoidable. We have previously proposed a "meta-matching" framework to translate models trained from large datasets to improve the prediction of new unseen phenotypes in small collection efforts. Meta-matching exploits correlations between phenotypes, yielding large improvement over classical machine learning when applied to prediction models using resting-state functional connectivity as input features. Here, we adapt the two best performing meta-matching variants ("meta-matching finetune" and "meta-matching stacking") from our previous study to work with T1-weighted MRI data by changing the base neural network architecture to a 3D convolution neural network. We compare the two meta-matching variants with elastic net and classical transfer learning using the UK Biobank (N = 36,461), Human Connectome Project Young Adults (HCP-YA) dataset (N = 1,017) and HCP-Aging dataset (N = 656). We find that meta-matching outperforms elastic net and classical transfer learning by a large margin, both when translating models within the same dataset, as well as translating models across datasets with different MRI scanners, acquisition protocols and demographics. For example, when translating a UK Biobank model to 100 HCP-YA participants, meta-matching finetune yielded a 136% improvement in variance explained over transfer learning, with an average absolute gain of 2.6% (minimum = -0.9%, maximum = 17.6%) across 35 phenotypes. Overall, our results highlight the versatility of the meta-matching framework.

neuroscience↗

bioRxiv2023

Multilayer meta-matching: translating phenotypic prediction models from multiple datasets to small data

Resting-state functional connectivity (RSFC) is widely used to predict phenotypic traits in individuals. Large sample sizes can significantly improve prediction accuracies. However, for studies of certain clinical populations or focused neuroscience inquiries, small-scale datasets often remain a necessity. We have previously proposed a "meta-matching" approach to translate prediction models from large datasets to predict new phenotypes in small datasets. We demonstrated large improvement of meta-matching over classical kernel ridge regression (KRR) when translating models from a single source dataset (UK Biobank) to the Human Connectome Project Young Adults (HCP-YA) dataset. In the current study, we propose two meta-matching variants ("meta-matching with dataset stacking" and "multilayer meta-matching") to translate models from multiple source datasets across disparate sample sizes to predict new phenotypes in small target datasets. We evaluate both approaches by translating models trained from five source datasets (with sample sizes ranging from 862 participants to 36,834 participants) to predict phenotypes in the HCP-YA and HCP-Aging datasets. We find that multilayer meta-matching modestly outperforms meta-matching with dataset stacking. Both meta-matching variants perform better than the original "meta-matching with stacking" approach trained only on the UK Biobank. All meta-matching variants outperform classical KRR and transfer learning by a large margin. In fact, KRR is better than classical transfer learning when less than 50 participants are available for finetuning, suggesting the difficulty of classical transfer learning in the very small sample regime. The multilayer meta-matching model is publicly available at GITHUB_LINK.

neuroscience↗

bioRxiv2023

A "through-DNA" mechanism for metal uptake-vs.-efflux regulation

Transition metals like Zn are essential for all organisms including bacteria, but fluctuations of their concentrations in the cell can be lethal. Organisms have thus evolved complex mechanisms for cellular metal homeostasis. One mechanistic paradigm involves pairs of transcription regulators sensing intracellular metal concentrations to regulate metal uptake and efflux. Here we report that Zur and ZntR, a prototypical pair of regulators for Zn uptake and efflux in E. coli, respectively, can coordinate their regulation through DNA, besides sensing cellular Zn2+ concentrations. Using a combination of live-cell single-molecule tracking and in vitro single-molecule FRET measurements, we show that unmetallated ZntR can enhance the unbinding kinetics of Zur from DNA by directly acting on Zur-DNA complexes, possibly through forming heteromeric ternary and quaternary complexes that involve both protein-DNA and protein-protein interactions. This through-DNA mechanism may functionally facilitate the switching in Zn uptake regulation when bacteria encounter changing Zn environments; it could also be relevant for regulating the uptake-vs.-efflux of various metals across different bacterial species and yeast.

biophysics↗

bioRxiv2023

Engineered Bacillus subtilis as oral probiotics to target circulating lactic acid

Elevated lactate concentrations are implicated in various acute and chronic diseases such as sepsis and mitochondrial dysfunction, respectively. Conversely, ineffective lactate clearance is associated with poor clinical prognoses and high mortality in these diseases. While several groups have proposed using small molecule inhibitors and enzyme replacement to reduce circulating lactate, there are few practical and effective ways to manage this condition. Recent evidence suggests that lactate is exchanged between systemic circulation and the gut, allowing bidirectional modulation between the gut microbiota and peripheral tissues. Inspired by these findings, this work seeks to engineer spore-forming probiotic B. subtilis strains to enable intestinal delivery of lactate oxidase as a therapeutic enzyme. After strain optimization, we showed that oral administration of engineered B. subtilis spores to the gut of mice reduced elevations in blood lactate in two different mouse models involving exogenous challenge or pharmacologic perturbation without disrupting gut microbiota composition, liver function, or immune homeostasis. Taken together, through the oral delivery of engineered probiotic spores to the gastrointestinal tract, our proof-of-concept study offers a practical strategy to aid in the management of disease states with elevated blood lactate and provides a new approach to knocking down circulating metabolites to help understand their roles in host physiological and pathological processes. Significance StatementThis study pioneers the use of engineered Bacillus subtilis spores as an oral probiotic therapy to enhance the clearance of elevated blood lactate, a condition linked to severe health issues like sepsis and metabolic disorders. By genetically modifying these spores to deliver therapeutic enzymes directly to the gut, we demonstrated a practical, effective method to modulate systemic lactate levels. This approach leverages the natural exchange between the gut microbiota and systemic circulation, offering a new strategy for managing diseases associated with lactate dysregulation. The safety and efficacy of this method were validated in mouse models, providing a foundation for future clinical applications.

bioengineering↗

bioRxiv2023

Multifrequency control of Faraday wave bioassembly for constructing multiscale hPSC-derived neuronal networks

Bioassembly is recently regarded as a critical alternative biofabrication technical route to bioprinting since it can directly manipulate millions of live cells to form multicellular structures with close intercellular proximity, improving contact-dependent cell communication and promoting the emergence of tissue-specific functions. However, acoustic bioassembly techniques are currently limited to generating cytoarchitecture with a single characteristic length which cannot faithfully mimic the multiscale cellular structures in native tissues. To overcome this challenge, herein we report a novel acoustic bioassembly technique that employs multifrequency control of Faraday waves to form multiscale cellular structures. By superimposing multiple sine wave signals with proper amplitude ratios, Faraday waves containing multiple wavelengths can be induced and enabled to generate multiscale structures in few seconds. Using this technique, we construct functional neuronal networks with multiscale connectivity that display spontaneous neuroelectrical activities. We anticipate this technique will find wide applications in tissue engineering and regenerative medicine.

bioengineering↗

bioRxiv2023

Group-common and individual-specific effects of structure-function coupling in human brain networks with graph neural networks

The human cerebral cortex is organized into functionally segregated but synchronized regions bridged by the structural connectivity of white matter pathways. While structure-function coupling has been implicated in cognitive development and neuropsychiatric disorders, it remains unclear to what extent the structure-function coupling reflects a group-common characteristic or varies across individuals, at both the global and regional brain levels. By leveraging two independent, high-quality datasets, we found that the graph neural network accurately predicted unseen individuals functional connectivity from structural connectivity, reflecting a strong structure-function coupling. This coupling was primarily driven by network topology and was substantially stronger than that of the correlation approaches. Moreover, we observed that structure-function coupling was dominated by group-common effects, with subtle yet significant individual-specific effects. The regional group and individual effects of coupling were hierarchically organized across the cortex along a sensorimotor-association axis, with lower group and higher individual effects in association cortices. These findings emphasize the importance of considering both group and individual effects in understanding cortical structure-function coupling, suggesting insights into interpreting individual differences of the coupling and informing connectivity-guided therapeutics.

neuroscience↗

bioRxiv2023

The cell cycle controls spindle architecture in Arabidopsis by modulating the augmin pathway

To ensure an even segregation of chromosomes during somatic cell division, eukaryotes rely on specific microtubule structures called mitotic spindles. There are, however, striking differences in overall spindle organization among eukaryotic super groups, and in particular little is known about how spindle architecture is determined in plants. As a foundation for our work, we have measured prime characteristics of Arabidopsis mitotic spindles and built a three-dimensional dynamic model of the Arabidopsis mitotic spindle using Cytosim. Next, we identified the cell-cycle regulator CYCLIN-DEPENDENT KINASE B1 (CDKB1) together with its cyclin partner CYCB3;1 as key regulators of spindle shape and organization in Arabidopsis. Loss of CDKB1 function resulted in a high number of astral microtubules that are normally absent from plant spindles, as opposed to animal ones. We identified an augmin complex member, ENDOSPERM DEFECTIVE1 (EDE1), as a substrate of the CDKB1;1-CYCB3;1 complex. A non-phosphorylatable mutant of EDE1 displayed spindles with extended pole-to-pole distance, resembling the phenotypes of cycb3;1 and cdkb1 mutants. Moreover, we found that the mutated EDE1 version associated less efficiently with spindle microtubules. Consistently, reducing the level of augmin in Cytosim simulations largely recapitulated the spindle phenotypes observed in cycb3;1 and cdkb1 mutants. Our results emphasize the importance of cell cycle-dependent phospho-control of the mitotic spindle in plant cells. They also support the validity of our computational model as a framework for the exploration of mechanisms controlling the organization of the spindle in plants and in other species.

developmental biology↗

bioRxiv2023

De novo genome assemblies from two Indigenous Americans from Arizona identify new polymorphisms in non-reference sequences

There is a collective push to diversify human genetic studies by including underrepresented populations. However, analyzing DNA sequence reads involves the initial step of aligning the reads to the GRCh38/hg38 reference genome which is inadequate for non-European ancestries. To help address this issue, we created a modified hg38 reference map using de novo sequence assemblies from Indigenous Americans living in Arizona (IAZ). Using HiFi SMRT long-read sequencing technology, we generated de novo genome assemblies for one female and one male IAZ individual. Each assembly included [~]17 Mb of DNA sequence not present (non-reference sequence; NRS) in hg38, which consists mostly of repeat elements. Forty NRSs totaling 240 kb were uniquely anchored to the hg38 primary assembly generating a modified hg38-NRS reference genome. DNA sequence alignment and variant calling were then conducted with WGS sequencing data from 387 IAZ cohorts using both the hg38 and modified hg38-NRS reference maps. Variant calling with the hg38-NRS map identified [~]50,000 single nucleotide variants present in at least 5% of the WGS samples which were not detected with the hg38 reference map. We also directly assessed the NRSs positioned within genes. Seventeen NRSs anchored to regions including an identical 187 bp NRS found in both de novo assemblies. The NRS is located in HCN2 79 bp downstream of exon 3 and contains several putative transcriptional regulatory elements. Genotyping of the HCN2-NRS revealed that the insertion is enriched in IAZ (MAF = 0.45) compared to Caucasians (MAF = 0.15) and African Americans (MAF = 0.03). This study shows that inclusion of population-specific NRSs can dramatically change the variant profile in an under-represented ethnic groups and thereby lead to the discovery of previously missed common variations. AUTHOR SUMMARYGRCh38/hg38 reference genome has been the standard reference for large-scale human genetics studies. However, it does not adequately represent sequences of non-European ancestry. In this study, using long-read sequencing technology, we constructed de novo sequence assemblies from two Indigenous Americans from Arizona. We then compared the de novo assemblies to the hg38 reference genome to identify non-reference sequences (NRSs). We integrated these NRSs into our whole-genome sequencing (WGS) variant calling pipeline to improve read alignment and variant detection. We also directly assessed the NRSs positioned within genes. Inclusion of population-specific NRSs dramatically changed the variant profile of our study group with under-represented ethnicity, revealing common variation not detected by our previous population-level WGS and genotyping studies.

genomics↗

bioRxiv2023

Co-existence of blaKPC-2 and blaVIM-2 in highly carbapenem-resistant Pseudomonas aeruginosa isolated in the ICU of a public hospital

In this study, highly carbapenem-resistant Pseudomonas aeruginosa (h-CRPA) 18102011 [the minimum inhibitory concentration (MIC) value of carbapenem antimicrobial imipenem (IP) for h-CRPA is 4,096 g/mL] was isolated from the bile of an intensive care unit (ICU) burn patient in China, and genomic sequencing revealed a complete genome. The genomes molecular characteristics were analyzed to assess the genetic environment of blaKPC-2 and blaVIM-2. Average nucleotide identity (ANI) comparisons were used for precise species-level identification, while serotyping, multi-locus sequence typing, and the identification of acquired resistance genes, and virulence genes were also carried out. The h-CRPA 18102011 strain carrying blaKPC-2 and blaVIM-2 was identified as strain ST2374 and the O4 serotype. Virulence genes (plcH, exoST) and resistance genes (aph(3)-IIb, aac(6)-Ib-cr, ant(2)-Ia, blaOXA-396, blaPAO, blaKPC-2, blaVIM-2, blaPER-1, sul1, catB7, qnrVC6, fosA) were both identified in the genome. In addition, the IncpRBL16 type mega-plasmid pP2011-1 carrying blaVIM-2 and the IncP6 type plasmid pP2011-2 carrying blaKPC-2 were identified in the strain. The genetic environment of blaVIM-2 and blaKPC-2 was specifically evaluated to assess their origins. blaVIM-2 was located in the region of In2075 (a novel type 1 integron) that was inserted into plasmid pP2011-1, this plasmid contained 3 novel recombination sites, as well as the typical recombination site 2 (umuC) observed for IncpRBL16 type plasmids. However, the core module Tn3-ISKpn27-blaKPC-{Delta}ISKpn6 was identified as the blaKPC-2 platform in plasmid pP2011-2. Conjugation experiments revealed that the plasmids pP2011-1 and pP2011-2 of the h-CRPA 18102011 strain could be transferred into Escherichia coli with a conjugation transfer efficiency of 10-6. The E. coli transconjugant carried blaKPC-2 and blaVIM-2 from the donor and the MIC value of IP to the E. coli transconjugant was 4,096 g/mL, which was the same as observed for the donor. Overall, this study revealed the molecular characteristics of a VIM-2 and KPC-2-co-producing strain that was typed as O4 and ST2374. The continuous monitoring of bacteria, such as the strain investigated here, that co-harbor different types of carbapenemase genes is critical for preventing the spread of these genes.

genomics↗

bioRxiv2023

Cell autonomous role of leucine-rich repeat kinase in protection of dopaminergic neuron survival

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinsons disease (PD), which is the leading neurodegenerative movement disorder characterized by the progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). However, whether LRRK2 mutations cause PD and degeneration of DA neurons via a toxic gain-of-function or a loss-of-function mechanism is unresolved and has pivotal implications for LRRK2-based PD therapies. In this study, we investigate whether LRRK2 and its functional homologue LRRK1 play an essential, intrinsic role in DA neuron survival through the development of DA neuron-specific LRRK conditional double knockout (cDKO) mice. We first generated and characterized floxed LRRK1 and LRRK2 mice and then confirmed that germline deletions of the floxed LRRK1 and LRRK2 alleles result in null mutations, as evidenced by the absence of LRRK1 and LRRK2 mRNA and protein in the respective homozygous deleted mutant mice. We further examined the specificity of Cre-mediated recombination driven by the dopamine transporter-Cre (DAT-Cre) knockin (KI) allele using a GFP reporter line and confirmed that DAT-Cre-mediated recombination is restricted to DA neurons in the SNpc. Crossing these validated floxed LRRK1 and LRRK2 mice with DAT-Cre KI mice, we then generated DA neuron-restricted LRRK cDKO mice and further showed that levels of LRRK1 and LRRK2 are reduced in dissected ventral midbrains of LRRK cDKO mice. While DA neuron-restricted LRRK cDKO mice of both sexes exhibit normal mortality and body weight, they develop age-dependent loss of DA neurons in the SNpc, as demonstrated by the progressive reduction of DA neurons in the SNpc of LRRK cDKO mice at the ages of 20 and 24 months but the unaffected number of DA neurons at the age of 15 months. Moreover, DA neurodegeneration is accompanied with increases of apoptosis and elevated microgliosis in the SNpc as well as decreases of DA terminals in the striatum, and is preceded by impaired motor coordination. Taken together, these findings provide the unequivocal evidence for the importance of LRRK in DA neurons and raise the possibility that LRRK2 mutations may impair its protection of DA neurons, leading to DA neurodegeneration in PD.

neuroscience↗

bioRxiv2023

Potential intrahospital dissemination of Pseudomonas aeruginosa carrying the blaIMP-1 gene within a Tn7-like transposon

We aimed to determine the molecular characteristics of carbapenem-resistant Pseudomonas aeruginosa 18081308 and 18083286 isolated from the urine and sputum of two Chinese patients respectively, and analyzed the formation mechanism of the genetic environment in which it carries blaIMP-1. Bacterial genome sequencing was carried out on strains 18081308 and 18083286 to obtain their whole genome sequence. Average nucleotide identity (ANI) was used for their precise species identification. Serotyping and multilocus sequence typing were performed. Furthermore, the acquired resistance genes, and virulence factors of these strains were identified. The carbapenem-resistant P. aeruginosa strains isolated in the present study were of sequence type ST865 and serotype O6. They all carried the same virulence factors (PLC, ExoSTY) and resistance genes (aacC2, tmrB, and blaIMP-1). Tn6411, a Tn7-like transposon carrying blaIMP-1, was found in both strains. Detailed genetic dissection was applied to this transposon to display the genetic environment of blaIMP-1. The aacC2-tmrB region remnant-Tn6411 backbone was the original structure of this type of transposon. A Tn402-like type 1 integron (intl1-aac(6)-II-blaIMP-1) was inserted into it and formed a stable structure, which was localized in the chromosome by TnsD for transmission within P. aeruginosa; the original structure of Tn7-like transposon was localized on the plasmid by TnsE for horizontal transmission between bacterial species. The intrahospital dissemination of P. aeruginosa ST865 isolated in this study was episodic. The blaIMP-1-carrying Tn7-like transposon might enhance their ability to survive under drug selection pressure and aggravate the difficulty in treating infections.

genomics↗

bioRxiv2023

A 3D Printed Ventilated Perfused Lung Model Platform to Dissect the Lung's Response to Viral Infection in the Presence of Respiration

In this study, we developed a three-dimensionally (3D) printed lung model that faithfully recapitulates the intricate lung environment. This 3D model incorporated alveolar and vascular components that allow for a comprehensive exploration of lung physiology and responses to infection in vitro. In particular, we investigated the intricate role of ventilation on formation of the alveolar epithelial layer and its response to viral infections. In this regard, we subjected our 3D printed, perfused lung model to a continuous respiratory cycle at the air-liquid interface (ALI) for up to 10 days followed by infection with two viruses: influenza virus (Pr8) and respiratory syncytial virus (RSV), at two different concentrations for 24 or 48 h. The results revealed that ventilation induced increased tight-junction formation with better epithelial barrier function over time, facilitated higher expression of alveolar epithelial specific genes, enabled higher level of infection with an increased progression of viral spread and replication over time, and modulated the production of pro-inflammatory cytokines and chemokines. Our findings represent a critical step forward in advancing our understanding of lung-specific viral responses and respiratory infections in response to ventilation, which sheds light on vital aspects of pulmonary physiology and pathobiology.

bioengineering↗

bioRxiv2023

Alpha-toxin elicited CX3CL1-release via ADAM10 in Staphylococcus aureus pneumoniaimpairs bactericidal function of human monocytes

Staphylococcus aureus is an important human pathogen causing severe invasive infections. Pathogenesis is attributed to a wide array of virulence factors, including several potent exotoxins such as the pore-forming alpha-toxin. In this study, we found that patients with S. aureus respiratory tract infections had elevated CX3CL1 levels in airway fluid and plasma. Using humanized organotypic lung models, we observed that stimulation of lung epithelium with alpha-toxin induce an intensified CX3CL1 expression apically in the epithelium as well as the release of CX3CL1. Blocking alpha-toxin or ADAM10 activity in organotypic lung using an alpha-toxin-blocking antibody or a specific ADAM-10 inhibitor confirmed their role in modulating CX3CL1 cleavage and release. Analyses of CD14+ human monocytes in combination with a CX3CR1 inhibitor revealed that alpha-toxin-mediated CX3CL1 release induce CX3CL1-dependent chemotaxis. In line with these data, lung tissue from patients with S. aureus respiratory tract infection showed elevated CX3CL1 and CD14 staining as compared to tissue from patients with non-infectious lung diseases. Functional studies of monocytes showed that CX3CL1 released by lung models resulted in upregulated CD83 and downregulated CD86, as well as impaired killing of phagocytosed S. aureus. Furthermore, stimulation of monocytes with soluble CX3CL1 hampered their reactive-oxygen and nitric-oxide production. Taken together, our data show that S. aureus triggers the release of lung epithelial CX3CL1; a process found to be dependent on the alpha-toxins effect on ADAM10 mediating cytotoxicity and resulting in impaired monocyte phagocytic killing. Hence, we identify an immunomodulatory effect of alpha-toxin involving the CX3CL1-ADAM10 axis extending beyond the cytolysis function.

microbiology↗

bioRxiv2023

Evolutionary prediction for new echolocators

It was suggested over 60 years ago that echolocation is widespread in animals. Although echolocation has been found to evolve independently in several mammalian lineages, this hypothesis remains largely untested due to the difficulty of determining the presence of echolocation. To address this issue, we combined molecular convergence analyses from 190 high-quality mammalian genomes with machine learning to predict potential new mammalian echolocators. Our model predicted three promising lineages of echolocating mammals. Behavioral experiments confirmed that the gracile shrew mole (Uropsilus gracilis), the highest- ranking species among predicted echolocators, as well as almost all shrew moles (Uropsilinae), are capable of echolocation through the use of ultrasonic pulses. In contrast to most bats that use laryngeal echolocation, the characteristics of calls, the morphology of the stylohyal bone, and the results of tongue ligation experiments all suggest that shrew moles produce ultrasonic clicks with their tongues for echolocation. Finally, we estimated at least 20% of all living mammalian orders with echolocation ability, thus empirically supporting Griffins hypothesis that echolocation is widespread among animals. Our findings not only provide evidence that three novel lineages of echolocating mammals, but also demonstrate that phylogenetically replicated phenotypes can be predicted through genetic convergence. One sentence summaryShrew moles are capable of echolocation.

evolutionary biology↗