Plant Biotechnol J. 2023 Oct 20. doi: 10.1111/pbi.14191. Online ahead of print.

NO ABSTRACT

PMID:37861059 | DOI:10.1111/pbi.14191

iScience. 2023 Sep 25;26(10):108042. doi: 10.1016/j.isci.2023.108042. eCollection 2023 Oct 20.

ABSTRACT

Machine learning (ML) has the potential to identify subsets of patients with distinct phenotypes from gene expression data. However, phenotype prediction using ML has often relied on identifying important genes without a systems biology context. To address this, we created an interpretable ML approach based on blood transcriptomics to predict phenotype in systemic lupus erythematosus (SLE), a heterogeneous autoimmune disease. We employed a sequential grouped feature importance algorithm to assess the performance of gene sets, including immune and metabolic pathways and cell types, known to be abnormal in SLE in predicting disease activity and organ involvement. Gene sets related to interferon, tumor necrosis factor, the mitoribosome, and T cell activation were the best predictors of phenotype with excellent performance. These results suggest potential relationships between the molecular pathways identified in each model and manifestations of SLE. This ML approach to phenotype prediction can be applied to other diseases and tissues.

PMID:37860757 | PMC:PMC10582499 | DOI:10.1016/j.isci.2023.108042

iScience. 2023 Sep 28;26(11):108080. doi: 10.1016/j.isci.2023.108080. eCollection 2023 Nov 17.

ABSTRACT

The SARS-CoV-2 genome encodes a multitude of accessory proteins. Using comparative genomic approaches, an additional accessory protein, ORF3c, has been predicted to be encoded within the ORF3a sgmRNA. Expression of ORF3c during infection has been confirmed independently by ribosome profiling. Despite ORF3c also being present in the 2002-2003 SARS-CoV, its function has remained unexplored. Here we show that ORF3c localizes to mitochondria, where it inhibits innate immunity by restricting IFN-β production, but not NF-κB activation or JAK-STAT signaling downstream of type I IFN stimulation. We find that ORF3c is inhibitory after stimulation with cytoplasmic RNA helicases RIG-I or MDA5 or adaptor protein MAVS, but not after TRIF, TBK1 or phospho-IRF3 stimulation. ORF3c co-immunoprecipitates with the antiviral proteins MAVS and PGAM5 and induces MAVS cleavage by caspase-3. Together, these data provide insight into an uncharacterized mechanism of innate immune evasion by this important human pathogen.

PMID:37860693 | PMC:PMC10583119 | DOI:10.1016/j.isci.2023.108080

Front Physiol. 2023 Oct 4;14:1233711. doi: 10.3389/fphys.2023.1233711. eCollection 2023.

ABSTRACT

Despite the important role of bitter taste for the rejection of potentially harmful food sources, birds have long been suspected to exhibit inferior bitter tasting abilities. Although more recent reports on the bitter recognition spectra of several bird species have cast doubt about the validity of this assumption, the bitter taste of avian species is still an understudied field. Previously, we reported the bitter activation profiles of three zebra finch receptors Tas2r5, -r6, and -r7, which represent orthologs of a single chicken bitter taste receptor, Tas2r1. In order to get a better understanding of the bitter tasting capabilities of zebra finches, we selected another Tas2r gene of this species that is similar to another chicken Tas2r. Using functional calcium mobilization experiments, we screened zebra finch Tas2r1 with 72 bitter compounds and observed responses for 7 substances. Interestingly, all but one of the newly identified bitter agonists were different from those previously identified for Tas2r5, -r6, and -r7 suggesting that the newly investigated receptor fills important gaps in the zebra finch bitter recognition profile. The most potent bitter agonist found in our study is cucurbitacin I, a highly toxic natural bitter substance. We conclude that zebra finch exhibits an exquisitely developed bitter taste with pronounced cucurbitacin I sensitivity suggesting a prominent ecological role of this compound for zebra finch.

PMID:37860623 | PMC:PMC10582322 | DOI:10.3389/fphys.2023.1233711

F1000Res. 2023 Apr 13;12:391. doi: 10.12688/f1000research.132952.1. eCollection 2023.

ABSTRACT

Superoxide dismutase [Cu-Zn] 1 (SOD1), is an antioxidant enzyme encoded by the gene SOD1, responsible for regulating oxidative stress levels by sequestering free radicals. Identified as the first gene with mutations in Amyotrophic lateral sclerosis (ALS), SOD1 is a determinant for studying diseases of aging and neurodegeneration. With guidance on well-characterized anti-SOD1 antibodies, the reproducibility of SOD1 research would be enhanced. In this study, we characterized eleven SOD1 commercial antibodies for Western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.

PMID:37860271 | PMC:PMC10582621 | DOI:10.12688/f1000research.132952.1

NAR Genom Bioinform. 2023 Oct 18;5(4):lqad092. doi: 10.1093/nargab/lqad092. eCollection 2023 Dec.

ABSTRACT

Given the current status of coronavirus disease 2019 (COVID-19) as a global pandemic, it is of high priority to gain a deeper understanding of the disease's development and how the virus impacts its host. Adenosine (A)-to-Inosine (I) RNA editing is a post-transcriptional modification, catalyzed by the ADAR family of enzymes, that can be considered part of the inherent cellular defense mechanism as it affects the innate immune response in a complex manner. It was previously reported that various viruses could interact with the host's ADAR enzymes, resulting in epigenetic changes both to the virus and the host. Here, we analyze RNA-seq of nasopharyngeal swab specimens as well as whole-blood samples of COVID-19 infected individuals and show a significant elevation in the global RNA editing activity in COVID-19 compared to healthy controls. We also detect specific coding sites that exhibit higher editing activity. We further show that the increment in editing activity during the disease is temporary and returns to baseline shortly after the symptomatic period. These significant epigenetic changes may contribute to the immune system response and affect adverse outcomes seen in post-viral cases.

PMID:37859800 | PMC:PMC10583280 | DOI:10.1093/nargab/lqad092

Exp Neurol. 2023 Oct 17:114578. doi: 10.1016/j.expneurol.2023.114578. Online ahead of print.

ABSTRACT

Traumatic brain injury leads to cellular and circuit changes in the dentate gyrus, a gateway to hippocampal information processing. Intrinsic granule cell firing properties and strong feedback inhibition in the dentate are proposed as critical to its ability to generate unique representation of similar inputs by a process known as pattern separation. Here we evaluate the impact of brain injury on cellular decorrelation of temporally patterned inputs in slices and behavioral discrimination of spatial locations in vivo one week after concussive lateral fluid percussion injury (FPI) in mice. Despite posttraumatic increases in perforant path evoked excitatory drive to granule cells and enhanced ΔFosB labeling, indicating sustained increase in excitability, the reliability of granule cell spiking was not compromised after FPI. Although granule cells continued to effectively decorrelate output spike trains recorded in response to similar temporally patterned input sets after FPI, their ability to decorrelate highly similar input patterns was reduced. In parallel, encoding of similar spatial locations in a novel object location task that involves the dentate inhibitory circuits was impaired one week after FPI. Injury induced changes in pattern separation were accompanied by loss of somatostatin expressing inhibitory neurons in the hilus. Together, these data suggest that the early posttraumatic changes in the dentate circuit undermine dentate circuit decorrelation of temporal input patterns as well as behavioral discrimination of similar spatial locations, both of which could contribute to deficits in episodic memory.

PMID:37858696 | DOI:10.1016/j.expneurol.2023.114578

J Pediatr Surg. 2023 Sep 26:S0022-3468(23)00564-X. doi: 10.1016/j.jpedsurg.2023.09.027. Online ahead of print.

ABSTRACT

PURPOSE: We explored the application of a machine learning algorithm for the timely detection of potential abusive head trauma (AHT) using the first free-text note of an encounter and demographic information.

METHODS: First free-text physician notes and demographic information were collected for children under 5 years of age at a Level 1 Trauma Center. The control group, which included patients with head/neck injury, was compared to those with AHT diagnosed by the Child Protective Team. Differential scores accounted for words overrepresented in AHT patient vs. control notes. Sentiment scores were reflective of note positivity/negativity and subjectivity scores accounted for note subjectivity/objectivity. The composite scores reflected the patient's differential score modified by the subjectivity score. Composite, sentiment, and subjectivity scores combined with demographic information trained a Random Forest (RF) machine learning algorithm to predict AHT.

RESULTS: Final composite scores with demographic information were highly associated with AHT in a test dataset. The control group included 587 patients and the test group included 193 patients. Combining composite scores with demographic information into the RF model improved AHT classification area under the curve (AUC) from 0.68 to 0.78, with an overall accuracy of 84%. Feature importance analysis of our RF model revealed that composite score, sentiment, age, and subjectivity were the most impactful predictors of AHT. The sentiment was not significantly different between control and AHT notes (p = 0.87), while subjectivity trended higher for AHT notes (p = 0.081).

CONCLUSION: We conclude that a machine learning algorithm can recognize patterns within free-text notes and demographic information that aid in AHT detection in children.

LEVEL OF EVIDENCE: III.

PMID:37858394 | DOI:10.1016/j.jpedsurg.2023.09.027

J Colloid Interface Sci. 2023 Oct 6:S0021-9797(23)01928-8. doi: 10.1016/j.jcis.2023.10.015. Online ahead of print.

ABSTRACT

The structure-function characteristics of isolated artificial organelles (AOs) in protocells are mainly known, but there are few reports on clustered or aggregated AOs. To imitate µm-sized complex and heterogeneous cell structures, approaches are needed that enable reversible changes in the aggregation state of colloidal structures in response to chemical, biological, and external stimuli. To construct adaptive organelle-like or cell-like reorganization characteristics, we present an advanced crosslinking strategy to fabricate clustered polymersomes as a platform based on host-guest interactions between azobenzene-containing polymersomes (Azo-Psomes) and a β-cyclodextrin-modified polymer (β-CD polymer) as a crosslinker. First, the reversible (dis)assembly of clustered Azo-Psomes is carried out by the alternating input of crosslinker and adamantane-PEG3000 as a decrosslinker. Moreover, cluster size dependence is demonstrated by environmental pH. These offer the controlled fabrication of various homogeneous and heterogeneous Azo-Psomes structures, including the size regulation and visualization of clustered AOs through a fluorescent enzymatic cascade reaction. Finally, a temperature-sensitive crosslinking agent with β-CD units can promote the coaggregation of Azo-Psomes mediated by temperature changes. Overall, these (co-)clustered Azo-Psomes and their successful transformation in AOs may provide new features for modelling biological systems for eukaryotic cells and systems biology.

PMID:37858368 | DOI:10.1016/j.jcis.2023.10.015

Genome Biol. 2023 Oct 19;24(1):236. doi: 10.1186/s13059-023-03067-9.

ABSTRACT

Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.

PMID:37858253 | DOI:10.1186/s13059-023-03067-9

BMC Biol. 2023 Oct 20;21(1):220. doi: 10.1186/s12915-023-01724-w.

ABSTRACT

BACKGROUND: Through alternative splicing, most human genes produce multiple isoforms in a cell-, tissue-, and disease-specific manner. Numerous studies show that alternative splicing is essential for development, diseases, and their treatments. Despite these important examples, the extent and biological relevance of splicing are currently unknown.

RESULTS: To solve this problem, we developed pairedGSEA and used it to profile transcriptional changes in 100 representative RNA-seq datasets. Our systematic analysis demonstrates that changes in splicing, on average, contribute to 48.1% of the biological signal in expression analyses. Gene-set enrichment analysis furthermore indicates that expression and splicing both convey shared and distinct biological signals.

CONCLUSIONS: These findings establish alternative splicing as a major regulator of the human condition and suggest that most contemporary RNA-seq studies likely miss out on critical biological insights. We anticipate our results will contribute to the transition from a gene-centric to an isoform-centric research paradigm.

PMID:37858135 | DOI:10.1186/s12915-023-01724-w

Nat Genet. 2023 Oct 19. doi: 10.1038/s41588-023-01529-1. Online ahead of print.

ABSTRACT

Most signals in genome-wide association studies (GWAS) of complex traits implicate noncoding genetic variants with putative gene regulatory effects. However, currently identified regulatory variants, notably expression quantitative trait loci (eQTLs), explain only a small fraction of GWAS signals. Here, we show that GWAS and cis-eQTL hits are systematically different: eQTLs cluster strongly near transcription start sites, whereas GWAS hits do not. Genes near GWAS hits are enriched in key functional annotations, are under strong selective constraint and have complex regulatory landscapes across different tissue/cell types, whereas genes near eQTLs are depleted of most functional annotations, show relaxed constraint, and have simpler regulatory landscapes. We describe a model to understand these observations, including how natural selection on complex traits hinders discovery of functionally relevant eQTLs. Our results imply that GWAS and eQTL studies are systematically biased toward different types of variant, and support the use of complementary functional approaches alongside the next generation of eQTL studies.

PMID:37857933 | DOI:10.1038/s41588-023-01529-1

Nat Metab. 2023 Oct 19. doi: 10.1038/s42255-023-00908-6. Online ahead of print.

ABSTRACT

Metabolic regulation is integral to the proper functioning of innate lymphoid cells, yet the underlying mechanisms remain elusive. Here, we show that disruption of exogenous proline uptake, either through dietary restriction or by deficiency of the proline transporter Slc6a7, in lymphoid tissue inducer (LTi) cells, impairs LTi activation and aggravates dextran sodium sulfate-induced colitis in mice. With an integrative transcriptomic and metabolomic analysis, we profile the metabolic characteristics of various innate lymphoid cell subsets and reveal a notable enrichment of proline metabolism in LTi cells. Mechanistically, defective proline uptake diminishes the generation of reactive oxygen species, previously known to facilitate LTi activation. Additionally, LTi cells deficient in Slc6a7 display downregulation of Cebpb and Kdm6b, resulting in compromised transcriptional and epigenetic regulation of interleukin-22. Furthermore, our study uncovers the therapeutic potential of proline supplementation in alleviating colitis. Therefore, these findings shed light on the role of proline in facilitating LTi activation and ultimately contributing to gut homeostasis.

PMID:37857730 | DOI:10.1038/s42255-023-00908-6

Sci Rep. 2023 Oct 19;13(1):17874. doi: 10.1038/s41598-023-44426-7.

ABSTRACT

Efficacious stem cell-based therapies for traumatic brain injury (TBI) depend on successful delivery, migration, and engraftment of stem cells to induce neuroprotection. L-myc expressing human neural stem cells (LMNSC008) demonstrate an inherent tropism to injury sites after intranasal (IN) administration. We hypothesize that IN delivered LMNSC008 cells migrate to primary and secondary injury sites and modulate biomarkers associated with neuroprotection and tissue regeneration. To test this hypothesis, immunocompetent adult female rats received either controlled cortical impact injury or sham surgery. LMNSC008 cells or a vehicle were administered IN on postoperative days 7, 9, 11, 13, 15, and 17. The distribution and migration of eGFP-expressing LMNSC008 cells were quantified over 1 mm-thick optically cleared (CLARITY) coronal brain sections from TBI and SHAM controls. NSC migration was observed along white matter tracts projecting toward the hippocampus and regions of TBI. ELISA and Nanostring assays revealed a shift in tissue gene expression in LMNSC008 treated rats relative to controls. LMNSC008 treatment reduced expression of genes and pathways involved in inflammatory response, microglial function, and various cytokines and receptors. Our proof-of-concept studies, although preliminary, support the rationale of using intranasal delivery of LMNSC008 cells for functional studies in preclinical models of TBI and provide support for potential translatability in TBI patients.

PMID:37857701 | DOI:10.1038/s41598-023-44426-7

Sci Rep. 2023 Oct 19;13(1):17881. doi: 10.1038/s41598-023-45018-1.

ABSTRACT

We present a miniature oblique back-illumination microscope (mOBM) for imaging the microcirculation of human oral mucosa, enabling real-time, label-free phase contrast imaging of individual leukocytes circulating in the bloodstream, as well as their rolling and adhesion on vascular walls-the initial steps in leukocyte recruitment that is a hallmark of inflammation. Using the mOBM system, we studied the leukocyte-endothelial interactions in healthy and locally inflamed tissue and observed drastic changes in leukocyte movement (velocity and displacement profile). Our findings suggest that real-time imaging of leukocyte dynamics can provide new diagnostic insights (assessment of inflammation, temporal progression of disease, evaluation of therapeutic response, etc.) that are not available using conventional static parameters such as cell number and morphology.

PMID:37857684 | DOI:10.1038/s41598-023-45018-1

NPJ Syst Biol Appl. 2023 Oct 19;9(1):51. doi: 10.1038/s41540-023-00312-6.

ABSTRACT

Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims to unravel the complex relationships between genes and their regulators. Deciphering these networks plays a critical role in understanding the underlying regulatory crosstalk that drives many cellular processes and diseases. Recent advances in sequencing technology have led to the development of state-of-the-art GRN inference methods that exploit matched single-cell multi-omic data. By employing diverse mathematical and statistical methodologies, these methods aim to reconstruct more comprehensive and precise gene regulatory networks. In this review, we give a brief overview on the statistical and methodological foundations commonly used in GRN inference methods. We then compare and contrast the latest state-of-the-art GRN inference methods for single-cell matched multi-omics data, and discuss their assumptions, limitations and opportunities. Finally, we discuss the challenges and future directions that hold promise for further advancements in this rapidly developing field.

PMID:37857632 | DOI:10.1038/s41540-023-00312-6

Bone Res. 2023 Oct 20;11(1):52. doi: 10.1038/s41413-023-00291-8.

ABSTRACT

Mineral and bone disorder (MBD) in chronic kidney disease (CKD) is tightly linked to cardiovascular disease (CVD). In this study, we aimed to compare the prognostic value of nine MBD biomarkers to determine those associated best with adverse cardiovascular (CV) outcomes and mortality. In 5 217 participants of the German CKD (GCKD) study enrolled with an estimated glomerular filtration rate (eGFR) between 30-60 mL·min-1 per 1.73 m2 or overt proteinuria, serum osteoprotegerin (OPG), C-terminal fibroblast growth factor-23 (FGF23), intact parathyroid hormone (iPTH), bone alkaline phosphatase (BAP), cross-linked C-telopeptide of type 1 collagen (CTX1), procollagen 1 intact N-terminal propeptide (P1NP), phosphate, calcium, and 25-OH vitamin D were measured at baseline. Participants with missing values among these parameters (n = 971) were excluded, leaving a total of 4 246 participants for analysis. During a median follow-up of 6.5 years, 387 non-CV deaths, 173 CV deaths, 645 nonfatal major adverse CV events (MACEs) and 368 hospitalizations for congestive heart failure (CHF) were observed. OPG and FGF23 were associated with all outcomes, with the highest hazard ratios (HRs) for OPG. In the final Cox regression model, adjusted for CV risk factors, including kidney function and all other investigated biomarkers, each standard deviation increase in OPG was associated with non-CV death (HR 1.76, 95% CI: 1.35-2.30), CV death (HR 2.18, 95% CI: 1.50-3.16), MACE (HR 1.38, 95% CI: 1.12-1.71) and hospitalization for CHF (HR 2.05, 95% CI: 1.56-2.69). Out of the nine biomarkers examined, stratification based on serum OPG best identified the CKD patients who were at the highest risk for any adverse CV outcome and mortality.

PMID:37857629 | DOI:10.1038/s41413-023-00291-8

Nat Commun. 2023 Oct 19;14(1):6628. doi: 10.1038/s41467-023-42238-x.

ABSTRACT

Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7×10-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.

PMID:37857613 | DOI:10.1038/s41467-023-42238-x

PLoS Comput Biol. 2023 Oct 19;19(10):e1011549. doi: 10.1371/journal.pcbi.1011549. Online ahead of print.

ABSTRACT

Protein allocation determines the activity of cellular pathways and affects growth across all organisms. Therefore, different experimental and machine learning approaches have been developed to quantify and predict protein abundance and how they are allocated to different cellular functions, respectively. Yet, despite advances in protein quantification, it remains challenging to predict condition-specific allocation of enzymes in metabolic networks. Here, using protein-constrained metabolic models, we propose a family of constrained-based approaches, termed PARROT, to predict how much of each enzyme is used based on the principle of minimizing the difference between a reference and an alternative growth condition. To this end, PARROT variants model the minimization of enzyme reallocation using four different (combinations of) distance functions. We demonstrate that the PARROT variant that minimizes the Manhattan distance between the enzyme allocation of a reference and an alternative condition outperforms existing approaches based on the parsimonious distribution of fluxes or enzymes for both Escherichia coli and Saccharomyces cerevisiae. Further, we show that the combined minimization of flux and enzyme allocation adjustment leads to inconsistent predictions. Together, our findings indicate that minimization of protein allocation rather than flux redistribution is a governing principle determining steady-state pathway activity for microorganism grown in alternative growth conditions.

PMID:37856550 | DOI:10.1371/journal.pcbi.1011549

Dev Growth Differ. 2023 Oct 19. doi: 10.1111/dgd.12897. Online ahead of print.

ABSTRACT

With advances in high-throughput, large-scale in vivo measurement and genome modification techniques at the single-nucleotide level, there is an increasing demand for the development of new technologies for the flexible design and control of cellular systems. Computer-aided design is a powerful tool to design new cells. Whole-cell modeling aims to integrate various cellular subsystems, determine their interactions and cooperative mechanisms, and predict comprehensive cellular behaviors by computational simulations on a genome-wide scale. It has been applied to prokaryotes, yeasts, and higher eukaryotic cells, and utilized in a wide range of applications, including production of valuable substances, drug discovery, and controlled differentiation. Whole-cell modeling, consisting of several thousand elements with diverse scales and properties, requires innovative model construction, simulation, and analysis techniques. Furthermore, whole-cell modeling has been extended to multiple scales, including high-resolution modeling at the single-nucleotide and single-amino acid levels and multicellular modeling of tissues and organs. This review presents an overview of the current state of whole-cell modeling, discusses the novel computational and experimental technologies driving it, and introduces further developments toward multihierarchical modeling on a whole-genome scale. This article is protected by copyright. All rights reserved.

PMID:37856476 | DOI:10.1111/dgd.12897