Proc Natl Acad Sci U S A. 2023 Sep 12;120(37):e2302275120. doi: 10.1073/pnas.2302275120. Epub 2023 Sep 5.

ABSTRACT

Alerting for imminent earthquakes is particularly challenging due to the high nonlinearity and nonstationarity of geodynamical phenomena. In this study, based on spatiotemporal information (STI) transformation for high-dimensional real-time data, we developed a model-free framework, i.e., real-time spatiotemporal information transformation learning (RSIT), for extending the nonlinear and nonstationary time series. Specifically, by transforming high-dimensional information of the global navigation satellite system into one-dimensional dynamics via the STI strategy, RSIT efficiently utilizes two criteria of the transformed one-dimensional dynamics, i.e., unpredictability and instability. Such two criteria contemporaneously signal a potential critical transition of the geodynamical system, thereby providing early-warning signals of possible upcoming earthquakes. RSIT explores both the spatial and temporal dynamics of real-world data on the basis of a solid theoretical background in nonlinear dynamics and delay-embedding theory. The effectiveness of RSIT was demonstrated on geodynamical data of recent earthquakes from a number of regions across at least 4 y and through further comparison with existing methods.

PMID:37669376 | DOI:10.1073/pnas.2302275120

Elife. 2023 Sep 5;12:RP87133. doi: 10.7554/eLife.87133.

ABSTRACT

The application of next-generation sequencing (NGS) has transformed cancer research. As costs have decreased, NGS has increasingly been applied to generate multiple layers of molecular data from the same samples, covering genomics, transcriptomics, and methylomics. Integrating these types of multi-omics data in a combined analysis is now becoming a common issue with no obvious solution, often handled on an ad hoc basis, with multi-omics data arriving in a tabular format and analyzed using computationally intensive statistical methods. These methods particularly ignore the spatial orientation of the genome and often apply stringent p-value corrections that likely result in the loss of true positive associations. Here, we present GENIUS (GEnome traNsformatIon and spatial representation of mUltiomicS data), a framework for integrating multi-omics data using deep learning models developed for advanced image analysis. The GENIUS framework is able to transform multi-omics data into images with genes displayed as spatially connected pixels and successfully extract relevant information with respect to the desired output. We demonstrate the utility of GENIUS by applying the framework to multi-omics datasets from the Cancer Genome Atlas. Our results are focused on predicting the development of metastatic cancer from primary tumors, and demonstrate how through model inference, we are able to extract the genes which are driving the model prediction and are likely associated with metastatic disease progression. We anticipate our framework to be a starting point and strong proof of concept for multi-omics data transformation and analysis without the need for statistical correction.

PMID:37669321 | DOI:10.7554/eLife.87133

PLoS Pathog. 2023 Sep 5;19(9):e1011630. doi: 10.1371/journal.ppat.1011630. Online ahead of print.

ABSTRACT

Streptococcus pneumoniae is a leading cause of community-acquired pneumonia and bacteraemia and is capable of remarkable phenotypic plasticity, responding rapidly to environmental change. Pneumococcus is a nasopharyngeal commensal, but is responsible for severe, acute infections following dissemination within-host. Pneumococcus is adept at utilising host resources, but the airways are compartmentalised and those resources are not evenly distributed. Challenges and opportunities in metabolite acquisition within different airway niches may contribute to the commensal-pathogen switch when pneumococcus moves from nasopharynx into lungs. We used NMR to characterise the metabolic landscape of the mouse airways, in health and during infection. Using paired nasopharynx and lung samples from naïve animals, we identified fundamental differences in metabolite bioavailability between airway niches. Pneumococcal pneumonia was associated with rapid and dramatic shifts in the lung metabolic environment, whilst nasopharyngeal carriage led to only modest change in upper airway metabolite profiles. NMR spectra derived from the nasopharynx of mice infected with closely-related pneumococcal strains that differ in their colonisation potential could be distinguished from one another using multivariate dimensionality reduction methods. The resulting models highlighted that increased branched-chain amino acid (BCAA) bioavailability in nasopharynx is a feature of infection with the high colonisation potential strain. Subsequent analysis revealed increased expression of BCAA transport genes and increased intracellular concentrations of BCAA in that same strain. Movement from upper to lower airway environments is associated with shifting challenges in metabolic resource allocation for pneumococci. Efficient biosynthesis, liberation or acquisition of BCAA is a feature of adaptation to nasopharyngeal colonisation.

PMID:37669280 | DOI:10.1371/journal.ppat.1011630

STAR Protoc. 2023 Sep 4;4(3):102508. doi: 10.1016/j.xpro.2023.102508. Online ahead of print.

ABSTRACT

Quantification of intracellular proteins is essential to understand signaling. Here, we describe quantification of the expression and phosphorylation of the transcription factor STAT3. We present isolation of total and phosphorylated STAT3 from cell lysates by immunoprecipitation, followed by SDS-PAGE and western blot together with known amounts of a calibrator protein that shares an epitope with the precipitated proteins. Finally, we explain how to relate the amount of precipitated protein to the amount of calibrator protein considering the efficiency of immunoprecipitation. For complete details on the use and execution of this protocol, please refer to Dittrich et al. (2012)1 and Reeh et al. (2019).2.

PMID:37669163 | DOI:10.1016/j.xpro.2023.102508

J Exp Bot. 2023 Sep 5:erad348. doi: 10.1093/jxb/erad348. Online ahead of print.

ABSTRACT

Plants often face simultaneous abiotic and biotic stress conditions. However, physiological and transcriptional responses of plants under combined stress situations still need to be understood. Spring barley is susceptible to Fusarium Head Blight (FHB), which is strongly affected by weather conditions. We therefore studied the potential influence of drought on FHB severity and responses in three differently susceptible spring barley varieties. We found strongly reduced FHB severity in susceptible varieties under drought. The number of differentially expressed genes (DEGs) and strength of transcriptomic regulation reflected the concentration of physiological stress markers such as abscisic acid or fungal DNA contents. Infection-related gene expression is associated with susceptibility rather than resistance. Weighted gene correlation network analysis uncovered 18 modules of co-expressed genes, which reflect the pathogen or drought response in the used varieties. A generally infection-related module contained co-expressed genes for defence, programmed cell death and mycotoxin-detoxification indicating that diverse genotypes use a similar defence strategy towards FHB, albeit with different success. Further, DEGs showed co-expression in drought or genotype-associated modules correlating with measured phytohormones or the osmolyte proline. The combination of drought stress with infection led to the highest numbers of DEGs and provoked a modular composition of single stress responses rather than a specific transcriptional readout.

PMID:37668551 | DOI:10.1093/jxb/erad348

Physiology (Bethesda). 2023 Sep 5. doi: 10.1152/physiol.00010.2023. Online ahead of print.

ABSTRACT

The array of ion channels and transporters expressed in cell membranes-collectively referred to as the transportome-is a complex and multifunctional molecular machinery; in particular, at the plasma membrane level it finely tunes the exchange of biomolecules and ions acting as a functionally adaptive interface that accounts for dynamic plasticity in the response to environmental fluctuations and stressors. The transportome is responsible for the definition of membrane potential and its variations, participates in the transduction of extracellular signals, and acts as a filter for most of the substances entering and leaving the cell, thus enabling the homeostasis of many cellular parameters. For all these reasons, physiologists have long been interested in the expression and functionality of ion channels and transporters, both in physiological and pathological settings, and across the different domains of life. Today, thanks to the high-throughput technologies of the post-genomic era, the omics approach to the study of the transportome is becoming increasingly popular in different areas of biomedical research, allowing for a more comprehensive, integrated, and functional perspective of this complex cellular apparatus. This paper represents a first effort for a systematic review of the scientific literature on this topic. Here we report a brief overview of all those studies-both primary and meta-analyses-that looked at the transportome as a whole, regardless of the biological problem or the models they used. A later section is devoted to the methodological aspect by reviewing the most important public databases with transporter annotations. Before conclusions, limitations and future perspectives are also discussed.

PMID:37668550 | DOI:10.1152/physiol.00010.2023

Biotechnol J. 2023 Sep 5:e2300033. doi: 10.1002/biot.202300033. Online ahead of print.

ABSTRACT

Amino acids are the building blocks of proteins. In this respect, a reciprocal effect of recombinant protein production on amino acid biosynthesis as well as the impact of the availability of free amino acids on protein production can be anticipated. In this study, the impact of engineering the amino acid metabolism on the production of recombinant proteins was investigated in the yeast Pichia pastoris (syn Komagataella phaffii). Based on comprehensive systems-level analyses of the metabolomes and transcriptomes of different P. pastoris strains secreting antibody fragments, cell engineering targets were selected. Our working hypothesis that increasing intracellular amino acid levels could help unburden cellular metabolism and improve recombinant protein production was examined by constitutive overexpression of genes related to amino acid metabolism. In addition to twelve genes involved in specific amino acid biosynthetic pathways, the transcription factor GCN4 responsible for regulation of amino acid biosynthetic genes was overexpressed. The production of the used model protein, a secreted carboxylesterase (CES) from Sphingopyxis macrogoltabida, was increased by overexpression of pathway genes for alanine and for aromatic amino acids, and most pronounced, when overexpressing the regulator GCN4. The analysis of intracellular amino acid levels of selected clones indicated a direct linkage of improved recombinant protein production to the increased availability of intracellular amino acids. Finally, fed batch cultures showed that overexpression of GCN4 increased CES titers 2.6-fold, while the positive effect of other amino acid synthesis genes could not be transferred from screening to bioreactor cultures. This article is protected by copyright. All rights reserved.

PMID:37668396 | DOI:10.1002/biot.202300033

J Exp Bot. 2023 Sep 5:erad344. doi: 10.1093/jxb/erad344. Online ahead of print.

ABSTRACT

Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets in certain species represents an opportunity to explore underutilized network aggregation approaches. In fact, aggregated GCNs (aggGCNs) highlight robust co-expression interactions and improve functional connectivity. We applied and evaluated two different aggregation methods on public grapevine RNA-Seq datasets belonging to three different tissue conditions (leaf, berry and 'all organs'). Our results show that co-occurrence-based aggregation generally yielded the best-performing networks. We applied aggGCNs to study several TF gene families, showing their capacity of detecting both already-described and novel regulatory relationships between R2R3-MYBs, bHLH/MYC and multiple specialized metabolic pathways. Specifically, TF gene- and pathway-centered network analyses successfully ascertained the previously established role of VviMYBPA1 in controlling the accumulation of proanthocyanidins while providing insights into its novel role as a regulator of p-coumaroyl-CoA biosynthesis as well as the shikimate and aromatic amino-acid pathways. This network was validated using DNA Affinity Purification Sequencing data, demonstrating that co-expression networks of transcriptional activators can serve as a proxy of gene regulatory networks. This study presents an open repository to reproduce networks in other crops and a GCN application within the Vitviz platform, a user-friendly tool for exploring co-expression relationships.

PMID:37668374 | DOI:10.1093/jxb/erad344

IUCrJ. 2023 Sep 1;10(Pt 5):519-520. doi: 10.1107/S2052252523006759.

ABSTRACT

Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. During the last ten years, cryoEM has become widely available and has provided a major boost to structure determination of membrane proteins and large multi-protein complexes. Many of the structures have now been made available at resolutions around 2 Å, where fundamental questions regarding enzyme mechanisms can be addressed. Over the years, the abbreviation cryoEM has been understood to stand for different things. We wish the wider community to engage and clarify the definition of cryoEM so that the expanding literature involving cryoEM is unified.

PMID:37668213 | DOI:10.1107/S2052252523006759

New Phytol. 2023 Sep 5. doi: 10.1111/nph.19225. Online ahead of print.

ABSTRACT

Biocrusts are phototroph-driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth-promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host-microbe co-culture experiments between biocrust communities/biocrust isolates and a model grass (Brachypodium distachyon) or a dominant biocrust cyanobacterium (Microcoleus vaginatus), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates (Bosea sp._L1B56, Pseudarthrobacter sp._L1D14 and Pseudarthrobacter picheli_L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B. distachyon exudates, and supplementation of plant growth medium with this metabolite increased B. distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth-promoting microbes and metabolites.

PMID:37668195 | DOI:10.1111/nph.19225

MedComm (2020). 2023 Sep 3;4(5):e361. doi: 10.1002/mco2.361. eCollection 2023 Oct.

ABSTRACT

The profile of antibodies against antigenic epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during neutralizing antibody (NAb) decay has not been clarified. Using a SARS-CoV-2 proteome microarray that contained viral antigenic peptides, we analyzed the characteristics of the humoral response in patients with coronavirus disease 19 (COVID-19) in a longitudinal study. A total of 89 patients were recruited, and 226 plasma samples were serially collected in 2020. In the antigenic peptide microarray, the level of immunoglobulin G (IgG) antibodies against peptides within the S2 subunit (S-82) and a conserved gene region in variants of interest, open reading frame protein 10 (ORF10-3), were closely associated with the presence of SARS-CoV-2 NAbs. In an independent evaluation cohort of 232 plasma samples collected from 116 COVID-19 cases in 2020, S82-IgG titers were higher in NAbs-positive samples (p = 0.002) than in NAbs-negative samples using enzyme-linked immunosorbent assay. We further collected 66 plasma samples from another cohort infected by Omicron BA.1 virus in 2022. Compared with the samples with lower S82-IgG titers, NAb titers were significantly higher in the samples with higher S82-IgG titers (p = 0.04). Our findings provide insights into the understanding of the decay-associated signatures of SARS-CoV-2 NAbs.

PMID:37667740 | PMC:PMC10475218 | DOI:10.1002/mco2.361

Clin Transl Med. 2023 Sep;13(9):e1400. doi: 10.1002/ctm2.1400.

NO ABSTRACT

PMID:37667528 | DOI:10.1002/ctm2.1400

Arthritis Res Ther. 2023 Sep 4;25(1):161. doi: 10.1186/s13075-023-03148-x.

ABSTRACT

Curcumin, a component of the South-Asian spice turmeric, elicits anti-inflammatory functions. We have previously demonstrated that a highly bioavailable formulation of cucurmin, Cureit/Acumin™ (CUR), can suppress disease onset and severity, in a collagen-induced arthritis (CIA) mouse model. In a previous study, we have also shown that the abundance of antimicrobial host defence peptides, specifically cathelicidin (CRAMP) and calprotectin (S100A8 and S100A9), is significantly increased in the joint tissues of CIA mice. Elevated levels of cathelicidin and calprotectin have been associated with the pathogenesis of rheumatoid arthritis. Therefore, in this study, we examined the effect CUR administration on the abundance of cathelicidin and calprotectin in the joints, in a CIA mouse model. Here, we demonstrate that daily oral administration of CUR significantly reduces the elevated levels of CRAMP and calprotectin to baseline in the joints of CIA mice. We also show a linear correlation between the abundance of these peptides in the joints with serum inflammatory cytokines TNFα, IFNγ, and MCP-1. Overall, our results suggest that oral administration of a bioavailable CUR can suppress cathelicidin and calprotectin in the joints and regulate both local (joints) and systemic (serum) inflammation, in inflammatory arthritis.

PMID:37667385 | DOI:10.1186/s13075-023-03148-x

Nat Immunol. 2023 Sep 4. doi: 10.1038/s41590-023-01601-2. Online ahead of print.

ABSTRACT

Millions of people are suffering from Long COVID or post-acute sequelae of COVID-19 (PASC). Several biological factors have emerged as potential drivers of PASC pathology. Some individuals with PASC may not fully clear the coronavirus SARS-CoV-2 after acute infection. Instead, replicating virus and/or viral RNA-potentially capable of being translated to produce viral proteins-persist in tissue as a 'reservoir'. This reservoir could modulate host immune responses or release viral proteins into the circulation. Here we review studies that have identified SARS-CoV-2 RNA/protein or immune responses indicative of a SARS-CoV-2 reservoir in PASC samples. Mechanisms by which a SARS-CoV-2 reservoir may contribute to PASC pathology, including coagulation, microbiome and neuroimmune abnormalities, are delineated. We identify research priorities to guide the further study of a SARS-CoV-2 reservoir in PASC, with the goal that clinical trials of antivirals or other therapeutics with potential to clear a SARS-CoV-2 reservoir are accelerated.

PMID:37667052 | DOI:10.1038/s41590-023-01601-2

Hepatol Int. 2023 Sep 4. doi: 10.1007/s12072-023-10581-2. Online ahead of print.

ABSTRACT

BACKGROUND: Elevated bile acid levels have been associated with liver tumors in fatty liver. Ileal bile acid transporter inhibitors may inhibit bile acid absorption in the distal ileum and increase bile acid levels in the colon, potentially decreasing the serum and hepatic bile acid levels. This study aimed to investigate the impact of these factors on liver tumor.

METHODS: C57BL/6J mice received a one-time intraperitoneal injection of 25-mg/kg diethylnitrosamine. They were fed a choline-deficient high-fat diet for 20 weeks starting from 8 weeks of age, with or without elobixibat (EA Pharma, Tokyo, Japan).

RESULTS: Both groups showed liver fat accumulation and fibrosis, with no significant differences between the two groups. However, mice with elobixibat showed fewer liver tumors. The total serum bile acid levels, including free, tauro-conjugated, glyco-conjugated, and tauro-α/β-muricholic acids in the liver, were noticeably reduced following elobixibat treatment. The proportion of gram-positive bacteria in feces was significantly lower in the group treated with elobixibat (5.4%) than in the group without elobixibat (33.7%).

CONCLUSION: Elobixibat suppressed tumor growth by inhibiting bile acid reabsorption, and decreasing total bile acid and primary bile acid levels in the serum and liver. Additionally, the presence of bile acids in the colon may have led to a significant reduction in the proportion of gram-positive bacteria, potentially resulting in decreased secondary bile acid synthesis.

PMID:37666952 | DOI:10.1007/s12072-023-10581-2

Sci Rep. 2023 Sep 4;13(1):14589. doi: 10.1038/s41598-023-41767-1.

ABSTRACT

The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of a network to permit variations of the complex formation rate vector at steady state, irrespective of the network kinetics. However, the deficiency is by definition completely insensitive to the fine details of the directionality of reactions as well as bounds on reaction fluxes. While the classical definition of deficiency can be readily applied in the analysis of unconstrained, weakly reversible networks, it only provides an upper bound in the cases where relevant constraints on reaction fluxes are imposed. Here we propose the concept of effective deficiency, which provides a more accurate assessment of the network's capacity to permit steady state variations at the complex level for constrained networks of any reversibility patterns. The effective deficiency relies on the concept of nonstoichiometric balanced complexes, which we have already shown to be present in real-world biochemical networks operating under flux constraints. Our results demonstrate that the effective deficiency of real-world biochemical networks is smaller than the classical deficiency, indicating the effects of reaction directionality and flux bounds on the variation of the complex formation rate vector at steady state.

PMID:37666891 | DOI:10.1038/s41598-023-41767-1

Sci Rep. 2023 Sep 4;13(1):14573. doi: 10.1038/s41598-023-40568-w.

ABSTRACT

In the last century, a plethora of species have shown rapid phenological changes in response to climate change. Among animals, amphibians exhibit some of the greatest responses since their activity strongly depends on temperature and rainfall regimes. These shifts in phenology can have negative consequences for amphibian fitness. Thus, understanding phenological changes in amphibians is pivotal to design conservation actions to mitigate climate change effects. We used data on Common Spadefoot Toad (Pelobates fuscus) reproductive migration to wetlands over a period of 8 years in Italy to (i) identify the factors related to breeding migrations, (ii) assess potential phenological shifts in the breeding period, and (iii) determine which climatic factors are related to the observed phenological shifts. Our results showed that toads migrate to spawning sites preferably in early spring, on rainy days with temperatures of 9-14 °C, and with high humidity. Furthermore, despite an increase in average temperature across the study period, we observed a delay in the start of breeding migrations of 12.4 days over 8 years. This counterintuitive pattern was the result of a succession of hot and dry years that occurred in the study area, highlighting that for ephemeral pond breeders, precipitation could have a larger impact than temperature on phenology. Our results belie the strong presumption that climate change will shift amphibian phenology toward an earlier breeding migration and underline the importance of closely investigating the environmental factors related to species phenology.

PMID:37666849 | DOI:10.1038/s41598-023-40568-w

Sci Rep. 2023 Sep 4;13(1):14547. doi: 10.1038/s41598-023-40996-8.

ABSTRACT

Microorganisms colonize all possible ecological habitats, including those subjected to harsh stressors such as UV radiation. Hospitals, in particular the UV cabins used in phototherapy units, constitute an environment in which microbes are intermittently subjected to UV irradiation. This selective pressure, in addition to the frequent use of antibiotics by patients, may represent a threat in the context of the increasing problem of antimicrobial resistance. In this work, a collection of microorganisms has been established in order to study the microbiota associated to the inner and outer surfaces of UV cabins and to assess their resistance to UV light and the antibiotics frequently used in the Dermatology Service of a Spanish hospital. Our results show that UV cabins harbor a relatively diverse biocenosis dominated by typically UV-resistant microorganisms commonly found in sun-irradiated environments, such as Kocuria, Micrococcus or Deinococcus spp., but also clinically relevant taxa, such as Staphylococcus or Pseudomonas spp. The UV-radiation assays revealed that, although some isolates displayed some resistance, UV is not a major factor shaping the biocenosis living on the cabins, since a similar pool of resistant microorganisms was identified on the external surface of the cabins. Interestingly, some Staphylococcus spp. displayed resistance to one or more antibiotics, although the hospital reported no cases of antibiotic-resistance infections of the patients using the cabins. Finally, no association between UV and antibiotic resistances was found.

PMID:37666842 | DOI:10.1038/s41598-023-40996-8

Cell Rep. 2023 Sep 3;42(9):113087. doi: 10.1016/j.celrep.2023.113087. Online ahead of print.

ABSTRACT

Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.

PMID:37665664 | DOI:10.1016/j.celrep.2023.113087

Methods Mol Biol. 2023;2718:167-179. doi: 10.1007/978-1-0716-3457-8_10.

ABSTRACT

Proteins are crucial for controlling different cellular processes by perceiving and converting external environmental cues into cellular responses. Therefore, regulation of protein activities is pivotal for the development and survival of an organism. This is often mediated by posttranslational modifications, which usually are carried out on specific residues of a target protein by a "writer" protein. The (reversible) modifications of different residues may lead to different signaling outputs. In the case of protein phosphorylation, one of the most common posttranslational modifications, this writer protein is a protein kinase. In this chapter, we report a comprehensive and versatile workflow to identify the phosphorylation profile of a target protein in plants from a putative kinase-target pair by combining an in planta phosphorylation assay and mass spectrometry analysis.

PMID:37665460 | DOI:10.1007/978-1-0716-3457-8_10