Allergy. 2021 Mar 11. doi: 10.1111/all.14811. Online ahead of print.

ABSTRACT

BACKGROUND: Early detection/prediction offlare-ups in asthma, commonly triggered by viruses, would enable timely treatment. Previous studies on exhaled breath analysis by electronic nose(eNose) technology could discriminate between stable and unstable episodes of asthma,using single/few time-points. To investigate its monitoring propertiesduring these episodes, we examined day-to-day fluctuations in exhaled breath profiles, before and after a rhinovirus-16(RV16) challenge, in healthy and asthmatic adults.

METHODS: In this proof-of-concept study, 12 atopic asthmatic and 12 non-atopic healthy adultswere prospectively followed thrice weekly,60 days before and 30 days after a RV16challenge. Exhaled breath profiles were detected using an eNose, consisting of 7 different sensors.Per sensor, individual means were calculated usingpre-challenge visits. Absolute deviations(|%|) from thisbaselinewere derived for all visits. Within-group comparisons were tested with Mann-Whitney U testsand receiver operating characteristics(ROC) analysis. Finally, Spearman's correlationsbetween the total change in eNose deviations and fractional exhaled nitric oxide(FeNO), cold-like symptoms and pro-inflammatory cytokines, were examined.

RESULTS: Both groups had significantly increased eNosefluctuationspost-challenge, which in asthma started one day post-challenge, before the onset of symptoms. Discrimination between pre- and post-challenge reached an area under the ROC curve of 0.82 (95%CI=0.65-0.99) in healthy and 0.97 (95%CI=0.91-1.00) in asthmaticadults.The total change in eNose deviationsmoderately correlated withIL-8 and TNFα (ρ≈0.50-0.60)in asthmatics.

CONCLUSION: eNose fluctuations rapidly increase after a RV16challenge, with distinct differences between healthy and asthmatic adults, suggesting that this technologycould be useful in monitoring virus-driven unstable episodes in asthma.

PMID:33704785 | DOI:10.1111/all.14811

Emerg Top Life Sci. 2021 Mar 11:ETLS20200271. doi: 10.1042/ETLS20200271. Online ahead of print.

ABSTRACT

Untargeted metabolomics enables the identification of key changes to standard pathways, but also aids in revealing other important and possibly novel metabolites or pathways for further analysis. Much progress has been made in this field over the past decade and yet plant metabolomics seems to still be an emerging approach because of the high complexity of plant metabolites and the number one challenge of untargeted metabolomics, metabolite identification. This final and critical stage remains the focus of current research. The intention of this review is to give a brief current state of LC-MS based untargeted metabolomics approaches for plant specific samples and to review the emerging solutions in mass spectrometer hardware and computational tools that can help predict a compound's molecular structure to improve the identification rate.

PMID:33704399 | DOI:10.1042/ETLS20200271

Invest Ophthalmol Vis Sci. 2021 Mar 1;62(3):16. doi: 10.1167/iovs.62.3.16.

ABSTRACT

PURPOSE: Aurora kinase B (AURKB) plays a pivotal role in the regulation of mitosis and is gaining prominence as a therapeutic target in cancers; however, the role of AURKB in retinoblastoma (RB) has not been studied. The purpose of this study was to determine if AURKB plays a role in RB, how its expression is regulated, and whether it could be specifically targeted.

METHODS: The protein expression of AURKB was determined using immunohistochemistry in human RB patient specimens and immunoblotting in cell lines. Pharmacological inhibition and shRNA-mediated knockdown were used to understand the role of AURKB in cell viability, apoptosis, and cell cycle distribution. Cell viability in response to AURKB inhibition was also assessed in enucleated RB specimens. Immunoblotting was employed to determine the protein levels of phospho-histone H3, p53, p21, and MYCN. Chromatin immunoprecipitation-qPCR was performed to verify the binding of MYCN on the promoter region of AURKB.

RESULTS: The expression of AURKB was found to be markedly elevated in human RB tissues, and the overexpression significantly correlated with optic nerve and anterior chamber invasion. Targeting AURKB with small-molecule inhibitors and shRNAs resulted in reduced cell survival and increased apoptosis and cell cycle arrest at the G2/M phase. More importantly, primary RB specimens showed decreased cell viability in response to pharmacological AURKB inhibition. Additional studies have demonstrated that the MYCN oncogene regulates the expression of AURKB in RB.

CONCLUSIONS: AURKB is overexpressed in RB, and targeting it could serve as a novel therapeutic strategy to restrict tumor cell growth.

PMID:33704359 | DOI:10.1167/iovs.62.3.16

Environ Sci Pollut Res Int. 2021 Mar 10. doi: 10.1007/s11356-021-12671-w. Online ahead of print.

ABSTRACT

Cereal-based foods are utilized as an essential food segment worldwide. Nevertheless, their contamination by mycotoxins, also fumonisins, could pose a critical health risk. The present research provides the first systematic review regarding the prevalence and concentration of fumonisins in cereal-based food with the aid of a meta-analysis. In this regard, some international databases PubMed, Web of Science, Google Scholar, and Scopus were explored during the last 30 years. Among 9729 screened articles, 73 articles (which meet the proposed inclusion criteria), including 11,132 data, were incorporated in the performed meta-analysis. The overall rank order regarding the concentration of fumonisins in cereal-based foods was corn-based foods > wheat-based foods > other cereal foods > barley-based foods > rice-based foods > oat-based foods. Based on the prevalence of fumonisins, the overall rank order was other cereal foods > corn-based foods > rice-based foods > wheat-based foods > oat-based foods > barley-based food. The present meta-analysis results can be a beneficial database for risk assessment model progress, which can help industries and organizations decrease the presence of fumonisins in cereal-based food.

PMID:33694116 | DOI:10.1007/s11356-021-12671-w

Plant Physiol. 2021 Mar 9:kiab115. doi: 10.1093/plphys/kiab115. Online ahead of print.

ABSTRACT

The world-wide distribution of Arabidopsis (Arabidopsis thaliana) accessions imposes different types of evolutionary pressures, which contributes to various responses of these accessions to environmental stresses. Responses to drought stress have mostly been studied in the Columbia accession, which is predominantly used in plant research. However, the reactions to drought stress are complex and our understanding of the responses that contribute to maintaining plant growth during mild drought is very limited. Here, we studied the mechanisms with which natural accessions react to mild drought at a physiological and molecular level during early leaf development. We documented variations in mild drought responses among natural accessions and used transcriptome sequencing of a drought-sensitive accession, ICE163, and a drought-insensitive accession, Yeg-1, to gain insights into the mechanisms underlying this discrepancy. This revealed that ICE163 preferentially induces jasmonate- and anthocyanin-related pathways, which are beneficial in biotic stress defense, whereas Yeg-1 has a more pronounced activation of abscisic acid signaling, the classical abiotic stress response. Related physiological traits, including content of proline, anthocyanins and reactive oxygen species, stomatal closure and cellular leaf parameters, were investigated and linked to the transcriptional responses. We can conclude that most of these processes constitute general drought response mechanisms that are regulated similarly in drought-insensitive and -sensitive accessions. However, the capacity to close stomata and maintain cell expansion under mild drought appeared to be major factors that allow to better sustain leaf growth under mild drought.

PMID:33693949 | DOI:10.1093/plphys/kiab115

Nucleic Acids Res. 2021 Mar 8:gkab102. doi: 10.1093/nar/gkab102. Online ahead of print.

ABSTRACT

Single cell chromatin accessibility assays reveal epigenomic variability at cis-regulatory elements among individual cells. We previously developed a single-cell DNase-seq assay (scDNase-seq) to profile accessible chromatin in a limited number of single cells. Here, we report a novel indexing strategy to resolve single-cell DNase hypersensitivity profiles based on bulk cell analysis. This new technique, termed indexing single-cell DNase sequencing (iscDNase-seq), employs the activities of terminal DNA transferase (TdT) and T4 DNA ligase to add unique cell barcodes to DNase-digested chromatin ends. By a three-layer indexing strategy, it allows profiling genome-wide DHSs for >15 000 single-cells in a single experiment. Application of iscDNase-seq to human white blood cells accurately revealed specific cell types and inferred regulatory transcription factors (TF) specific to each cell type. We found that iscDNase-seq detected DHSs with specific properties related to gene expression and conservation missed by scATAC-seq for the same cell type. Also, we found that the cell-to-cell variation in accessibility computed using iscDNase-seq data is significantly correlated with the cell-to-cell variation in gene expression. Importantly, this correlation is significantly higher than that between scATAC-seq and scRNA-seq, suggesting that iscDNase-seq data can better predict the cellular heterogeneity in gene expression compared to scATAC-seq. Thus, iscDNase-seq is an attractive alternative method for single-cell epigenomics studies.

PMID:33693880 | DOI:10.1093/nar/gkab102

G3 (Bethesda). 2021 Feb 9;11(2):jkaa068. doi: 10.1093/g3journal/jkaa068.

ABSTRACT

Microbial growth characteristics have long been used to investigate fundamental questions of biology. Colony-based high-throughput screens enable parallel fitness estimation of thousands of individual strains using colony growth as a proxy for fitness. However, fitness estimation is complicated by spatial biases affecting colony growth, including uneven nutrient distribution, agar surface irregularities, and batch effects. Analytical methods that have been developed to correct for these spatial biases rely on the following assumptions: (1) that fitness effects are normally distributed, and (2) that most genetic perturbations lead to minor changes in fitness. Although reasonable for many applications, these assumptions are not always warranted and can limit the ability to detect small fitness effects. Beneficial fitness effects, in particular, are notoriously difficult to detect under these assumptions. Here, we developed the linear interpolation-based detector (LI Detector) framework to enable sensitive colony-based screening without making prior assumptions about the underlying distribution of fitness effects. The LI Detector uses a grid of reference colonies to assign a relative fitness value to every colony on the plate. We show that the LI Detector is effective in correcting for spatial biases and equally sensitive toward increase and decrease in fitness. LI Detector offers a tunable system that allows the user to identify small fitness effects with unprecedented sensitivity and specificity. LI Detector can be utilized to develop and refine gene-gene and gene-environment interaction networks of colony-forming organisms, including yeast, by increasing the range of fitness effects that can be reliably detected.

PMID:33693606 | DOI:10.1093/g3journal/jkaa068

G3 (Bethesda). 2021 Feb 9;11(2):jkaa061. doi: 10.1093/g3journal/jkaa061.

ABSTRACT

The Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the evolution and genetic basis of quantitative traits. We have expanded the resource with new lines and new populations, and here report the genotype and haplotype composition of CeMEE version 2, including a large set of putative de novo mutations, and updated additive and epistatic mapping simulations. Additive quantitative trait loci explaining 4% of trait variance are detected with >80% power, and the median detection interval approaches single-gene resolution on the highly recombinant chromosome arms. Although CeMEE populations are derived from a long-term evolution experiment, genetic structure is dominated by variation present in the ancestral population.

PMID:33693602 | DOI:10.1093/g3journal/jkaa061

Bioinformatics. 2021 Mar 8:btab160. doi: 10.1093/bioinformatics/btab160. Online ahead of print.

ABSTRACT

SUMMARY: Here, we propose Fourier ring correlation-based quality estimation (FRC-QE) as a new metric for automated image quality estimation in 3 D fluorescence microscopy acquisitions of cleared organoids that yields comparable measurements across experimental replicates, clearing protocols and works for different microscopy modalities.

AVAILABILITY AND IMPLEMENTATION: FRC-QE is written in ImgLib2/Java and provided as an easy-to-use and macro-scriptable plugin in Fiji. Code, documentation, sample images and further information can be found under https://github.com/PreibischLab/FRC-QE.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:33693580 | DOI:10.1093/bioinformatics/btab160

Cardiovasc Res. 2021 Mar 6:cvab058. doi: 10.1093/cvr/cvab058. Online ahead of print.

NO ABSTRACT

PMID:33693568 | DOI:10.1093/cvr/cvab058

Biosci Biotechnol Biochem. 2021 Mar 9:zbab034. doi: 10.1093/bbb/zbab034. Online ahead of print.

ABSTRACT

The C-terminal of GPCRs is now recognized as being important for G protein activation and signaling function. To detect the role of C-terminal tail in receptor activation, we used the α1b-AR, which has a long C-terminal of 164 amino acids. We constructed the intramolecular FRET sensors, in which the C-terminal was truncated to 10 (∆C-10), 20 (∆C-20), 30 (∆C-30), 50 (∆C-50), 70 (∆C-70) or 90 (∆C-90). The truncated mutants of ∆C-10, ∆C-20 or ∆C-30 cannot induce FRET signal changes and downstream ERK1/2 phosphorylation. However, the truncated mutants of ∆C-50, ∆C-70 or ∆C-90 induce significant FRET signal changes and downstream ERK1/2 phosphorylation, especially ∆C-90. This is particularly true in the case of the ∆C-90, ∆C-70, or ∆C-50 which retained the potential phosphorylation sites (Ser401, Ser404, Ser408 or Ser410). The ∆C-90 showed an increase in agonist-induced FRET signal changes and ERK1/2 phosphorylation in PKC- or endocytosis-dependent and EGFR-, src- or β-arrestin 2-independent.

PMID:33693487 | DOI:10.1093/bbb/zbab034

Front Genet. 2021 Feb 22;12:626403. doi: 10.3389/fgene.2021.626403. eCollection 2021.

ABSTRACT

Unaffected relatives of individuals with non-syndromic cleft lip with or without cleft palate (NSCL/P) show distinctive facial features. The presence of this facial endophenotype is potentially an expression of underlying genetic susceptibility to NSCL/P in the larger unselected population. To explore this hypothesis, we first partitioned the face into 63 partially overlapping regions representing global-to-local facial morphology and then defined endophenotypic traits by contrasting the 3D facial images from 264 unaffected parents of individuals with NSCL/P versus 3,171 controls. We observed distinct facial features between parents and controls across 59 global-to-local facial segments at nominal significance (p ≤ 0.05) and 52 segments at Bonferroni corrected significance (p < 1.2 × 10-3), respectively. Next, we quantified these distinct facial features as univariate traits in another dataset of 8,246 unaffected European individuals and performed a genome-wide association study. We identified 29 independent genetic loci that were associated (p < 5 × 10-8) with at least one of the tested endophenotypic traits, and nine genetic loci also passed the study-wide threshold (p < 8.47 × 10-10). Of the 29 loci, 22 were in proximity of loci previously associated with normal facial variation, 18 were near genes that show strong evidence in orofacial clefting (OFC), and another 10 showed some evidence in OFC. Additionally, polygenic risk scores for NSCL/P showed associations with the endophenotypic traits. This study thus supports the hypothesis of a shared genetic architecture of normal facial development and OFC.

PMID:33692830 | PMC:PMC7937973 | DOI:10.3389/fgene.2021.626403

Front Plant Sci. 2021 Feb 22;12:640914. doi: 10.3389/fpls.2021.640914. eCollection 2021.

ABSTRACT

Hyperspectral imaging is a promising tool for non-destructive phenotyping of plant physiological traits, which has been transferred from remote to proximal sensing applications, and from manual laboratory setups to automated plant phenotyping platforms. Due to the higher resolution in proximal sensing, illumination variation and plant geometry result in increased non-biological variation in plant spectra that may mask subtle biological differences. Here, a better understanding of spectral measurements for proximal sensing and their application to study drought, developmental and diurnal responses was acquired in a drought case study of maize grown in a greenhouse phenotyping platform with a hyperspectral imaging setup. The use of brightness classification to reduce the illumination-induced non-biological variation is demonstrated, and allowed the detection of diurnal, developmental and early drought-induced changes in maize reflectance and physiology. Diurnal changes in transpiration rate and vapor pressure deficit were significantly correlated with red and red-edge reflectance. Drought-induced changes in effective quantum yield and water potential were accurately predicted using partial least squares regression and the newly developed Water Potential Index 2, respectively. The prediction accuracy of hyperspectral indices and partial least squares regression were similar, as long as a strong relationship between the physiological trait and reflectance was present. This demonstrates that current hyperspectral processing approaches can be used in automated plant phenotyping platforms to monitor physiological traits with a high temporal resolution.

PMID:33692820 | PMC:PMC7937976 | DOI:10.3389/fpls.2021.640914

Front Immunol. 2021 Feb 22;12:641588. doi: 10.3389/fimmu.2021.641588. eCollection 2021.

ABSTRACT

Chronic neuropathic pain (CNP) is caused by a lesion or disease of the somatosensory nervous system. It affects ~8% of the general population and negatively impacts a person's level of functioning and quality of life. Its resistance to available pain therapies makes CNP a major unmet medical need. Immune cells have been shown to play a role for development, maintenance and recovery of CNP and therefore are attractive targets for novel pain therapies. In particular, in neuropathic mice and humans, microglia are activated in the dorsal horn and peripheral immune cells infiltrate the nervous system to promote chronic neuroinflammation and contribute to the initiation and progression of CNP. Importantly, immunity not only controls pain development and maintenance, but is also essential for pain resolution. In particular, regulatory T cells, a subpopulation of T lymphocytes with immune regulatory function, and macrophages were shown to be important contributors to pain recovery. In this review we summarize the interactions of the peripheral immune system with the nervous system and outline their contribution to the development and recovery of pain.

PMID:33692810 | PMC:PMC7937804 | DOI:10.3389/fimmu.2021.641588

Front Immunol. 2021 Feb 22;12:619776. doi: 10.3389/fimmu.2021.619776. eCollection 2021.

ABSTRACT

Parasitic helminths, comprising the flatworms (tapeworms and flukes) and nematodes (roundworms), have plagued humans persistently over a considerable period of time. It is now known that the degree of exposure to these and other pathogens inversely correlates with the incidence of both T helper 1 (Th1)-mediated autoimmunity and Th2-mediated allergy. Accordingly, there has been recent increased interest in utilizing active helminth worm infections and helminth-derived products for the treatment of human autoimmune and inflammatory diseases and to alleviate disease severity. Indeed, there is an accumulating list of novel helminth derived molecules, including proteins, peptides, and microRNAs, that have been shown to exhibit therapeutic potential in a variety of disease models. Here we consider the blood-dwelling schistosome flukes, which have evolved subtle immune regulatory mechanisms that promote parasite survival but at the same time minimize host tissue immunopathology. We review and discuss the recent advances in using schistosome infection and schistosome-derived products as therapeutics to treat or mitigate human immune-related disorders, including allergic asthma, arthritis, colitis, diabetes, sepsis, cystitis, and cancer.

PMID:33692793 | PMC:PMC7937812 | DOI:10.3389/fimmu.2021.619776

Nat Biotechnol. 2021 Mar 10. doi: 10.1038/s41587-021-00847-1. Online ahead of print.

NO ABSTRACT

PMID:33692517 | DOI:10.1038/s41587-021-00847-1

Cell Mol Immunol. 2021 Mar 10. doi: 10.1038/s41423-021-00659-y. Online ahead of print.

NO ABSTRACT

PMID:33692480 | DOI:10.1038/s41423-021-00659-y

J Immunother Cancer. 2021 Mar;9(3):e001610. doi: 10.1136/jitc-2020-001610.

ABSTRACT

BACKGROUND: Neoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC.

METHODS: We analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets.

RESULTS: Gene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature.

CONCLUSIONS: Taken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.

PMID:33692216 | DOI:10.1136/jitc-2020-001610

Sci Transl Med. 2021 Mar 10;13(584):eabe1433. doi: 10.1126/scitranslmed.abe1433.

ABSTRACT

Macrophages play a central role in the pathogenesis of atherosclerosis. The inflammatory properties of these cells are dictated by their metabolism, of which the mechanistic target of rapamycin (mTOR) signaling pathway is a key regulator. Using myeloid cell-specific nanobiologics in apolipoprotein E-deficient (Apoe -/-) mice, we found that targeting the mTOR and ribosomal protein S6 kinase-1 (S6K1) signaling pathways rapidly diminished plaque macrophages' inflammatory activity. By investigating transcriptome modifications, we identified Psap, a gene encoding the lysosomal protein prosaposin, as closely related with mTOR signaling. Subsequent in vitro experiments revealed that Psap inhibition suppressed both glycolysis and oxidative phosphorylation. Transplantation of Psap -/- bone marrow to low-density lipoprotein receptor knockout (Ldlr -/-) mice led to a reduction in atherosclerosis development and plaque inflammation. Last, we confirmed the relationship between PSAP expression and inflammation in human carotid atherosclerotic plaques. Our findings provide mechanistic insights into the development of atherosclerosis and identify prosaposin as a potential therapeutic target.

PMID:33692130 | DOI:10.1126/scitranslmed.abe1433

Genome Biol. 2021 Mar 10;22(1):81. doi: 10.1186/s13059-021-02295-1.

ABSTRACT

Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.

PMID:33691770 | DOI:10.1186/s13059-021-02295-1