Front Neurosci. 2023 Mar 24;17:1052079. doi: 10.3389/fnins.2023.1052079. eCollection 2023.

ABSTRACT

INTRODUCTION: Obese rodents e.g., the leptin-deficient (ob/ob) mouse exhibit remarkable behavioral changes and are therefore ideal models for evaluating mental disorders resulting from obesity. In doing so, female as well as male ob/ob mice at 8, 24, and 40 weeks of age underwent two common behavioral tests, namely the Open Field test and Elevated Plus Maze, to investigate behavioral alteration in a sex- and age dependent manner. The accuracy of these tests is often dependent on the observer that can subjectively influence the data.

METHODS: To avoid this bias, mice were tracked with a video system. Video files were further analyzed by the compared use of two software, namely EthoVision (EV) and DeepLabCut (DLC). In DLC a Deep Learning application forms the basis for using artificial intelligence in behavioral research in the future, also with regard to the reduction of animal numbers.

RESULTS: After no sex and partly also no age-related differences were found, comparison revealed that both software lead to almost identical results and are therefore similar in their basic outcomes, especially in the determination of velocity and total distance movement. Moreover, we observed additional benefits of DLC compared to EV as it enabled the interpretation of more complex behavior, such as rearing and leaning, in an automated manner.

DISCUSSION: Based on the comparable results from both software, our study can serve as a starting point for investigating behavioral alterations in preclinical studies of obesity by using DLC to optimize and probably to predict behavioral observations in the future.

PMID:37034162 | PMC:PMC10079875 | DOI:10.3389/fnins.2023.1052079

Front Microbiol. 2023 Mar 23;14:1117779. doi: 10.3389/fmicb.2023.1117779. eCollection 2023.

ABSTRACT

INTRODUCTION: The human respiratory tract is considered to be a polymicrobial niche, and an imbalance in the microorganism composition is normally associated with several respiratory diseases. In addition to the well-studied bacteriome, the existence of fungal species in the respiratory tract has drawn increasing attention and has been suggested to have a significant clinical impact. However, the understanding of the respiratory fungal microbiota (mycobiome) in pulmonary diseases is still insufficient.

METHODS: In this study, we investigated the fungal community composition of oropharynx swab (OS) samples from patients with five kinds of pulmonary disease, including interstitial lung disease (ILD), bacterial pneumonia (BP), fungal pneumonia (FP), asthma (AS) and lung cancer (LC), and compared them with healthy controls (HCs), based on high-throughput sequencing of the amplified fungal internal transcribed spacer (ITS) region.

RESULTS: The results showed significant differences in fungal composition and abundance between disease groups and HCs. Malassezia was the most significant genus, which was much more abundant in pulmonary diseases than in the control. In addition, many common taxa were shared among different disease groups, but differences in taxa abundance and specific species in distinct disease groups were also observed. Based on linear discriminant analysis effect size (LefSe), each group had its characteristic species. Furthermore, some species showed a significant correlation with the patient clinical characteristics.

DISCUSSION: Our study deepened our understanding of the respiratory tract mycobiome in some diseases that are less studied and identified the commonalities and differences among different kinds of pulmonary disease. These results would provide the solid basis for further investigation of the association between the mycobiome and pathogenicity of pulmonary diseases.

PMID:37032908 | PMC:PMC10076636 | DOI:10.3389/fmicb.2023.1117779

Synth Biol (Oxf). 2023 Apr 8;8(1):ysad006. doi: 10.1093/synbio/ysad006. eCollection 2023.

ABSTRACT

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.

PMID:37073284 | PMC:PMC10105873 | DOI:10.1093/synbio/ysad006

Cell Rep Med. 2023 Mar 31:101007. doi: 10.1016/j.xcrm.2023.101007. Online ahead of print.

ABSTRACT

Pancreatic ductal adenocarcinomas (PDACs) frequently harbor KRAS mutations. Although MEK inhibitors represent a plausible therapeutic option, most PDACs are innately resistant to these agents. Here, we identify a critical adaptive response that mediates resistance. Specifically, we show that MEK inhibitors upregulate the anti-apoptotic protein Mcl-1 by triggering an association with its deubiquitinase, USP9X, resulting in acute Mcl-1 stabilization and protection from apoptosis. Notably, these findings contrast the canonical positive regulation of Mcl-1 by RAS/ERK. We further show that Mcl-1 inhibitors and cyclin-dependent kinase (CDK) inhibitors, which suppress Mcl-1 transcription, prevent this protective response and induce tumor regression when combined with MEK inhibitors. Finally, we identify USP9X as an additional potential therapeutic target. Together, these studies (1) demonstrate that USP9X regulates a critical mechanism of resistance in PDAC, (2) reveal an unexpected mechanism of Mcl-1 regulation in response to RAS pathway suppression, and (3) provide multiple distinct promising therapeutic strategies for this deadly malignancy.

PMID:37030295 | DOI:10.1016/j.xcrm.2023.101007

Plant J. 2023 Apr 8. doi: 10.1111/tpj.16242. Online ahead of print.

ABSTRACT

The plant secondary cell wall is a thickened matrix of polysaccharides and lignin deposited at the cessation of growth in some cells. It forms the majority of carbon in lignocellulosic biomass, and it is an abundant and renewable source for forage, fiber, materials, fuels, and bioproducts. The complex structure and arrangement of the cell wall polymers mean that the carbon is difficult to access in an economical and sustainable way. One solution is to alter cell wall polymer structure so that it is more suited to downstream processing. However, it remains difficult to predict what the effects of this engineering will have on the assembly, architecture and properties of the cell wall. Here, we make use of Arabidopsis plants expressing a suite of genes to increase pectic galactan chain length in the secondary cell wall. Using multi-dimensional solid-state NMR, we show that increasing galactan chain length enhances pectin-cellulose spatial contacts and increases cellulose crystallinity. We also find the increased galactan content leads to fewer spatial contacts of cellulose with xyloglucan and the backbone of pectin. Hence, we propose that the elongated galactan side chains compete with xyloglucan and the pectic backbone for cellulose interactions. Due to the galactan topology, this may result in comparatively weaker interactions and disrupts the cell wall architecture. Therefore, introduction of this strategy into trees or other bioenergy crops would benefit from cell-specific expression strategies to avoid negative effects on plant growth.

PMID:37029760 | DOI:10.1111/tpj.16242

J Biomol Struct Dyn. 2023 Apr 8:1-11. doi: 10.1080/07391102.2023.2193999. Online ahead of print.

ABSTRACT

The calcium/calmodulin dependent protein kinase kinase 2 (CAMKK2) plays a key role in regulation of intracellular calcium levels and signaling pathways. It is involved in activation of downstream signaling pathways that regulate various cellular processes. Dysregulation of CAMKK2 activity has been linked to various diseases including cancer, suggesting that CAMKK2 inhibitors might be beneficial in oncological, metabolic and inflammatory indications. The most pressing issues in small molecule discovery are synthesis feasibility, novel chemical structure and desired biological characteristics. To circumvent this constraint, we employed 'DrugspaceX' for rapid lead identification, followed by repositioning seven FDA-approved drugs for CAMKK2 inhibition. Further, first-level transformation (Set1 analogues) was performed in 'DrugspaceX', followed by virtual screening. The t-SNE visualization revealed that the transformations surrounding Rucaparib, Treprostinil and Canagliflozin are more promising for developing CAMKK2 inhibitors. Second, using the top-ranked Set1 analogues, Set2 analogues were generated, and virtual screening revealed the top-ranked five analogues. Among the top five Set2 analogues, DE273038_5 had the lowest docking score of -11.034 kcal/mol and SA score of 2.59, retaining the essential interactions with Hotspot residues LYS194 and VAL270 across 250 ns simulation period. When compared to the other four compounds, the ligand effectiveness score was 0.409, and the number of rotatable penalties was only three. Further, DE273038_5 after two rounds of transformations was discovered to be novel and had not been previously described in other databases. These data suggest that the new candidate DE273038_5 is likely to have inhibitory activity at the CAMKK2 active site, implying potential therapeutic use.Communicated by Ramaswamy H. Sarma.

PMID:37029757 | DOI:10.1080/07391102.2023.2193999

J Physiol. 2023 Apr 7. doi: 10.1113/JP284111. Online ahead of print.

ABSTRACT

The carotid bodies are the principal sensory organs for detecting changes in arterial blood oxygen concentration, and the carotid body chemoreflex is a major regulator of the sympathetic tone, blood pressure and breathing. Intermittent hypoxia is a hallmark manifestation of obstructive sleep apnea (OSA), which is a widespread respiratory disorder. The first part of this review discuss the role of carotid bodies in heightened sympathetic tone and hypertension in rodents treated with intermittent hypoxia, and the underlying cellular, molecular, and epigenetic mechanisms. We also present evidence for hitherto uncharacterized role of carotid body afferents in triggering cellular and molecular changes by intermittent hypoxia. The second part of the review presents evidence for contribution of hypersensitive carotid body to OSA and potential therapeutic intervention to mitigate OSA in a murine model. Abstract figure legend OSA = obstructive sleep apnea; IH = intermittent hypoxia; ROS = reactive oxygen species; CB = carotid body; SNA = sympathetic nerve activity; HO-2 = hemeoxygenase 2; CSE = cystathionine-ϒ-lyase. This article is protected by copyright. All rights reserved.

PMID:37029496 | DOI:10.1113/JP284111

Stem Cell Reports. 2023 Apr 7:S2213-6711(23)00101-7. doi: 10.1016/j.stemcr.2023.03.013. Online ahead of print.

ABSTRACT

The molecular mechanisms allowing hair follicles to periodically activate their stem cells (HFSCs) are incompletely characterized. Here, we identify the transcription factor IRX5 as a promoter of HFSC activation. Irx5-/- mice have delayed anagen onset, with increased DNA damage and diminished HFSC proliferation. Open chromatin regions form near cell cycle progression and DNA damage repair genes in Irx5-/- HFSCs. DNA damage repair factor BRCA1 is an IRX5 downstream target. Inhibition of FGF kinase signaling partially rescues the anagen delay in Irx5-/- mice, suggesting that the Irx5-/- HFSC quiescent phenotype is partly due to failure to suppress Fgf18 expression. Interfollicular epidermal stem cells also show decreased proliferation and increased DNA damage in Irx5-/-mice. Consistent with a role for IRX5 as a promoter of DNA damage repair, we find that IRX genes are upregulated in many cancer types and that there is a correlation between IRX5 and BRCA1 expression in breast cancer.

PMID:37084727 | DOI:10.1016/j.stemcr.2023.03.013

World J Microbiol Biotechnol. 2023 Apr 8;39(6):151. doi: 10.1007/s11274-023-03603-6.

ABSTRACT

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

PMID:37029313 | DOI:10.1007/s11274-023-03603-6

Sci Rep. 2023 Apr 7;13(1):5712. doi: 10.1038/s41598-023-32666-6.

ABSTRACT

Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation of particular steady-state properties; however, the underlying factors leading to the formation of balanced complexes have not been studied, yet. Here, we present a number of factorizations providing insights in mechanisms that lead to the origins of the corresponding balanced complexes. The proposed factorizations enable us to categorize balanced complexes into four distinct classes, each with specific origins and characteristics. They also provide the means to efficiently determine if a balanced complex in large-scale networks belongs to a particular class from the categorization. The results are obtained under very general conditions and irrespective of the network kinetics, rendering them broadly applicable across variety of network models. Application of the categorization shows that all classes of balanced complexes are present in large-scale metabolic models across all kingdoms of life, therefore paving the way to study their relevance with respect to different properties of steady states supported by these networks.

PMID:37029206 | DOI:10.1038/s41598-023-32666-6

Sci Data. 2023 Apr 7;10(1):193. doi: 10.1038/s41597-023-02108-z.

ABSTRACT

Defining cellular and subcellular structures in images, referred to as cell segmentation, is an outstanding obstacle to scalable single-cell analysis of multiplex imaging data. While advances in machine learning-based segmentation have led to potentially robust solutions, such algorithms typically rely on large amounts of example annotations, known as training data. Datasets consisting of annotations which are thoroughly assessed for quality are rarely released to the public. As a result, there is a lack of widely available, annotated data suitable for benchmarking and algorithm development. To address this unmet need, we release 105,774 primarily oncological cellular annotations concentrating on tumor and immune cells using over 40 antibody markers spanning three fluorescent imaging platforms, over a dozen tissue types and across various cellular morphologies. We use readily available annotation techniques to provide a modifiable community data set with the goal of advancing cellular segmentation for the greater imaging community.

PMID:37029126 | DOI:10.1038/s41597-023-02108-z

Food Chem Toxicol. 2023 Apr 5:113760. doi: 10.1016/j.fct.2023.113760. Online ahead of print.

ABSTRACT

Food-grade titanium dioxide (TiO2-FG) is a widespread metal oxide used in the food industries. Recently, the European Food Safety Authority concluded that TiO2-FG cannot be considered safe for consumption due to its genotoxicity; however, its effect on the gut microbiota has not yet been completely unraveled. We studied the effects of TiO2-FG (0.125 mg/mL) on Lactobacillus rhamnosus GG (LGG) and Enterococcus faecium NCIMB10415 (Ent), in particular some physiological and phenotypic traits (growth kinetics, bile salts, and ampicillin resistance) and their interactions with the host (auto-aggregation, biofilm formation, and adhesion on Caco-2/TC7 monolayers) and other gut microorganisms (antimicrobial activity towards pathogens). The results obtained revealed that TiO2-FG alters both LGG and Ent growth and lowers bile resistance (62 and 34.5%, respectively) and adhesion on Caco-2/TC7 monolayers (34.8 and 14.16%, respectively). The other outcomes were strictly species-specific: Ent showed a lower ampicillin sensitivity (14.48%) and auto-aggregation (38.1%), while LGG showed a reduced biofilm formation (37%) and antimicrobial activity towards Staphylococcus aureus (35.73%). Overall, these results suggest an adverse effect of TiO2-FG on both the endogenous and exogenously administered probiotics, contributing to the argument against using TiO2-FG as a food additive.

PMID:37028743 | DOI:10.1016/j.fct.2023.113760

Am J Med. 2023 Apr 5:S0002-9343(23)00208-5. doi: 10.1016/j.amjmed.2023.03.004. Online ahead of print.

NO ABSTRACT

PMID:37028693 | DOI:10.1016/j.amjmed.2023.03.004

Curr Opin Immunol. 2023 Apr 5;82:102323. doi: 10.1016/j.coi.2023.102323. Online ahead of print.

ABSTRACT

Single-cell technologies have revealed the extensive heterogeneity and complexity of the immune system. Systems biology approaches in immunology have taken advantage of the high-parameter, high-throughput data and analyzed immune cell types in a 'bottom-up' data-driven method. This approach has discovered previously unrecognized cell types and functions. Especially for human immunology, in which experimental manipulations are challenging, systems approach has become a successful means to investigate physiologically relevant contexts. This review focuses on the recent findings in lymphocyte biology, from their development, differentiation into subsets, and heterogeneity in their functions, enabled by these systems approaches. Furthermore, we review examples of the application of findings from systems approach studies and discuss how now to leave the rich dataset in the curse of high dimensionality.

PMID:37028221 | DOI:10.1016/j.coi.2023.102323

Neural Netw. 2023 Apr 5;163:64. doi: 10.1016/j.neunet.2023.03.027. Online ahead of print.

NO ABSTRACT

PMID:37028155 | DOI:10.1016/j.neunet.2023.03.027

Sci Immunol. 2023 Apr 14;8(82):eabg2200. doi: 10.1126/sciimmunol.abg2200. Epub 2023 Apr 7.

ABSTRACT

Neoantigens are tumor-specific peptide sequences resulting from sources such as somatic DNA mutations. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Accurate neoantigen identification is thus critical for both designing cancer vaccines and predicting response to immunotherapies. Neoantigen identification and prioritization relies on correctly predicting whether the presenting peptide sequence can successfully induce an immune response. Because most somatic mutations are single-nucleotide variants, changes between wild-type and mutated peptides are typically subtle and require cautious interpretation. A potentially underappreciated variable in neoantigen prediction pipelines is the mutation position within the peptide relative to its anchor positions for the patient's specific MHC molecules. Whereas a subset of peptide positions are presented to the T cell receptor for recognition, others are responsible for anchoring to the MHC, making these positional considerations critical for predicting T cell responses. We computationally predicted anchor positions for different peptide lengths for 328 common HLA alleles and identified unique anchoring patterns among them. Analysis of 923 tumor samples shows that 6 to 38% of neoantigen candidates are potentially misclassified and can be rescued using allele-specific knowledge of anchor positions. A subset of anchor results were orthogonally validated using protein crystallography structures. Representative anchor trends were experimentally validated using peptide-MHC stability assays and competition binding assays. By incorporating our anchor prediction results into neoantigen prediction pipelines, we hope to formalize, streamline, and improve the identification process for relevant clinical studies.

PMID:37027480 | DOI:10.1126/sciimmunol.abg2200

Chin Med J (Engl). 2023 Apr 7. doi: 10.1097/CM9.0000000000002250. Online ahead of print.

NO ABSTRACT

PMID:37026872 | DOI:10.1097/CM9.0000000000002250

Adv Sci (Weinh). 2023 Apr 7:e2204514. doi: 10.1002/advs.202204514. Online ahead of print.

ABSTRACT

As a type of immunogenic cell death, ferroptosis participates in the creation of immunoactive tumor microenvironments. However, knowledge of spatial location of tumor cells with ferroptosis signature in tumor environments and the role of ferroptotic stress in inducing the expression of immune-related molecules in cancer cells is limited. Here the spatial association of the transcriptomic signatures is demonstrated for ferroptosis and inflammation/immune activation located in the invasive front of head and neck squamous cell carcinoma (HNSCC). The association between ferroptosis signature and inflammation/immune activation is more prominent in HPV-negative HNSCC compared to HPV-positive ones. Ferroptotic stress induces PD-L1 expression through reactive oxygen species (ROS)-elicited NF-κB signaling pathway and calcium influx. Priming murine HNSCC with the ferroptosis inducer sensitizes tumors to anti-PD-L1 antibody treatment. A positive correlation between the ferroptosis signature and the active immune cell profile is shown in the HNSCC samples. This study reveals a subgroup of ferroptotic HNSCC with immune-active signatures and indicates the potential of priming HNSCC with ferroptosis inducers to increase the antitumor efficacy of immune checkpoint inhibitors.

PMID:37026630 | DOI:10.1002/advs.202204514

Front Public Health. 2023 Mar 21;11:1069906. doi: 10.3389/fpubh.2023.1069906. eCollection 2023.

ABSTRACT

INTRODUCTION: The metabolomic changes caused by airborne fine particulate matter (PM2.5) exposure in patients with chronic obstructive pulmonary disease (COPD) remain unclear. The aim of this study was to determine whether it is possible to predict PM2.5-induced acute exacerbation of COPD (AECOPD) using metabolic markers.

METHODS: Thirty-eight patients with COPD diagnosed by the 2018 Global Initiative for Obstructive Lung Disease were selected and divided into high exposure and low exposure groups. Questionnaire data, clinical data, and peripheral blood data were collected from the patients. Targeted metabolomics using liquid chromatography-tandem mass spectrometry was performed on the plasma samples to investigate the metabolic differences between the two groups and its correlation with the risk of acute exacerbation.

RESULTS: Metabolomic analysis identified 311 metabolites in the plasma of patients with COPD, among which 21 metabolites showed significant changes between the two groups, involving seven pathways, including glycerophospholipid, alanine, aspartate, and glutamate metabolism. Among the 21 metabolites, arginine and glycochenodeoxycholic acid were positively associated with AECOPD during the three months of follow-up, with an area under the curve of 72.50% and 67.14%, respectively.

DISCUSSION: PM2.5 exposure can lead to changes in multiple metabolic pathways that contribute to the development of AECOPD, and arginine is a bridge between PM2.5 exposure and AECOPD.

PMID:37026137 | PMC:PMC10070744 | DOI:10.3389/fpubh.2023.1069906

Front Immunol. 2023 Mar 21;14:1183969. doi: 10.3389/fimmu.2023.1183969. eCollection 2023.

ABSTRACT

[This corrects the article DOI: 10.3389/fimmu.2023.1122409.].

PMID:37026016 | PMC:PMC10071529 | DOI:10.3389/fimmu.2023.1183969