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

Nat Microbiol. 2023 Oct 26. doi: 10.1038/s41564-023-01497-6. Online ahead of print.

ABSTRACT

Malaria-associated pathogenesis such as parasite invasion, egress, host cell remodelling and antigenic variation requires concerted action by many proteins, but the molecular regulation is poorly understood. Here we have characterized an essential Plasmodium-specific Apicomplexan AP2 transcription factor in Plasmodium falciparum (PfAP2-P; pathogenesis) during the blood-stage development with two peaks of expression. An inducible knockout of gene function showed that PfAP2-P is essential for trophozoite development, and critical for var gene regulation, merozoite development and parasite egress. Chromatin immunoprecipitation sequencing data collected at timepoints matching the two peaks of pfap2-p expression demonstrate PfAP2-P binding to promoters of genes controlling trophozoite development, host cell remodelling, antigenic variation and pathogenicity. Single-cell RNA sequencing and fluorescence-activated cell sorting revealed de-repression of most var genes in Δpfap2-p parasites. Δpfap2-p parasites also overexpress early gametocyte marker genes, indicating a regulatory role in sexual stage conversion. We conclude that PfAP2-P is an essential upstream transcriptional regulator at two distinct stages of the intra-erythrocytic development cycle.

PMID:37884813 | DOI:10.1038/s41564-023-01497-6

Nat Aging. 2023 Oct 26. doi: 10.1038/s43587-023-00511-0. Online ahead of print.

NO ABSTRACT

PMID:37884766 | DOI:10.1038/s43587-023-00511-0

Nat Nanotechnol. 2023 Oct 26. doi: 10.1038/s41565-023-01523-y. Online ahead of print.

ABSTRACT

Commencing with the breakdown of immune tolerance, multiple pathogenic factors, including synovial inflammation and harmful cytokines, are conjointly involved in the progression of rheumatoid arthritis. Intervening to mitigate some of these factors can bring a short-term therapeutic effect, but other unresolved factors will continue to aggravate the disease. Here we developed a ceria nanoparticle-immobilized mesenchymal stem cell nanovesicle hybrid system to address multiple factors in rheumatoid arthritis. Each component of this nanohybrid works individually and also synergistically, resulting in comprehensive treatment. Alleviation of inflammation and modulation of the tissue environment into an immunotolerant-favourable state are combined to recover the immune system by bridging innate and adaptive immunity. The therapy is shown to successfully treat and prevent rheumatoid arthritis by relieving the main symptoms and also by restoring the immune system through the induction of regulatory T cells in a mouse model of collagen-induced arthritis.

PMID:37884660 | DOI:10.1038/s41565-023-01523-y

Sci Rep. 2023 Oct 26;13(1):18365. doi: 10.1038/s41598-023-45694-z.

ABSTRACT

The design of biomaterials able to facilitate cell adhesion is critical in the field of tissue engineering. Precise control of surface chemistry at the material/tissue interface plays a major role in enhancing the interactions between a biomaterial and living cells. Bio-integration is particularly important in case of various electrotherapies, since a close contact between tissue and electrode's surface facilitates treatment. A promising approach towards surface biofunctionalization involves the electrografting of diazonium salts followed by the modification of organic layer with pro-adhesive polypeptides. This study focuses on the modification of platinum electrodes with a 4-nitrobenzenediazonium layer, which is then converted to the aminobenzene moiety. The electrodes are further biofunctionalized with polypeptides (polylysine and polylysine/laminin) to enhance cell adhesion. This study also explores the differences between physical and chemical coupling of selected polypeptides to modulate pro-adhesive nature of Pt electrodes with respect to human neuroblastoma SH-SY5Y cells and U87 astrocytes. Our results demonstrate the significant enhancement in cell adhesion for biofunctionalized electrodes, with more amplified adhesion noted for covalently coupled polypeptides. The implications of this research are crucial for the development of more effective and functional biomaterials, particularly biomedical electrodes, which have the potential to advance the field of bioelectronics and improve patients' outcomes.

PMID:37884622 | DOI:10.1038/s41598-023-45694-z

eNeuro. 2023 Oct 26;10(10):ENEURO.0340-23.2023. doi: 10.1523/ENEURO.0340-23.2023. Print 2023 Oct.

NO ABSTRACT

PMID:37884345 | DOI:10.1523/ENEURO.0340-23.2023

Cell Rep. 2023 Oct 17:113279. doi: 10.1016/j.celrep.2023.113279. Online ahead of print.

ABSTRACT

Antigen-specific CD8+ T cells mediate pathogen clearance. T cell phenotype is influenced by T cell receptor (TCR) sequences and environmental signals. Quantitative comparisons of these factors in human disease, while challenging to obtain, can provide foundational insights into basic T cell biology. Here, we investigate the phenotype kinetics of 679 CD8+ T cell clonotypes, each with specificity against one of three immunogenic viral antigens. Data were collected from a longitudinal study of 68 COVID-19 patients with antigens from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cytomegalovirus (CMV), and influenza. Each antigen is associated with a different type of immune activation during COVID-19. We find TCR sequence to be by far the most important factor in shaping T cell phenotype and persistence for populations specific to any of these antigens. Our work demonstrates the important relationship between TCR sequence and T cell phenotype and persistence and helps explain why T cell phenotype often appears to be determined early in an infection.

PMID:37883974 | DOI:10.1016/j.celrep.2023.113279