Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Dihydropyrimidine Dehydrogenase as a Novel Regulator of Hepatic Steatosis

Pyrimidine catabolism is implicated in hepatic steatosis. Dihydropyrimidine Dehydrogenase (DPYD) is an enzyme responsible for uracil and thymine catabolism, and DPYD human genetic variability affects clinically observed toxicity following 5-Fluorouracil (5-FU) administration. In an in vitro model of diet-induced steatosis, the pharmacologic inhibition of DPYD resulted in protection from lipid accumulation. Additionally, a gain-of-function mutation of DPYD, created through clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) engineering, led to an increased lipid burden, which was associated with altered mitochondrial functionality in a hepatocarcionma cell line. The studies presented herein describe a novel role for DPYD in hepatocyte metabolic regulation as a modulator of hepatic steatosis.
A positive role of task-deactivated default mode network in narrative

57 Psychological theories have implicated an active role of the default mode network 58 (DMN) in natural speech comprehension. However, as listeners need to keep tracking 59 the external audio streams, the DMN is regularly de-activated and anticorrelated with 60 externally-oriented networks. Such a pattern has been interpreted as the suppression of 61 the DMN to support externally-oriented cognitive processes. The current study aims to 62 resolve this seeming contradiction. Brain activities from a speaker telling 63 autobiographical stories and a group of participants (N = 62) listening to the recordings 64 were collected with fMRI. By analyzing the listeners’ brains alone, we found the DMN 65 was deactivated during speech listening relative to a fixation period and anticorrelated 66 with the task-positive perisylvian language network (pLN). Dynamic Causal Modeling 67 showed the pLN had inhibitory influence on the DMN, whereas the DMN had 68 excitatory influence on the pLN. Further between-brain analyses revealed the activities 69 of DMN in the listener’s brain were tightly coupled with the activities of the 70 homologous network in the speaker’s brain. Significant interbrain couplings were also 71 observed in the pLN, but were weaker and faded quicker. Moreover, listeners showing 72 stronger coupling responses to the speaker in the DMN understood the speech better, 73 and tended to exhibit more positive DMN → pLN effective connections. We conclude 74 that the DMN may occupy an internal system that works cooperatively with the 75 externally-oriented pLN to support narrative speech comprehension. 76
Pro-inflammatory alveolar macrophages associated with allograft dysfunction after lung transplantation

Purpose Lung transplant (LT) recipients experience episodes of immune-mediated acute lung allograft dysfunction (ALAD). We have applied single-cell RNA sequencing (scRNAseq) to bronchoalveolar lavage (BAL) cells of stable and ALAD patients to determine key cellular elements in dysfunctional lung allografts. Our particular focus here is on studying alveolar macrophages (AMs) as scRNAseq enables us to elucidate their heterogeneity and possible association with ALAD where our knowledge from cytometry-based assays is very limited. Methods Fresh bronchoalveolar lavage (BAL) cells from 6 LT patients, 3 with stable lung function (3044 ± 1519 cells) and 3 undergoing an episode of ALAD (2593 ± 904 cells) were used for scRNAseq. R Bioconductor and Seurat were used to perform QC, dimensionality reduction, annotation, pathway analysis, and trajectory. Donor and recipient deconvolution was performed using single nucleotide variations. Results Our data revealed that AMs are highly heterogeneous (12 transcriptionally distinct subsets in stable). We identified two AM subsets uniquely represented in ALAD. Based on pathway analysis and the top differentially expressed genes in BAL we annotated them as pro-inflammatory interferon-stimulated genes (ISG) and metallothioneins-mediated inflammatory (MT). Pseudotime analysis suggested that ISG AMs represent an earlier stage of differentiation which may suggest them as monocyte drive macrophages. Our functional analysis on an independent set of BAL samples shows that ALAD samples have significantly higher expression of CXCL10, a marker of ISG AM, as we as higher secretion of pro-inflammatory cytokines. Single nucleotide variation calling algorithm has allowed us to identify macrophages of donor origin and demonstrated that donor AMs are lost with time post-transplant. Conclusion Using scRNAseq, we observed AMs heterogeneity and identified specific subsets that may be associated with allograft dysfunction. Further exploration with scRNAseq will shed light on LT immunobiology and the role of AMs in allograft injury and dysfunction.
The Borrelia burgdorferi adenylyl cyclase, CyaB, is important for virulence factor production and mammalian infection

Borrelia burgdorferi, the causative agent of Lyme disease, traverses through vastly distinct environments between the tick vector and the multiple phases of the mammalian infection that requires genetic adaptation for the progression of pathogenesis. Borrelial gene expression is highly responsive to changes in specific environmental signals that initiate the RpoS regulon for mammalian adaptation, but the mechanism(s) for direct detection of environmental cues has yet to be identified. Secondary messenger cyclic adenosine monophosphate (cAMP) produced by adenylate cyclase is responsive to environmental signals, such as carbon source and pH, in many bacterial pathogens to promote virulence by altering gene regulation. B. burgdorferi encodes a single non-toxin class IV adenylate cyclase (bb0723, cyaB). This study investigates cyaB expression along with its influence on borrelial virulence regulation and mammalian infectivity. Expression of cyaB was specifically induced with co-incubation of mammalian host cells that was not observed with cultivated tick cells suggesting that cyaB expression is influenced by cellular factor(s) unique to mammalian cell lines. The 3’ end of cyaB also encodes a small RNA, SR0623, in the same orientation that overlaps with bb0722. The differential processing of cyaB and SR0623 transcripts may alter the ability to influence function in the form of virulence determinant regulation and infectivity. Two independent cyaB deletion B31 strains were generated in 5A4-NP1 and ML23 backgrounds and complemented with the cyaB ORF alone that truncates SR0623, cyaB with intact SR0623, or cyaB with a mutagenized full length SR0623 to evaluate the influence on transcriptional and post-transcriptional regulation of borrelial virulence factors and infectivity. In the absence of cyaB, expression and production of ospC was significantly reduced, while the protein levels for BosR and DbpA were substantially lower than parental strains. Infectivity studies with both independent cyaB mutants demonstrated an attenuated phenotype with reduced colonization of tissues during early disseminated infection. This work suggests that B. burgdorferi utilizes cyaB and potentially cAMP as a regulatory pathway to modulate borrelial gene expression and protein production to promote borrelial virulence and dissemination in the mammalian host.
Maturation signatures of conventional dendritic cells in COVID-19 reflect direct viral sensing

Growing evidence suggests that conventional dendritic cells (cDCs) undergo aberrant maturation in COVID-19, and this adversely affects T cell activation. Here, we find that cDC2 subtypes show similar infection-induced gene signatures with an increasing gradient of expression of interferon-stimulated genes from mild to severe patients and a down-regulation of major histocompatibility complex class II (MHC class II) molecules and some inflammatory cytokines compared to the baseline level of healthy donors. In vitro, the direct exposure of cDC2s to the virus recapitulates the type of activation observed in vivo. Our findings provide evidence that SARS-CoV-2 can directly interact with cDC2s and, by down-regulating crucial molecules required for T cell activation, implements an efficient immune escape mechanism. One-Sentence Summary Type 2 conventional dendritic cell functions are altered by direct interaction with SARS-CoV-2
Detection of ESKAPE pathogens and Clostridioides difficile in Simulated Skin Transmission Events with Metagenomic and Metatranscriptomic Sequencing

Background Antimicrobial resistance is a significant global threat, posing major public health risks and economic costs to healthcare systems. Bacterial cultures are typically used to diagnose healthcare-acquired infections (HAI); however, culture-dependent methods provide limited presence/absence information and are not applicable to all pathogens. Next generation sequencing (NGS) has the capacity to detect a wide variety of pathogens, virulence elements, and antimicrobial resistance (AMR) signatures in healthcare settings without the need for culturing, but few research studies have explored how NGS could be used to detect viable human pathogen transmission events under different HAI-relevant scenarios. Methods The objective of this project was to assess the capability of NGS-based methods to detect the direct and indirect transmission of high priority healthcare-related pathogens. DNA was extracted and sequenced from a previously published study exploring pathogen transfer with simulated skin containing background microorganisms, which allowed for complementary culture and metagenomic analysis comparisons. RNA was also isolated from an additional set of samples to evaluate metatranscriptomic analysis methods at different concentrations. Results Using various analysis methods and custom reference databases, both pathogenic and non-pathogenic members of the microbial community were taxonomically identified. Virulence and AMR genes known to reside within the community were also routinely detected. Ultimately, pathogen abundance within the overall microbial community played the largest role in successful taxonomic classification and gene identification. Conclusions These results illustrate the utility of metagenomic analysis in clinical settings or for epidemiological studies, but also highlight the limits associated with the detection and characterization of pathogens at low abundance in a microbial community.
TAFKAP: An improved method for probabilistic decoding of cortical activity

Cortical activity can be difficult to interpret. Neural responses to the same stimulus vary between presentations, due to random noise and other sources of variability. This unreliable relationship to external stimuli renders any pattern of activity open to a multitude of plausible interpretations. We have previously shown that this uncertainty in cortical stimulus representations can be characterized using a probabilistic decoding algorithm, which inverts a generative model of stimulus-evoked cortical responses. Here, we improve upon this method in two important ways, which both target the precision with which the generative model can be estimated from limited, noisy training data. We show that these improvements lead to considerably better estimation of the presented stimulus and its associated uncertainty. Estimates of the presented stimulus are recovered with an accuracy that exceeds that of standard decoding methods (SVMs), and in some cases even approaches the behavioral accuracy of human observers. Moreover, the uncertainty in the decoded probability distributions better characterizes the precision of cortical stimulus information from trial to trial.
The cryptic gonadotropin-releasing hormone neuronal system of human basal ganglia

Human reproduction is controlled by ∼2,000 hypothalamic gonadotropin-releasing hormone (GnRH) neurons. Here we report the discovery and characterization of additional 150-200,000 GnRH-synthesizing cells in the human basal ganglia and basal forebrain. Extrahypothalamic GnRH neurons were cholinergic. Though undetectable in adult rodents, the GnRH-GFP transgene was expressed transiently by caudate-putamen cholinergic interneurons in newborn transgenic mice. In slice electrophysiological studies, GnRH inhibited these interneurons via GnRHR1 autoreceptors. Whole-transcriptome analysis of cholinergic interneurons and medium spiny projection neurons laser-microdissected from the human putamen confirmed selective expression of GNRH1 and GNRHR1 autoreceptors in cholinergic cells and uncovered the detailed transcriptome profile and molecular connectome of these two cell types. Higher- order non-reproductive functions regulated by GnRH under physiological conditions in the human basal ganglia and basal forebrain require clarification. GnRH/GnRHR1 signaling as a potential therapeutic target in the treatment of neurodegenerative disorders affecting cholinergic neurocircuitries, including Parkinson’s and Alzheimer’s diseases, needs to be explored.
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

The open sharing of genomic data provides an incredibly rich resource for the study of bacterial evolution and function, and even anthropogenic activities such as the widespread use of antimicrobials. Whilst these archives are rich in data, considerable processing is required before biological questions can be addressed. Here, we assembled and characterised 661,405 bacterial genomes using a uniform standardised approach, retrieved from the European Nucleotide Archive (ENA) in November of 2018. A searchable COBS index has been produced, facilitating the easy interrogation of the entire dataset for a specific gene or mutation. Additional MinHash and pp-sketch indices support genome-wide comparisons and estimations of genomic distance. An analysis on this scale revealed the uneven species composition in the ENA/public databases, with just 20 of the total 2,336 species making up 90% of the genomes. The over-represented species tend to be acute/common human pathogens. This aligns with research priorities at different levels from individuals with targeted but focused research questions, areas of focus for the funding bodies or national public health agencies, to those identified globally as priority pathogens by the WHO for their resistance to front and last line antimicrobials. Understanding the actual and potential biases in bacterial diversity depicted in this snapshot, and hence within the data being submitted to the public sequencing archives, is essential if we are to target and fill gaps in our understanding of the bacterial kingdom.
Interstitial leukocyte navigation through a search and run response to gradients

Migrating cells must interpret chemical gradients to guide themselves within tissues. A general premise has been that gradients influence the direction of leading-edge protrusions. However, recent evidence indicates that actin flows correlate better with directed motion than protrusions. A unified chemotaxis model that integrates the role of protrusions and actin flows and that accounts for in vivo cell motion patterns is lacking. Here, we provide direct experimental evidence of how neutrophils sense gradients in real-time in vivo and demonstrate a two-stage process: first a ‘search’ phase, that requires actin network expansion by Arp2/3, whereby cells slow down, explore the environment and execute path corrections. This is followed by a ‘run’ phase, that requires Myosin-II-driven contractility and fast actin flows, whereby cells accelerate and persist in the source direction. Thus, protrusive forces support chemotaxis by enhancing signal detection, while actin flows act as the ultimate output of gradient processing.
Autism spectrum disorder: understanding the impact of SNPs on biological pathways in the fetal and adult cortex

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by significant and complex genetic etiology. GWAS studies have identified genetic variants associated with ASD, but the functional impacts of these variants remain unknown. Here, we integrated four distinct levels of biological information (GWAS, eQTL, spatial genome organization and protein-protein interactions) to identify potential regulatory impacts of ASD-associated SNPs (p < 5×10-8) on biological pathways within fetal and adult cortical tissues. We found 80 and 58 SNPs that mark regulatory regions (i.e. expression quantitative trait loci or eQTLs) in the fetal and adult cortex, respectively. These eQTLs were also linked to other psychiatric disorders (e.g. schizophrenia, ADHD, bipolar disorder). Functional annotation of ASD-associated eQTLs revealed that they are involved in diverse regulatory processes. In particular, we found significant enrichment of eQTLs within regions repressed by Polycomb proteins in the fetal cortex compared to the adult cortex. Furthermore, we constructed fetal and adult cortex-specific protein-protein interaction networks and identified that ASD-associated regulatory SNPs impact on immune pathways, fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and spliceosome in the fetal cortex. By contrast in the adult cortex, they largely affect immune pathways. Overall, our findings highlight potential regulatory mechanisms and pathways important for the etiology of ASD in early brain development and adulthood. This approach, in combination with clinical studies on ASD, will contribute to individualized mechanistic understanding of ASD development.
Application of inductively coupled plasma mass spectrometry to phospholipid analysis

Phospholipids are the main constituents of membranes in all types of prokaryotic and eukariotic cells. Due to their complexity and heterogeneity in biological samples, qualitative and quantitative analyses of membrane phospholipids in cellular extracts represent major analytical challenges, mainly due to suitable and sensitive detection methods. The inductively coupled plasma mass spectrometer (ICP-MS) is a suitable detector for selective determination of phospholipids as they all contain phosphorus. Phospholipids are extractable with organic solvents, therefore liquid chromatography with an organic mobile phase was used for separation of different lipid species. Solvent load to the plasma was reduced by splitting the mobile phase prior to reaching the nebulizer, by chilling the spray chamber to −5 °C and by optimisation of carrier gas flow for maximum condensation of organic vapours. Despite desolvation, oxygen was added to prevent carbon deposition on interface cones. To reduce polyatomic interferences at m/z ratio 31 (e.g.31CH3O+) and to improve detection limits, helium was used as a collision gas. The achieved absolute detection limits were between 0.21 and 1.2 ng of phosphorus and were superior to those obtained by an evaporative light scattering detector, which provides an alternative detection system for lipid analysis. The usefulness of the developed method was demonstrated by analysis of lipid extracts from the yeast Saccharomyces cerevisiae.
Novel Paju Apodemus Paramyxovirus 1 and 2, Harbored by Apodemus agrarius in The Republic of Korea

Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a potential threat to public health. Currently, 78 species and 17 genera of paramyxoviruses are classified and harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Jeilongvirus has been proposed as a novel paramyxovirus genus containing J-, Beilong, and Tailam viruses, found in wild rodents. Using RT-PCR, 824 Apodemus agrarius individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was detected in 108 (13.1%) rodents captured at 14 trapping sites in Korea. We first present two genetically distinct novel paramyxoviruses (genus Jeilongvirus), Paju Apodemus paramyxoviruses 1 (PAPV-1) and 2 (PAPV-2), from A. agrarius. Six PAPV strains were completely sequenced using next-generation and Sanger sequencing. PAPV-1 genome comprised 19,716 nucleotides, with eight genes (3′-N-P/V/C-M-F-SH-TM-G-L-5′), whereas PAPV-2 genome contained 17,475 nucleotides, with seven genes (3′-N-P/V/C-M-F-TM-G-L-5′). The disparity between PAPV-1 and -2 revealed the presence of the SH gene and length of the G gene in the genome organization. The phylogenies of PAPV-1 and -2 belong to distinct genetic lineages of Jeilongvirus despite being from the same natural host. PAPV-1 clustered with Beilong and Tailam viruses, while PAPV-2 formed a genetic lineage with Mount Mabu Lophuromys virus-1. PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. Therefore, this study provides profound insights into the molecular epidemiology, virus-host interactions, and zoonotic potential of novel rodent-borne paramyxoviruses. Importance Paramyxoviruses are a critical public health and socio-economic burden to humans. Rodents play a crucial role in transmitting pathogens to humans. In the last decade, novel paramyxoviruses have been discovered in different rodents. Here, we found that Apodemus agrarius harbored two distinct genotypes of the novel paramyxoviruses, Paju Apodemus paramyxovirues 1 (PAPV-1) and 2 (PAPV-2), possessing unique genome structures that are responsible for encoding TM and G proteins of different sizes. In addition, PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III IFNs, ISGs, and proinflammatory cytokines. Thus, this study provides significant insights into molecular prevalence, virus-host interactions of paramyxoviruses. These observations raise the awareness of physicians and scientists about the emergence of new rodent-borne paramyxoviruses.
Ribosome-Profiling Reveals Restricted Post Transcriptional Expression of Antiviral Cytokines and Transcription Factors during SARS-CoV-2 Infection

The global COVID-19 pandemic caused by SARS-CoV-2 has resulted in over 2.2 million deaths. Disease outcomes range from asymptomatic to severe with, so far, minimal genotypic change to the virus so understanding the host response is paramount. Transcriptomics has become incredibly important in understanding host-pathogen interactions; however, post-transcriptional regulation plays an important role in infection and immunity through translation and mRNA stability, allowing tight control over potent host responses by both the host and the invading virus. Here we apply ribosome profiling to assess post-transcriptional regulation of host genes during SARS-CoV-2 infection of a human lung epithelial cell line (Calu-3). We have identified numerous transcription factors (JUN, ZBTB20, ATF3, HIVEP2 and EGR1) as well as select antiviral cytokine genes, namely IFNB1, IFNL1,2 and 3, IL-6 and CCL5, that are restricted at the post-transcriptional level by SARS-CoV-2 infection and discuss the impact this would have on the host response to infection. This early phase restriction of antiviral transcripts in the lungs may allow high viral load and consequent immune dysregulation typically seen in SARS-CoV-2 infection.