Elife. 2023 Oct 27;12:e81406. doi: 10.7554/eLife.81406. Online ahead of print.

ABSTRACT

Candida albicans, an opportunistic human pathogen, poses a significant threat to human health and is associated with significant socio-economic burden. Current antifungal treatments fail, at least in part, because C. albicans can initiate a strong drug tolerance response that allows some cells to grow at drug concentrations above their minimal inhibitory concentration. To better characterize this cytoprotective tolerance program at the molecular single cell level, we used a nano-liter droplet-based transcriptomics platform to profile thousands of individual fungal cells and establish their subpopulation characteristics in the absence and presence of antifungal drugs. Profiles of untreated cells exhibit heterogeneous expression that correlates with cell cycle stage with distinct metabolic and stress responses. At two days post-fluconazole exposure (a time when tolerance is measurable), surviving cells bifurcate into two major subpopulations: one characterized by the upregulation of genes encoding ribosomal proteins, rRNA processing machinery and mitochondrial cellular respiration capacity, termed the Ribo-dominant (Rd) state; and the other enriched for genes encoding stress responses and related processes, termed the Stress-dominant (Sd) state. This bifurcation persists at 3 and 6 days post treatment. We provide evidence that the Ribosome Assembly Stress Response (RASTR) is activated in these subpopulations and may facilitate cell survival.

PMID:37888959 | DOI:10.7554/eLife.81406

Toxics. 2023 Sep 30;11(10):827. doi: 10.3390/toxics11100827.

ABSTRACT

Benzophenone-3 (BP-3) is a lipophilic organic compound that occurs naturally in flower pigments. Since it adsorbs ultraviolet (UV) radiation in the UVA and UVB regions, it is one of the most common UV filters found in sunscreen and cosmetic products. We explored by in vivo micronuclei (MNi) assay the genotoxic effects of BP-3 on hemocytes from the freshwater gastropod Lymnaea stagnalis. We also studied its possible toxic effects on life-history traits: body growth in L. stagnalis and egg production of both L. stagnalis and the marine polychaete worm Ophryotrocha diadema. Adult individuals were exposed to increasing concentrations of BP-3 (0.025, 0.050, 0.100, and 0.200 mg/L) once a week for 4 weeks. In L. stagnalis, exposure to BP-3 at concentrations of both 0.2 and 0.1 mg/L produced genotoxic effects on the micronuclei frequencies, but only concentrations of 0.2 mg/L affected the NBUDs frequencies. Similarly, negative effects on body growth were observed at the concentrations of 0.2 and 0.1 mg/L and a significant reduction of egg production at 0.2 mg/L. In O. diadema, a negative correlation between egg production and increasing BP-3 concentrations was observed. Our findings suggest the need for more stringent measures to reduce the presence of BP-3 in the environment.

PMID:37888678 | DOI:10.3390/toxics11100827

Toxics. 2023 Sep 28;11(10):817. doi: 10.3390/toxics11100817.

ABSTRACT

The Arieş River (Western Romania) represents one of the most important affluents of the Mureş River, with great significance in the Mureş Tisza basin. The environmental quality of the Arieş basin is significantly affected by both historic mining activities and contemporary impacts. Thus, an evaluation of the effects of the main contaminants found in water (organochlorine pesticides-OCPs, monocyclic aromatic hydrocarbons-MAHs, polycyclic aromatic hydrocarbons-PAHs, and metals) on cyanobacteria and plants was performed. Among OCPs, hexachlorocyclohexane isomers, dichlorodiphenyltrichloroethane, and derivatives were detected in plants while admissible concentrations were detected in water. Among MAHs, high levels of benzene were detected both in water and in plants. The levels of PAHs exceeded the allowable values in all samples. Increased concentrations of metals in water were found only at Baia de Arieş, but in plants, all metal concentrations were high. The pH, nitrates, nitrites, and phosphates, as well as metals, pesticides, and aromatic hydrocarbons, influenced the physiological characteristics of algae, test plants, and aquatic plants exposed to various compounds dissolved in water. Considering that the Arieş River basin is the site of intense past mining activities, these data provide information about the impact on water quality as a consequence of pollution events.

PMID:37888668 | DOI:10.3390/toxics11100817

Mol Syst Biol. 2023 Oct 27:e11566. doi: 10.15252/msb.202311566. Online ahead of print.

ABSTRACT

The Escherichia coli genome-scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision-recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene-protein-reaction mapping as a key source of inaccurate predictions. A machine learning approach further identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy. This work outlines improved practices for the assessment of GEM accuracy with high-throughput mutant fitness data and highlights promising areas for future model refinement in E. coli and beyond.

PMID:37888487 | DOI:10.15252/msb.202311566

Membranes (Basel). 2023 Oct 17;13(10):833. doi: 10.3390/membranes13100833.

ABSTRACT

Electric potentials referred to as the gravielectric effect (∆ΨS) are generated in a double-membrane system containing identical polymer membranes set in horizontal planes and separating non-homogenous electrolyte solutions. The gravielectric effect depends on the concentration and composition of the solutions and is formed due to the gravitational field breaking the symmetry of membrane complexes/concentration boundary layers formed under concentration polarization conditions. As a part of the Kedem-Katchalsky formalism, a model of ion transport was developed, containing the transport parameters of membranes and solutions and taking into account hydrodynamic (convective) instabilities. The transition from non-convective to convective or vice versa can be controlled by a dimensionless concentration polarization factor or concentration Rayleigh number. Using the original measuring set, the time dependence of the membrane potentials was investigated. For steady states, the ∆ΨS was calculated and then the concentration characteristics of this effect were determined for aqueous solutions of NaCl and ethanol. The results obtained from the calculations based on the mathematical model of the gravitational effect are consistent with the experimental results within a 7% error range. It has been shown that a positive or negative gravielectric effect appeared when a density of the solution in the inter-membrane compartment was higher or lower than the density in the outer compartments. The values of the ∆ΨS were in a range from 0 to 27 mV. It was found that, the lower the concentration of solutions in the outer compartments of the two-membrane system (C0), for the same values of Cm/C0, the higher the ∆ΨS, which indicates control properties of the double-membrane system. The considered two-membrane electrochemical system is a source of electromotive force and functions as an electrochemical gravireceptor.

PMID:37888005 | DOI:10.3390/membranes13100833

Pathogens. 2023 Oct 17;12(10):1250. doi: 10.3390/pathogens12101250.

ABSTRACT

This manuscript elucidates the occurrence of glanders in an asymptomatic mare from Brazil presenting positive Burkholderia mallei antibody titers. The diagnosis was established through a multi-pronged approach encompassing microbiological culture, mass spectrometry, and genome sequencing. The outbreak occurred in 2019 in Tatuí, São Paulo, Brazil, and the infected mare, despite displaying no clinical symptoms, had multiple miliary lesions in the liver, as well as intense catarrhal discharge in the trachea. Samples were collected from various organs and subjected to bacterial isolation, molecular detection, and identification. The strain was identified as B. mallei using PCR and confirmed by MALDI-TOF mass spectrometry. Whole-genome sequencing revealed a genome size of 5.51 Mb with a GC content of 65.8%, 5871 genes (including 4 rRNA and 53 tRNA genes), and 5583 coding DNA sequences (CDSs). Additionally, 227 predicted pseudogenes were detected. In silico analysis of different genomic loci that allow for differentiation with Burkholderia pseudomallei confirmed the identity of the isolate as B. mallei, in addition to the characteristic genome size. The BAC 86/19 strain was identified as lineage 3, sublineage 2, which includes other strains from Brazil, India, and Iran. The genome sequencing of this strain provides valuable information that can be used to better understand the pathogen and its epidemiology, as well as to develop diagnostic tools for glanders.

PMID:37887766 | DOI:10.3390/pathogens12101250

Pathogens. 2023 Oct 3;12(10):1215. doi: 10.3390/pathogens12101215.

ABSTRACT

After many decades of research, a schistosome vaccine still looks to be a distant prospect. These helminths can live in the human bloodstream for years, even decades, surrounded by and feeding on the components of the immune response they provoke. The original idea of a vaccine based on the killing of invading cercariae in the skin has proven to be illusory. There has also been a realisation that even if humans develop some protection against infection over a protracted period, it very likely involves IgE-mediated responses that cannot provide the basis for a vaccine. However, it has also become clear that both invasive migrating larvae and adult worms must expose proteins and release secretions into the host environment as part of their normal biological activities. The application of modern 'omics approaches means that we now have a much better idea of the identity of these potential immune targets. This review looks at three animal models in which acquired immunity has been demonstrated and asks whether the mechanisms might inform our vaccine strategies to achieve protection in model hosts and humans. Eliciting responses, either humoral or cellular, that can persist for many months is a challenge. Arming of the lungs with effector T cells, as occurs in mice exposed to the radiation-attenuated cercarial vaccine, is one avenue. Generating IgG antibody titres that reach levels at which they can exert sustained immune pressure to cause worm elimination, as occurs in rhesus macaques, is another. The induction of memory cell populations that can detect trickle invasions of larval stages remains to be explored. One promising approach is the analysis of protective antibodies using high-density peptide arrays of target proteins to identify reactive regions. These can be combined in multi-epitope constructs to immunise a host against many targets simultaneously and cheaply.

PMID:37887731 | DOI:10.3390/pathogens12101215

Metabolites. 2023 Oct 2;13(10):1048. doi: 10.3390/metabo13101048.

ABSTRACT

Trace metal elements are of vital importance for fundamental biological processes. They function in various metabolic pathways after the long evolution of living organisms. Glucose is considered to be one of the main sources of biological energy that supports biological activities, and its metabolism is tightly regulated by trace metal elements such as iron, zinc, copper, and manganese. However, there is still a lack of understanding of the regulation of glucose metabolism by trace metal elements. In particular, the underlying mechanism of action remains to be elucidated. In this review, we summarize the current concepts and progress linking trace metal elements and glucose metabolism, particularly for the trace metal elements zinc, copper, manganese, and iron.

PMID:37887373 | DOI:10.3390/metabo13101048

Biology (Basel). 2023 Oct 18;12(10):1344. doi: 10.3390/biology12101344.

ABSTRACT

Text mining methods are being developed to assimilate the volume of biomedical textual materials that are continually expanding. Understanding protein-protein interaction (PPI) deficits would assist in explaining the genesis of diseases. In this study, we designed an automated system to extract PPIs from the biomedical literature that uses a deep learning sentence classification model, a pretrained word embedding, and a BiLSTM recurrent neural network with additional layers, a conditional random field (CRF) named entity recognition (NER) model, and shortest-dependency path (SDP) model using the SpaCy library in Python. The automated system ensures that it targets sentences that contain PPIs and not just these proteins mentioned in the framework of disease discovery or other context. Our first model achieved 13% greater precision on the Aimed/BioInfr benchmark corpus than the previous state-of-the-art BiLSTM neural network models. The NER model presented in this study achieved 98% precision on the Aimed/BioInfr corpus over previous models. In order to facilitate the production of an accurate representation of the PPI network, the processes were developed to systematically map the protein interactions in the texts. Overall, evaluating our system through the use of 6027 abstracts pertaining to seven proteins associated with Autism Spectrum Disorder completed the manually curated PPI network for these proteins. When it comes to complicated diseases, these networks would assist in understanding how PPI deficits contribute to disease development while also emphasizing the influence of interactions on protein function and biological processes.

PMID:37887054 | DOI:10.3390/biology12101344

Biology (Basel). 2023 Oct 16;12(10):1338. doi: 10.3390/biology12101338.

ABSTRACT

Translation efficiency modulates gene expression in prokaryotes. The comparative analysis of translation elongation efficiency characteristics of Ralstonia genus bacteria genomes revealed that these characteristics diverge in accordance with the phylogeny of Ralstonia. The first branch of this genus is a group of bacteria commonly found in moist environments such as soil and water that includes the species R. mannitolilytica, R. insidiosa, and R. pickettii, which are also described as nosocomial infection pathogens. In contrast, the second branch is plant pathogenic bacteria consisting of R. solanacearum, R. pseudosolanacearum, and R. syzygii. We found that the soil Ralstonia have a significantly lower number and energy of potential secondary structures in mRNA and an increased role of codon usage bias in the optimization of highly expressed genes' translation elongation efficiency, not only compared to phytopathogenic Ralstonia but also to Cupriavidus necator, which is closely related to the Ralstonia genus. The observed alterations in translation elongation efficiency of orthologous genes are also reflected in the difference of potentially highly expressed gene' sets' content among Ralstonia branches with different lifestyles. Analysis of translation elongation efficiency characteristics can be considered a promising approach for studying complex mechanisms that determine the evolution and adaptation of bacteria in various environments.

PMID:37887048 | DOI:10.3390/biology12101338

Bioinform Adv. 2023 Oct 20;3(1):vbad147. doi: 10.1093/bioadv/vbad147. eCollection 2023.

NO ABSTRACT

PMID:37886713 | PMC:PMC10599964 | DOI:10.1093/bioadv/vbad147

Bioinform Adv. 2023 Oct 18;3(1):vbad150. doi: 10.1093/bioadv/vbad150. eCollection 2023.

ABSTRACT

SUMMARY: Gene set scoring (or enrichment) is a common dimension reduction task in bioinformatics that can be focused on the differences between groups or at the single sample level. Gene sets can represent biological functions, molecular pathways, cell identities, and more. Gene set scores are context dependent values that are useful for interpreting biological changes following experiments or perturbations. Single sample scoring produces a set of scores, one for each member of a group, which can be analyzed with statistical models that can include additional clinically important factors such as gender or age. However, the sparsity and technical noise of single-cell expression measures create difficulties for these methods, which were originally designed for bulk expression profiling (microarrays, RNAseq). This can be greatly remedied by first applying a smoothing transformation that shares gene measure information within transcriptomic neighborhoods. In this work, we use the nearest neighbor graph of cells for matrix smoothing to produce high quality gene set scores on a per-cell, per-group, level which is useful for visualization and statistical analysis.

AVAILABILITY AND IMPLEMENTATION: The gssnng software is available using the python package index (PyPI) and works with Scanpy AnnData objects. It can be installed using "pip install gssnng." More information and demo notebooks: see https://github.com/IlyaLab/gssnng.

PMID:37886712 | PMC:PMC10599965 | DOI:10.1093/bioadv/vbad150

Bioinform Adv. 2023 Aug 22;3(1):vbad109. doi: 10.1093/bioadv/vbad109. eCollection 2023.

ABSTRACT

MOTIVATION: Genetic biases in the human antibody repertoire result in publicly available antibody sequence datasets that contain many duplicate or highly similar sequences. Available datasets are further skewed by the predominance of studies focused on specific disease states, primarily cancer, autoimmunity, and a small number of infectious diseases that includes HIV, influenza, and SARS-CoV-2. These biases and redundancies are a barrier to rapid similarity searches and reduce the efficiency with which these datasets can be used to train statistical or machine-learning models. Identity-based clustering provides a solution; however, the extremely large size of available antibody sequence datasets makes such clustering operations computationally intensive and potentially out of reach for many scientists and researchers who would benefit from such data.

RESULTS: Antibody Reference Clusters (AntiRef), which is modeled after UniRef, provides clustered datasets of filtered human antibody sequences. Due to the modular nature of recombined antibody genes, the clustering thresholds used by UniRef for general protein sequences are suboptimal for antibody clustering. Starting with an input dataset of ∼451M full-length, productive human antibody sequences, AntiRef provides reference datasets clustered at a range of antibody-optimized identity thresholds. AntiRef90 is one-third the size of the input dataset and less than half the size of the non-redundant AntiRef100.

AVAILABILITY AND IMPLEMENTATION: AntiRef datasets are available on Zenodo (zenodo.org/record/7474336). All code used to generate AntiRef is available on GitHub (github.com/briney/antiref). The AntiRef versioning scheme (current version: v2022.12.14) refers to the date on which sequences were retrieved from OAS.

PMID:37886711 | PMC:PMC10598580 | DOI:10.1093/bioadv/vbad109

Hepatobiliary Surg Nutr. 2023 Oct 1;12(5):795-797. doi: 10.21037/hbsn-23-335. Epub 2023 Sep 15.

NO ABSTRACT

PMID:37886186 | PMC:PMC10598306 | DOI:10.21037/hbsn-23-335

Front Microbiol. 2023 Oct 11;14:1270487. doi: 10.3389/fmicb.2023.1270487. eCollection 2023.

ABSTRACT

Coordination of cell cycle with metabolism exists in all cell types that grow by division. It serves to build a new cell, (i) fueling building blocks for the synthesis of proteins, nucleic acids, and membranes, and (ii) producing energy through glycolysis. Cyclin-dependent kinases (Cdks) play an essential role in this coordination, thereby in the regulation of cell division. Cdks are functional homologs across eukaryotes and are the engines that drive cell cycle events and the clocks that time them. Their function is counteracted by stoichiometric inhibitors; specifically, inhibitors of cyclin-cyclin dependent kinase (cyclin/Cdk) complexes allow for their activity at specific times. Here, we provide a new perspective about the yet unknown cell cycle mechanisms impacting on metabolism. We first investigated the effect of the mitotic cyclin/Cdk1 complex Cyclin B/Cdk1-functional homolog in mammalian cells of the budding yeast Clb2/Cdk1-on yeast metabolic enzymes of, or related to, the glycolysis pathway. Six glycolytic enzymes (Glk1, Hxk2, Pgi1, Fba1, Tdh1, and Pgk1) were subjected to in vitro Cdk-mediated phosphorylation assays. Glucose-6-phosphate dehydrogenase (Zwf1), the first enzyme in the pentose phosphate pathway that is important for NADPH production, and 6-phospho-fructo-2-kinase (Pfk27), which catalyzes fructose-2,6-bisphosphate synthesis, a key regulator of glycolysis, were also included in the study. We found that, among these metabolic enzymes, Fba1 and Pgk1 may be phosphorylated by Cdk1, in addition to the known Cdk1-mediated phosphorylation of Gph1. We then investigated the possible effect of Sic1, stoichiometric inhibitor of mitotic cyclin/Cdk1 complexes in budding yeast, on the activities of three most relevant glycolytic enzymes: Hxk2, Glk1, and Tdh1. We found that Sic1 may have a negative effect on Hxk2. Altogether, we reveal possible new routes, to be further explored, through which cell cycle may regulate cellular metabolism. Because of the functional homology of cyclin/Cdk complexes and their stoichiometric inhibitors across evolution, our findings may be relevant for the regulation of cell division in eukaryotes.

PMID:37886071 | PMC:PMC10598772 | DOI:10.3389/fmicb.2023.1270487

Front Microbiol. 2023 Oct 10;14:1302833. doi: 10.3389/fmicb.2023.1302833. eCollection 2023.

ABSTRACT

[This corrects the article DOI: 10.3389/fmicb.2020.00366.].

PMID:37886070 | PMC:PMC10598376 | DOI:10.3389/fmicb.2023.1302833

J Open Source Softw. 2023;8(88):5545. doi: 10.21105/joss.05545. Epub 2023 Aug 2.

NO ABSTRACT

PMID:37885608 | PMC:PMC10600976 | DOI:10.21105/joss.05545

JACS Au. 2023 Oct 3;3(10):2873-2882. doi: 10.1021/jacsau.3c00421. eCollection 2023 Oct 23.

ABSTRACT

Dynamic monitoring of intracellular ubiquitin (Ub) conjugates is instrumental to understanding the Ub regulatory machinery. Although many biochemical approaches have been developed to characterize protein ubiquitination, chemical tools capable of temporal resolution probing of ubiquitination events remain to be developed. Here, we report the development of the first cell-permeable and stimuli-responsive Ub probe and its application for the temporal resolution profiling of ubiquitinated substrates in live cells. The probe carrying the photolabile group N-(2-nitrobenzyl)-Gly (Nbg) on the amide bond between Ub Gly75 and Gly76 is readily prepared through chemical synthesis and can be delivered to live cells by conjugation via a disulfide bond with the cyclic cell-penetrating peptide cR10D (i.e., 4-((4-(dimethylamino)phenyl)-azo)-benzoic acid-modified cyclic deca-arginine). Both in vitro and in vivo experiments showed that Ub-modifying enzymes (E1, E2s, and E3s) could not install the Ub probe onto substrate proteins prior to removal of the nitrobenzyl group, which was easily accomplished via photoirradiation. The utility and practicality of this probe were exemplified by the time-resolved biochemical and proteomic investigation of ubiquitination events in live cells during a H2O2-mediated oxidative stress response. This work shows a conceptually new family of chemical Ub tools for the time-resolved studies on dynamic protein ubiquitination in different biological processes and highlights the utility of modern chemical protein synthesis in obtaining custom-designed tools for biological studies.

PMID:37885572 | PMC:PMC10598832 | DOI:10.1021/jacsau.3c00421

Hum Vaccin Immunother. 2023 Dec 15;19(3):2267295. doi: 10.1080/21645515.2023.2267295. Epub 2023 Oct 26.

ABSTRACT

In the field of immunology, a systems biology approach is crucial to understanding the immune response to infection and vaccination considering the complex interplay between genetic, epigenetic, and environmental factors. Significant progress has been made in understanding the innate immune response, including cell players and critical signaling pathways, but many questions remain unanswered, including how the innate immune response dictates host/pathogen responses and responses to vaccines. To complicate things further, it is becoming increasingly clear that the innate immune response is not a linear pathway but is formed from complex networks and interactions. To further our understanding of the crosstalk and complexities, systems-level analyses and expanded experimental technologies are now needed. In this review, we discuss the most recent immunoprofiling techniques and discuss systems approaches to studying the global innate immune landscape which will inform on the development of personalized medicine and innovative vaccine strategies.

PMID:37885158 | DOI:10.1080/21645515.2023.2267295

BMC Genomics. 2023 Oct 26;24(1):641. doi: 10.1186/s12864-023-09743-1.

ABSTRACT

BACKGROUND: MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage.

RESULTS: We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development.

CONCLUSION: The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.

PMID:37884859 | DOI:10.1186/s12864-023-09743-1