Front Bioeng Biotechnol. 2024 Jun 24;12:1360740. doi: 10.3389/fbioe.2024.1360740. eCollection 2024.

ABSTRACT

Developing efficient bioprocesses requires selecting the best biosynthetic pathways, which can be challenging and time-consuming due to the vast amount of data available in databases and literature. The extension of the shikimate pathway for the biosynthesis of commercially attractive molecules often involves promiscuous enzymes or lacks well-established routes. To address these challenges, we developed a computational workflow integrating enumeration/retrosynthesis algorithms, a toolbox for pathway analysis, enzyme selection tools, and a gene discovery pipeline, supported by manual curation and literature review. Our focus has been on implementing biosynthetic pathways for tyrosine-derived compounds, specifically L-3,4-dihydroxyphenylalanine (L-DOPA) and dopamine, with significant applications in health and nutrition. We selected one pathway to produce L-DOPA and two different pathways for dopamine-one already described in the literature and a novel pathway. Our goal was either to identify the most suitable gene candidates for expression in Escherichia coli for the known pathways or to discover innovative pathways. Although not all implemented pathways resulted in the accumulation of target compounds, in our shake-flask experiments we achieved a maximum L-DOPA titer of 0.71 g/L and dopamine titers of 0.29 and 0.21 g/L for known and novel pathways, respectively. In the case of L-DOPA, we utilized, for the first time, a mutant version of tyrosinase from Ralstonia solanacearum. Production of dopamine via the known biosynthesis route was accomplished by coupling the L-DOPA pathway with the expression of DOPA decarboxylase from Pseudomonas putida, resulting in a unique biosynthetic pathway never reported in literature before. In the context of the novel pathway, dopamine was produced using tyramine as the intermediate compound. To achieve this, tyrosine was initially converted into tyramine by expressing TDC from Levilactobacillus brevis, which, in turn, was converted into dopamine through the action of the enzyme encoded by ppoMP from Mucuna pruriens. This marks the first time that an alternative biosynthetic pathway for dopamine has been validated in microbes. These findings underscore the effectiveness of our computational workflow in facilitating pathway enumeration and selection, offering the potential to uncover novel biosynthetic routes, thus paving the way for other target compounds of biotechnological interest.

PMID:38978715 | PMC:PMC11228882 | DOI:10.3389/fbioe.2024.1360740

Front Cell Neurosci. 2024 Jun 24;18:1403734. doi: 10.3389/fncel.2024.1403734. eCollection 2024.

ABSTRACT

Mitochondrial diseases are a group of severe pathologies that cause complex neurodegenerative disorders for which, in most cases, no therapy or treatment is available. These organelles are critical regulators of both neurogenesis and homeostasis of the neurological system. Consequently, mitochondrial damage or dysfunction can occur as a cause or consequence of neurodevelopmental or neurodegenerative diseases. As genetic knowledge of neurodevelopmental disorders advances, associations have been identified between genes that encode mitochondrial proteins and neurological symptoms, such as neuropathy, encephalomyopathy, ataxia, seizures, and developmental delays, among others. Understanding how mitochondrial dysfunction can alter these processes is essential in researching rare diseases. Three-dimensional (3D) cell cultures, which self-assemble to form specialized structures composed of different cell types, represent an accessible manner to model organogenesis and neurodevelopmental disorders. In particular, brain organoids are revolutionizing the study of mitochondrial-based neurological diseases since they are organ-specific and model-generated from a patient's cell, thereby overcoming some of the limitations of traditional animal and cell models. In this review, we have collected which neurological structures and functions recapitulate in the different types of reported brain organoids, focusing on those generated as models of mitochondrial diseases. In addition to advancements in the generation of brain organoids, techniques, and approaches for studying neuronal structures and physiology, drug screening and drug repositioning studies performed in brain organoids with mitochondrial damage and neurodevelopmental disorders have also been reviewed. This scope review will summarize the evidence on limitations in studying the function and dynamics of mitochondria in brain organoids.

PMID:38978706 | PMC:PMC11228165 | DOI:10.3389/fncel.2024.1403734

Front Plant Sci. 2024 Jun 24;15:1337388. doi: 10.3389/fpls.2024.1337388. eCollection 2024.

ABSTRACT

INTRODUCTION: In plant breeding, we often aim to improve multiple traits at once. However, without knowing the economic value of each trait, it is hard to decide which traits to focus on. This is where "desired gain selection indices" come in handy, which can yield optimal gains in each trait based on the breeder's prioritisation of desired improvements when economic weights are not available. However, they lack the ability to maximise the selection response and determine the correlation between the index and net genetic merit.

METHODS: Here, we report the development of an iterative desired gain selection index method that optimises the sampling of the desired gain values to achieve a targeted or a user-specified selection response for multiple traits. This targeted selection response can be constrained or unconstrained for either a subset or all the studied traits.

RESULTS: We tested the method using genomic estimated breeding values (GEBVs) for seven traits in a bread wheat (Triticum aestivum) reference breeding population comprising 3,331 lines and achieved prediction accuracies ranging between 0.29 and 0.47 across the seven traits. The indices were validated using 3,005 double haploid lines that were derived from crosses between parents selected from the reference population. We tested three user-specified response scenarios: a constrained equal weight (INDEX1), a constrained yield dominant weight (INDEX2), and an unconstrained weight (INDEX3). Our method achieved an equivalent response to the user-specified selection response when constraining a set of traits, and this response was much better than the response of the traditional desired gain selection indices method without iteration. Interestingly, when using unconstrained weight, our iterative method maximised the selection response and shifted the average GEBVs of the selection candidates towards the desired direction.

DISCUSSION: Our results show that the method is an optimal choice not only when economic weights are unavailable, but also when constraining the selection response is an unfavourable option.

PMID:38978519 | PMC:PMC11228337 | DOI:10.3389/fpls.2024.1337388

Br J Pharmacol. 2024 Jul 8. doi: 10.1111/bph.16495. Online ahead of print.

ABSTRACT

G protein-coupled receptors (GPCRs) are one of the major drug targets. In recent years, computational drug design for GPCRs has mainly focused on static structures obtained through X-ray crystallography, cryogenic electron microscopy (cryo-EM) or in silico modelling as a starting point for virtual screening campaigns. However, GPCRs are highly flexible entities with the ability to adopt different conformational states that elicit different physiological responses. Including this knowledge in the drug discovery pipeline can help to tailor novel conformation-specific drugs with an improved therapeutic profile. In this review, we outline our current knowledge about GPCR dynamics that is relevant for receptor activation, signalling bias and allosteric modulation. Ultimately, we highlight new technological implementations such as time-resolved X-ray crystallography and cryo-EM as well as computational algorithms that can contribute to a more comprehensive understanding of receptor dynamics and its relevance for GPCR functionality.

PMID:38978399 | DOI:10.1111/bph.16495

J Extracell Vesicles. 2024 Jul;13(7):e12479. doi: 10.1002/jev2.12479.

ABSTRACT

Although the isolation and counting of small extracellular vesicles (sEVs) are essential steps in sEV research, an integrated method with scalability and efficiency has not been developed. Here, we present a scalable and ready-to-use extracellular vesicle (EV) isolation and counting system (EVics) that simultaneously allows isolation and counting in one system. This novel system consists of (i) EVi, a simultaneous tandem tangential flow filtration (TFF)-based EV isolation component by applying two different pore-size TFF filters, and (ii) EVc, an EV counting component using light scattering that captures a large field-of-view (FOV). EVi efficiently isolated 50-200 nm-size sEVs from 15 µL to 2 L samples, outperforming the current state-of-the-art devices in purity and speed. EVc with a large FOV efficiently counted isolated sEVs. EVics enabled early observations of sEV secretion in various cell lines and reduced the cost of evaluating the inhibitory effect of sEV inhibitors by 20-fold. Using EVics, sEVs concentrations and sEV PD-L1 were monitored in a 23-day cancer mouse model, and 160 clinical samples were prepared and successfully applied to diagnosis. These results demonstrate that EVics could become an innovative system for novel findings in basic and applied studies in sEV research.

PMID:38978321 | DOI:10.1002/jev2.12479

Genome Biol. 2024 Jul 8;25(1):183. doi: 10.1186/s13059-024-03287-7.

ABSTRACT

BACKGROUND: Recent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficult to infer using conventional approaches because nORFs tend to be short, of recent de novo origins, and lowly expressed. Here we develop a dedicated coexpression analysis framework that accounts for low expression to investigate the transcriptional regulation, evolution, and potential cellular roles of nORFs in Saccharomyces cerevisiae.

RESULTS: Our results reveal that nORFs tend to be preferentially coexpressed with genes involved in cellular transport or homeostasis but rarely with genes involved in RNA processing. Mechanistically, we discover that young de novo nORFs located downstream of conserved genes tend to leverage their neighbors' promoters through transcription readthrough, resulting in high coexpression and high expression levels. Transcriptional piggybacking also influences the coexpression profiles of young de novo nORFs located upstream of genes, but to a lesser extent and without detectable impact on expression levels. Transcriptional piggybacking influences, but does not determine, the transcription profiles of de novo nORFs emerging nearby genes. About 40% of nORFs are not strongly coexpressed with any gene but are transcriptionally regulated nonetheless and tend to form entirely new transcription modules. We offer a web browser interface ( https://carvunislab.csb.pitt.edu/shiny/coexpression/ ) to efficiently query, visualize, and download our coexpression inferences.

CONCLUSIONS: Our results suggest that nORF transcription is highly regulated. Our coexpression dataset serves as an unprecedented resource for unraveling how nORFs integrate into cellular networks, contribute to cellular phenotypes, and evolve.

PMID:38978079 | DOI:10.1186/s13059-024-03287-7

BMC Psychiatry. 2024 Jul 8;24(1):493. doi: 10.1186/s12888-024-05942-6.

ABSTRACT

BACKGROUND: Existing evidence suggests that alterations in the gut microbiome are closely associated with major depressive disorder (MDD). We aimed to reveal the causal relationships between MDD and various microbial taxa in the gut.

METHODS: We used the two-sample Mendelian randomization (TSMR) to explore the bidirectional causal effects between gut microbiota and MDD. The genome-wide association studies summary results of gut microbiota were obtained from two large consortia, the MibioGen consortium and the Dutch Microbiome Project, which we analyzed separately.

RESULTS: Our TSMR analysis identified 10 gut bacterial taxa that were protective against MDD, including phylum Actinobacteria, order Clostridiales, and family Bifidobacteriaceae (OR: 0.96 ∼ 0.98). Ten taxa were associated with an increased risk of MDD, including phyla Firmicutes and Proteobacteria, class Actinobacteria, and genus Alistipes (OR: 1.01 ∼ 1.09). On the other hand, MDD may decrease the abundance of 12 taxa, including phyla Actinobacteria and Firmicutes, families Bifidobacteriaceae and Defluviitaleaceae (OR: 0.63 ∼ 0.88). MDD may increase the abundance of 8 taxa, including phylum Bacteroidetes, genera Parabacteroides, and Bacteroides (OR: 1.12 ∼ 1.43).

CONCLUSIONS: Our study supports that there are mutual causal relationships between certain gut microbiota and the development of MDD suggesting that gut microbiota may be targeted in the treatment of MDD.

PMID:38977973 | DOI:10.1186/s12888-024-05942-6

Commun Biol. 2024 Jul 8;7(1):832. doi: 10.1038/s42003-024-06458-1.

ABSTRACT

An important question in cell biology is how cytoskeletal proteins evolved and drove the development of novel structures and functions. Here we address the origin of SPIRE actin nucleators. Mammalian SPIREs work with RAB GTPases, formin (FMN)-subgroup actin assembly proteins and class-5 myosin (MYO5) motors to transport organelles along actin filaments towards the cell membrane. However, the origin and extent of functional conservation of SPIRE among species is unknown. Our sequence searches show that SPIRE exist throughout holozoans (animals and their closest single-celled relatives), but not other eukaryotes. SPIRE from unicellular holozoans (choanoflagellate), interacts with RAB, FMN and MYO5 proteins, nucleates actin filaments and complements mammalian SPIRE function in organelle transport. Meanwhile SPIRE and MYO5 proteins colocalise to organelles in Salpingoeca rosetta choanoflagellates. Based on these observations we propose that SPIRE originated in unicellular ancestors of animals providing an actin-myosin driven exocytic transport mechanism that may have contributed to the evolution of complex multicellular animals.

PMID:38977899 | DOI:10.1038/s42003-024-06458-1

Sci Rep. 2024 Jul 9;14(1):15760. doi: 10.1038/s41598-024-66591-z.

ABSTRACT

Manufacturing regenerative medicine requires continuous monitoring of pluripotent cell culture and quality assessment while eliminating cell destruction and contaminants. In this study, we employed a novel method to monitor the pluripotency of stem cells through image analysis, avoiding the traditionally used invasive procedures. This approach employs machine learning algorithms to analyze stem cell images to predict the expression of pluripotency markers, such as OCT4 and NANOG, without physically interacting with or harming cells. We cultured induced pluripotent stem cells under various conditions to induce different pluripotent states and imaged the cells using bright-field microscopy. Pluripotency states of induced pluripotent stem cells were assessed using invasive methods, including qPCR, immunostaining, flow cytometry, and RNA sequencing. Unsupervised and semi-supervised learning models were applied to evaluate the results and accurately predict the pluripotency of the cells using only image analysis. Our approach directly links images to invasive assessment results, making the analysis of cell labeling and annotation of cells in images by experts dispensable. This core achievement not only contributes for safer and more reliable stem cell research but also opens new avenues for real-time monitoring and quality control in regenerative medicine manufacturing. Our research fills an important gap in the field by providing a viable, noninvasive alternative to traditional invasive methods for assessing pluripotency. This innovation is expected to make a significant contribution to improving regenerative medicine manufacturing because it will enable a more detailed and feasible understanding of cellular status during the manufacturing process.

PMID:38977828 | DOI:10.1038/s41598-024-66591-z

J Hazard Mater. 2024 Jun 27;476:135053. doi: 10.1016/j.jhazmat.2024.135053. Online ahead of print.

ABSTRACT

The presence of microplastics in cosmetics and personal care products (C&PCPs) has been increasingly in the public eye since the early 2010s. Despite increasing research into the potential environmental and health effects of microplastics, most research to date on microplastics in C&PCPs has investigated "rinse-off" products, while the potential impacts of "leave-on" C&PCPs have been largely neglected, despite these products being purchased in greater volumes and often having two or more microplastic ingredients in their formulations(CosmeticsEurope, 2018b). This review aims to synthesize the current knowledge of microplastic in C&PCPs, assessing the potential environmental and human health impacts of C&PCPs and discussing the regulatory implications. The lack of studies on leave-on C&PCPs is significant, suggesting a severe knowledge gap regarding microplastic presence in, and emissions from, C&PCPs. There is a noticeable lack of studies on the (eco)toxicological consequences of microplastic exposure from C&PCPs. As a result, significant aspects of microplastic contamination may be overlooked in the microplastic legislations emerging globally (including from the European Commission), which intend to restrict microplastic use in C&PCPs but focus on rinse-off C&PCPs only. This review highlights the potential consequences of microplastics in leave-on C&PCPs for regulatory decision-making, particularly as alternatives to microplastics are considered during the phase-out periods and spotlights the need for sufficient monitoring and research on these alternatives, to avoid unforeseen consequences.

PMID:38976961 | DOI:10.1016/j.jhazmat.2024.135053

Int Immunopharmacol. 2024 Jul 7;138:112611. doi: 10.1016/j.intimp.2024.112611. Online ahead of print.

ABSTRACT

OBJECTIVE: Osteoporosis (OP) is a disease characterized by decreased bone mass, deteriorated microstructure, and increased fragility and fracture risk. The diagnosis and prevention of OP and its complications have become major public health challenges. Therefore, exploring the complex ecological connections between the immune and skeletal systems may provide new insights for clinical prevention and treatment strategies.

METHODS: First, we performed single-cell RNA sequencing on human lumbar lamina tissue and conducted clustering and subgroup analysis of quality-controlled single-cell transcriptome data to identify target subgroups. Subsequently, enrichment analysis and pseudotime analysis were performed. In addition, we conducted in-depth studies on the gene regulatory network between different cell subgroups and the communication between bone immune cells.

RESULTS: In this study, we identified several cell subgroups that may be involved in the progression of OP. For example, the CCL4+ NKT and CXCL8+ neutrophils subgroups promote OP progression by mediating an inflammatory environment that disrupts bone homeostasis, and the MNDA+ Mac subgroup promotes osteoclast differentiation to promote OP. Moreover, the TNFAIP6+ Obl, NR4A2+ B and HMGN2+ erythrocyte subgroups promoted the balance of bone metabolism and suppressed OP. In the cell communication network, Obl closely interacts with immune cell subgroups through the CXCR4-CXCL12, CTGF-ITGB2, and TNFSF14-TNFRSF14 axes.

CONCLUSION: Our research revealed specific subgroups and intercellular interactions that play crucial roles in the pathogenesis of OP, providing potential new insights for more precise therapeutic interventions for OP.

PMID:38976947 | DOI:10.1016/j.intimp.2024.112611

PLoS One. 2024 Jul 8;19(7):e0304947. doi: 10.1371/journal.pone.0304947. eCollection 2024.

ABSTRACT

The RNA-binding protein LIN28B represses the biogenesis of the tumor suppressor let-7. The LIN28B/let-7 axis regulates cell differentiation and is associated with various cancers. The RNA-binding protein Q (hnRNP Q) or SYNCRIP (Synaptotagmin Binding Cytoplasmic RNA Interacting Protein) has been implicated in mRNA splicing, mRNA transport, translation, and miRNAs biogenesis as well as metabolism in cancer. To determine whether hnRNP Q plays a role in the LIN28B/let-7 axis, we tested for interactions between hnRNP Q and LIN28B. We demonstrated that hnRNP Q interacts with LIN28B in an RNA-dependent manner. Knockdown of hnRNP Q caused reduced expression of a well-known let-7 target TRIM71, an E3 ubiquitin ligase that belongs to the RBCC/TRIM family, and also LIN28B, whose mRNA itself is down-regulated by let-7. In addition, hnRNP Q knockdown increased let-7 family miRNA levels and reduced the activity of luciferase reporters fused with the TRIM71 3'UTR or a synthetic 3'UTR carrying 8X let-7 complementary sites. Finally, depletion of hnRNP Q inhibited the proliferation of a hepatocellular carcinoma cell line, Huh7. This observation is consistent with the survival curve for liver cancer patients from the TCGA database, which indicates that high expression of hnRNP Q is a prognostic marker for a poor outcome in individuals afflicted with hepatocellular carcinoma. Together, our findings suggest that hnRNP Q interacts with LIN28B and modulates the LIN28B/let-7 axis in hepatocellular carcinoma.

PMID:38976670 | DOI:10.1371/journal.pone.0304947

Bioinformatics. 2024 Jul 8:btae443. doi: 10.1093/bioinformatics/btae443. Online ahead of print.

ABSTRACT

MOTIVATION: Understanding the dynamics of gene expression across different cellular states is crucial for discerning the mechanisms underneath cellular differentiation. Genes that exhibit variation in mean expression as a function of Pseudotime and between branching trajectories are expected to govern cell fate decisions. We introduce scMaSigPro, a method for the identification of differential gene expression patterns along Pseudotime and branching paths simultaneously.

RESULTS: We assessed the performance of scMaSigPro using synthetic and public datasets. Our evaluation shows that scMaSigPro outperforms existing methods in controlling the False Positive Rate and is computationally efficient.

AVAILABILITY AND IMPLEMENTATION: scMaSigPro is available as a free R package (version 4.0 or higher) under the GPL(≥2) license on GitHub at 'github.com/BioBam/scMaSigPro' and archived with version 0.03 on Zenodo at 'zenodo.org/records/12568922'.

PMID:38976653 | DOI:10.1093/bioinformatics/btae443

J Bacteriol. 2024 Jul 8:e0013624. doi: 10.1128/jb.00136-24. Online ahead of print.

ABSTRACT

Although members of the genus Pseudomonas share specific morphological, metabolic, and genomic traits, the diversity of niches and lifestyles adopted by the family members is vast. One species of the group, Pseudomonas putida, thrives as a colonizer of plant roots and frequently inhabits soils polluted with various types of chemical waste. Owing to a combination of historical contingencies and inherent qualities, a particular strain, P. putida KT2440, emerged time ago as an archetype of an environmental microorganism amenable to recombinant DNA technologies, which was also capable of catabolizing chemical pollutants. Later, the same bacterium progressed as a reliable platform for programming traits and activities in various biotechnological applications. This article summarizes the stepwise upgrading of P. putida KT2440 from being a system for fundamental studies on the biodegradation of aromatic compounds (especially when harboring the TOL plasmid pWW0) to its adoption as a chassis of choice in metabolic engineering and synthetic biology. Although there are remaining uncertainties about the taxonomic classification of KT2440, advanced genome editing capabilities allow us to tailor its genetic makeup to meet specific needs. This makes its traditional categorization somewhat less important, while also increasing the strain's overall value for contemporary industrial and environmental uses.

PMID:38975763 | DOI:10.1128/jb.00136-24

J Anim Sci Technol. 2024 May;66(3):443-456. doi: 10.5187/jast.2023.e133. Epub 2024 May 31.

ABSTRACT

In female tract, mammalian sperm develop hyperactivated motility which is a key physiological event for sperm to fertilize eggs. This motility change is triggered by Ca2+ influx via the sperm-specific Ca2+ channel, CatSper. Although previous studies in human and mice largely contributed to understanding CatSper and Ca2+ signaling for sperm hyperactivation, the differences on their activation mechanisms are not well understood yet. There are several studies to examine expression and significance of the CatSper channel in non-human and non-mouse models, such as domestic animals. In this review, I summarize key knowledge for the CatSper channel from previous studies and propose future aspects for CatSper study using sperm from domestic animals.

PMID:38975583 | PMC:PMC11222122 | DOI:10.5187/jast.2023.e133

Heliyon. 2024 Jun 11;10(12):e32828. doi: 10.1016/j.heliyon.2024.e32828. eCollection 2024 Jun 30.

ABSTRACT

OBJECTIVE: The interplay of gut microbiota with the kidney system in chronic kidney disease (CKD), is characterized by increased concentrations of uric acid in the gut, which in turn, may increase bacterial uricase activity and may lead to the generation of uremic toxins. Nevertheless, knowledge on these underlying bidirectional molecular mechanisms is still limited.

METHODS: In this exploratory study, proteomic analysis was performed on fecal samples, targeting to investigate this largely unexplored biological material as a source of information reflecting the gut-kidney axis. Specifically, fecal suspension samples from patients with CKD1 (n = 12) and CKD4 (n = 17) were analysed by LC-MS/MS, using both the Human and Bacterial UniProt RefSeq reviewed databases.

RESULTS: This fecal proteomic analysis collectively identified 701 human and 1011 bacterial proteins of high confidence. Differential expression analysis (CKD4/CKD1) revealed significant changes in human proteins (n = 8, including proteins such as galectin-3-binding protein and prolactin-inducible protein), that were found to be associated with inflammation and CKD. The differential protein expression of pancreatic alpha-amylase further suggested plausible reduced saccharolytic fermentation in CKD4/CKD1. Significant changes in bacterial proteins (n = 9, such as glyceraldehyde-3-phosphate dehydrogenase and enolase), participating in various carbohydrate and metabolic pathways important for the synthesis of butyrate, in turn suggested differential butyrate synthesis in CKD4/CKD1. Further, targeted quantification of fecal pancreatic alpha-amylase and butyrate in the same fecal suspension samples, supported these hypotheses.

CONCLUSION: Collectively, this exploratory fecal proteomic analysis highlighted changes in human and bacterial proteins reflecting inflammation and reduced saccharolytic fermentation in CKD4/CKD1, plausibly affecting the butyrate synthesis pathways in advanced stage kidney disease. Integrative multi-omics validation is planned.

PMID:38975221 | PMC:PMC11226915 | DOI:10.1016/j.heliyon.2024.e32828

iScience. 2024 May 27;27(7):110116. doi: 10.1016/j.isci.2024.110116. eCollection 2024 Jul 19.

ABSTRACT

Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. Decoding the interconnections among different biological axes of plasticity is crucial to understand the molecular origins of phenotypic heterogeneity. Here, we use multi-modal transcriptomic data-bulk, single-cell, and spatial transcriptomics-from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity-two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. Mathematical modeling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and identify interventions to restrict it.

PMID:38974967 | PMC:PMC11225361 | DOI:10.1016/j.isci.2024.110116

J Trop Med. 2024 Jun 28;2024:8564163. doi: 10.1155/2024/8564163. eCollection 2024.

ABSTRACT

BACKGROUND: Helminthiasis is endemic in Chad and constitutes a public health problem, particularly among school-age children. The aim of this study was to evaluate the anthelmintic activity of extracts of Khaya anthotheca and Faidherbia albida used in Chad by traditional healers for the treatment of helminthiasis.

METHODS: The anthelmintic activity was assessed against Heligmosomoides polygyrus and Caenorhabditis elegans larvae using the Worm Microtracker. Embryonated eggs, L1, L2, and L3 larvae of H. polygyrus were obtained after 24 h, 48 h, and 7 days of coproculture and L4 larvae of C. elegans culture using standard procedures. One hundred microliters of extracts at various concentrations, with albendazole and distilled water were, put in contact with 100 µL of H. polygyrus suspension (containing 50 parasites at various developmental stages) in a microplate and incubated for 20 h at 25°C in the Worm Microtracker. The same procedure was adopted for C. elegans, but with 180 µL of OP50. 19 µL of C. elegans suspension (containing 50 larvae) was put in contact with 1 µL of extract at various concentrations and incubated in the Worm Microtracker. Docking studies were carried out using the Schrodinger Maestro software's Glide module. The score function in the software was used to rank and group distinct possible adduct structures generated by molecular docking.

RESULTS: The aqueous and ethanolic extracts of F. albida at a concentration of 2.5 mg/mL showed the same activity as albendazole (100 ± 0.00) on hatching. The IC50s of the aqueous extracts of the two plants (IC50: 0.6212 mg/mL and 0.71 mg/mL, respectively) were comparable on egg hatching of H. polygyrus with no significant difference (p ≥ 0.05) with respect to the ethanol extracts (IC50: 0.70 mg/mL and 0.81 mg/mL, respectively). There was no significant difference between the percentage inhibition of extracts and albendazole on the L1 larvae of H. polygyrus (p ≥ 0.05). The aqueous extracts acted more effectively than the ethanol extracts on the L1 larvae of H. polygyrus with an IC50 of 0.5588 and ∼9.858e - 005 mg/ml, respectively, for K. anthotheca and F. albida. The aqueous extracts of K. anthotheca and F. albida on L3 larvae of H. polygyrus had inhibitory percentages of 92.6 ± 0.62 and 91.37 ± 0.8 at 2.5 mg/mL which were lower than albendazole (100 ± 0.00). The aqueous extracts of K. anthotheca and F. albida on C. elegance showed IC50 of 0.2775 µg/mL and 0.5115 µg/mL, respectively, and were more effective than the ethanol extracts. Examining K. anthotheca and F. albida through the interaction with the protein receptor and its results also confirmed our assumption that the compound used has hydroxyl and carbonyl groups as well as aromatic rings and is exposed to phenolic and flavonoid groups in a more specific way, and it shows a better inhibitory effect.

CONCLUSIONS: This study scientifically validates the use of extracts of the two plants in the traditional treatment of helminthiasis. However, it will be necessary to evaluate the in vivo anthelmintic activity and toxicity. Examining the ADME properties of these compounds also supports the potential of these ligands to be transformed into pharmaceutical forms.

PMID:38974476 | PMC:PMC11226339 | DOI:10.1155/2024/8564163

Int Immunopharmacol. 2024 Jul 6;138:112587. doi: 10.1016/j.intimp.2024.112587. Online ahead of print.

ABSTRACT

There is a growing trend of applying traditional Chinese medicine (TCM) to treat immune diseases. This study reveals the possible mechanism of luteolin, an active ingredient in the core prescription of TCM, in alleviating systemic sclerosis (SSc) inflammation. Bibliometrics was performed to retrieve the core keywords of SSc inflammation. The key inflammatory indicators in the serum samples of 50 SSc patients were detected by ELISA. Data mining was applied for correlation analysis, association rule analysis, and binary logistic regression analysis on the clinical indicators and medication of 50 SSc patients before and after treatment to determine the core prescription. Network pharmacology was used for identifying candidate genes and pathways; molecular docking was conducted to determine the core monomer components of the prescription, providing a basis for subsequent in vitro molecular mechanism research. The effect of luteolin on SSc-human dermal fibroblasts (HDF) viability and inflammatory factors was evaluated by means of ELISA, RT-PCR, and Western blot. The role of TNF in inflammation was explored by using a TNF overexpression vector, NF-κB inhibitor (PKM2), and SSc-HDF. The involvement of TNF/NF-κB pathway was validated by RT-PCR, Western blot, and immunofluorescence. TCM treatment partially corrected the inflammatory changes in SSc patients, indicating its anti-inflammatory effects in the body. Atractylodes, Yam, Astragalus root, Poria cocos, Pinellia ternata, Salvia miltiorrhiza, Safflower, Cassia twig, and Angelica were identified as the core prescriptions for improving inflammatory indicators. Luteolin was the main active ingredient in the prescription and showed a strong binding energy with TNF and NF-κB. Luteolin exerted anti-inflammatory effects in vitro by reducing inflammatory cytokines in SSc-HDF and inhibiting the activation of TNF/NF-κB. Mechanistically, luteolin inhibited the activation of the TNF/NF-κB pathway in SSc-HDF, as manifested by an increase in extranuclear p-P65 and TNF but a decrease in intranuclear p-P65. Interestingly, the addition of PKM2 augmented the therapeutic function of luteolin against inflammation in SSc-HDF. Our study showed the TCM alleviates the inflammatory response of SSc by inhibiting the activation of the TNF/NF-κB pathway and is an effective therapeutic agent for the treatment of SSc.

PMID:38972211 | DOI:10.1016/j.intimp.2024.112587

Nat Commun. 2024 Jul 7;15(1):5699. doi: 10.1038/s41467-024-50067-9.

ABSTRACT

Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conduct a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identifies three dominant lineages, each with unique gene sets potentially enhancing bacterial fitness in the environment. We find that recombination drives lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage reveal increased expression of lineage-specific genes under environmental conditions in two out of three lineages. This underscores the potential importance of environmental persistence for these dominant lineages. The study also highlights the influence of environmental factors such as terrain slope, altitude, and river direction on the geographical dispersal of B. pseudomallei. Collectively, our findings suggest that environmental persistence may play a role in facilitating the spread of B. pseudomallei, and as a prerequisite for exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.

PMID:38972886 | DOI:10.1038/s41467-024-50067-9