Iran J Basic Med Sci. 2024;27(12):1515-1528. doi: 10.22038/ijbms.2024.78787.17037.

ABSTRACT

OBJECTIVES: In recent years, microplastics (MPs), which are novel environmental contaminants measuring 5 mm in diameter, have garnered considerable attention. However, information regarding substances that can mitigate the dangers of MPs for animals remains extremely limited.

MATERIALS AND METHODS: Ninety days were devoted to the exposure of mature male mice to royal jelly (RJ) and 2 µm virgin polystyrene microplastics (PS-MPs) in this study. Pre-implantation embryo development; the structure of testis tissue; the gonadosomatic index; sperm parameters; RNA damage in germinal cells; the anti-oxidant capacity of the entire testis; and the activity of anti-oxidant enzymes in serum and testicular tissue, including TAC, SOD dismutase, CAT, GSH, and MDA, histomorphometric indices of the testis (tubular differentiation index, spermatogenesis index, and repopulation index), steroidogenic foci, and the quantity of apoptosis were assessed in the testis, respectively, through the measurement of pro-apoptosis (p53, Bax, and Caspase-3) and anti-apoptosis (Bcl-2) factors, as well as Hsp70 mediator.

RESULTS: The results indicate that concurrent administration of RJ can confer a protective effect on mice exposed to microplastics by maintaining the structure of mitochondria and enhancement of the anti-oxidant defense system. Furthermore, RJ co-treatment decreased apoptosis and oxidant/anti-oxidant status, enhanced pre-implantation embryo development, and improved sperm characteristics and RNA damage in germ cells.

CONCLUSION: The data confirm that royal jelly could protect the testis structure against polystyrene microplastic-induced testicular injury through anti-oxidant and anti-apoptotic properties.

PMID:39539451 | PMC:PMC11556760 | DOI:10.22038/ijbms.2024.78787.17037

ACS Pharmacol Transl Sci. 2024 Oct 19;7(11):3488-3501. doi: 10.1021/acsptsci.4c00405. eCollection 2024 Nov 8.

ABSTRACT

Monopolar spindle 1 (Mps1, also known as TTK) and Aurora kinase (AURK) A and B are critical regulators of mitosis and have been linked to the progression of various cancers. Here, we report the design, synthesis, and biological evaluation of a series of PROTACs (proteolysis-targeting chimeras) targeting TTK and AURKs. We synthesized various degrader molecules based on four different 2-aminoadenine-based ligands, recruiting either cereblon or VHL as the E3-ligase. Our research showed that the nature of the linker and modification of the ligand significantly influence the target specificity and degradation efficacy. Notably, compound 19, among the most potent degraders, demonstrated robust proteasome-mediated degradation of TTK with D max of 66.5% and DC50 value (6 h) of 17.7 nM as compared to its structurally akin inhibitor control, 23. The cytotoxicity of most of the synthesized chimeras against acute myeloid leukemia cell line MV4-11 was lower than that of the corresponding parent inhibitors. However, we could also identify degraders such as 15 and 26 that induce potent AURKA degradation and display comparable antiproliferative activities to their parent compound SF1. Compound 15 degrades AURKA with low DC50 value of 2.05 nM, which is 77-fold and 21-fold more selective toward AURKB and TTK and has an EC50 value of 39 nM against cancer MV4-11 cells. Overall, the observations we made with the degrader molecules we developed can further aid in the design and development of optimized TTK or AURK degraders for cancer therapy.

PMID:39539259 | PMC:PMC11555526 | DOI:10.1021/acsptsci.4c00405

Nature. 2024 Nov 13. doi: 10.1038/s41586-024-08187-1. Online ahead of print.

ABSTRACT

Pangenomes are collections of annotated genome sequences of multiple individuals of a species1. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants2. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.

PMID:39537924 | DOI:10.1038/s41586-024-08187-1

Sci Rep. 2024 Nov 13;14(1):27879. doi: 10.1038/s41598-024-78035-9.

ABSTRACT

We investigated associations between prenatal genocidal trauma, including maternal rape, and postnatal adverse childhood experiences (ACEs) on DNA methylation of genes associated with the stress response. In a comparative cross-sectional study of 91 Rwandan young adults, categorized by prenatal exposure to genocide and maternal rape, genocide without rape, and unexposed controls, we analyzed DNA methylation from dried blood spots and assessed ACEs and depression and anxiety symptoms at age 24. Prenatal exposure to maternal rape was associated with DNA methylation changes in BDNF and SLC6A4, with the association in BDNF attenuated after including ACE exposure in the model. Genocide exposure without rape was associated with methylation changes in PRDM8 after adjusting for early adversity. Methylation in BDNF and SLC6A4 correlated with depression and anxiety symptoms. These findings underscore the impact of prenatal and postnatal trauma on DNA methylation and mental wellbeing, emphasizing the need for continued support for survivors in the decades after conflict.

PMID:39537739 | DOI:10.1038/s41598-024-78035-9

Nat Commun. 2024 Nov 13;15(1):9792. doi: 10.1038/s41467-024-53933-8.

ABSTRACT

Multidrug-resistant tuberculosis (MDR-TB), defined as resistance to the first-line drugs isoniazid and rifampin, is a growing source of global mortality and threatens global control of tuberculosis disease. The diarylquinoline bedaquiline has recently emerged as a highly efficacious drug against MDR-TB and kills Mycobacterium tuberculosis by inhibiting mycobacterial ATP synthase. However, the mechanisms underlying bedaquiline's efficacy against MDR-TB remain unknown. Here we investigate bedaquiline hyper-susceptibility in drug-resistant Mycobacterium tuberculosis using systems biology approaches. We discovered that MDR clinical isolates are commonly sensitized to bedaquiline. This hypersensitization is caused by several physiological changes induced by deficient catalase activity. These include enhanced accumulation of reactive oxygen species, increased susceptibility to DNA damage, induction of sensitizing transcriptional programs, and metabolic repression of several biosynthetic pathways. In this work we demonstrate how resistance-associated changes in bacterial physiology can mechanistically induce collateral antimicrobial drug sensitivity and reveal druggable vulnerabilities in antimicrobial resistant pathogens.

PMID:39537610 | DOI:10.1038/s41467-024-53933-8

Nat Commun. 2024 Nov 13;15(1):9827. doi: 10.1038/s41467-024-53452-6.

ABSTRACT

Several cardiovascular traits and diseases co-occur with Alzheimer's disease. We mapped their shared genetic architecture using multi-trait genome-wide association studies. Subsequent fine-mapping and colocalisation highlighted 16 genetic loci associated with both Alzheimer's and cardiovascular diseases. We prioritised rs11786896, which colocalised with Alzheimer's disease, atrial fibrillation and expression of PLEC in the heart left ventricle, and rs7529220, which colocalised with Alzheimer's disease, atrial fibrillation and expression of C1Q family genes. Single-cell RNA-sequencing data, co-expression network and protein-protein interaction analyses provided evidence for different mechanisms of PLEC, which is upregulated in left ventricular endothelium and cardiomyocytes with heart failure and in brain astrocytes with Alzheimer's disease. Similar common mechanisms are implicated for C1Q in heart macrophages with heart failure and in brain microglia with Alzheimer's disease. These findings highlight inflammatory and pleomorphic risk determinants for the co-occurrence of Alzheimer's and cardiovascular diseases and suggest PLEC, C1Q and their interacting proteins as potential therapeutic targets.

PMID:39537608 | DOI:10.1038/s41467-024-53452-6

BMJ Open Ophthalmol. 2024 Nov 12;9(1):e001915. doi: 10.1136/bmjophth-2024-001915.

ABSTRACT

OBJECTIVE: Glaucoma is an optic neuropathy and the leading cause of irreversible blindness worldwide. However, the early detection of glaucoma remains challenging, as chronic forms of glaucoma remain largely asymptomatic until considerable irreversible visual field deficits have ensued. Thus, biomarkers that facilitate early diagnosis and treatment for glaucoma patients with a high risk of progression are pressing.

METHODS AND ANALYSIS: Human disease-biomarker interactions network and human disease-target-drug interactions network were first constructed based on multiomics data. The greedy search algorithm was used to search for the hub biomarkers and drug targets for glaucoma. Genome-wide association studies and epidemiological data from the UK Biobank were used to verify our results. Biological network and functional analysis was conducted to find common network features and pathways.

RESULTS: We identified 10 hub biomarkers/drug targets for the diagnosis, treatment and prognosis for glaucoma. These results were verified by text mining and genomic/epidemiology data. We also predicted the new application of BMP1 and MMP9 to diagnose glaucoma and confirm the theory of hub biomarkers with multiple clinical applications. Further, relevant pivotal pathways for these hub biomolecules were discovered, which may serve as foundations for future biomarker and drug target prediction for glaucoma.

CONCLUSION: We have used a network-based approach to identify hub diagnostic and therapeutic biomarkers for glaucoma and detected relationships between glaucoma and associated diseases. Several hub biomarkers were identified and verified, which may play more important roles in the diagnosis and treatment of glaucoma.

PMID:39537208 | DOI:10.1136/bmjophth-2024-001915

Life Sci. 2024 Nov 11:123238. doi: 10.1016/j.lfs.2024.123238. Online ahead of print.

ABSTRACT

Metabolomics is an emerging field involving the systematic identification and quantification of numerous metabolites in biological samples. Precision medicine applies multiomics systems biology to individual patients for reliable diagnostic classification, disease monitoring, and treatment. Multiomics systems biology encompasses genomics, transcriptomics, proteomics, epigenomics, and metabolomics. Therefore, metabolomic techniques could be highly valuable for future clinical decision-making. This review provides a technical overview of two commonly used techniques for metabolomics measurements: mass spectrometry (MS) and proton nuclear magnetic resonance (1H NMR) spectroscopy. We also discuss recent clinical advances in these techniques. Individuals with inflammatory bowel disease (IBD) exhibit significant variability in prognosis and response to treatment. Since both genetic predisposition and environmental factors contribute to this condition, targeting the metabolome may provide key insights for distinguishing and profiling patients with different clinical needs. Additionally, the considerable overlap in the clinical presentation of various disease subtypes emphasizes the need for enhanced diagnostic methods to improve patient care.

PMID:39537099 | DOI:10.1016/j.lfs.2024.123238

Acta Trop. 2024 Nov 11:107461. doi: 10.1016/j.actatropica.2024.107461. Online ahead of print.

ABSTRACT

This study aimed to assess the baseline genetic diversity of the Plasmodium vivax population in an endemic area of northeast Myanmar at the onset of the malaria elimination campaign in the Greater Mekong Subregion. We genotyped 125 P. vivax clinical samples at two merozoite surface protein loci, PvMSP1 and PvMSP3α, by amplicon deep sequencing. Our study revealed that the parasite population in this region was highly diverse, identifying 60 PvMSP1 and 98 PvMSP3α haplotypes, with haplotype diversity of 0.929 and 0.944, respectively. Remarkably, 97.6% (122/125) of the patients harbored multiclonal infections with a mean multiplicity of infection of 4.18, indicating a relatively high transmission intensity. Neutrality tests and network analysis suggested a recent parasite population expansion, consistent with the concurrent malaria outbreak in the region. These findings underscore the existence of a highly diverse P. vivax population at the China-Myanmar border, highlighting the need for effective malaria control strategies to achieve the goal of regional malaria elimination.

PMID:39536889 | DOI:10.1016/j.actatropica.2024.107461

Sci Total Environ. 2024 Nov 11:177505. doi: 10.1016/j.scitotenv.2024.177505. Online ahead of print.

ABSTRACT

Coastal marine and estuarine systems are subject to enormous endogenous and exogenous pressures, particularly climate change, while at the same time being highly productive sources and nurseries for fish populations. Interactions between host and microbiome are increasingly recognized for their importance for fish health, with growing evidence indicating that increasing environmental pressures impact host resilience and favor the raise of opportunistic bacterial taxa. The microbial composition of the gill mucus reflects environmental conditions and represents an entry route for pathogens into the fish body. High-throughput sequencing of prokaryotic populations from 250 samples of two fish species with highly different habitat preferences, as well as seasonal and spatial distributions in the Elbe estuary system, allowed us to describe the variation of the microbiota along a salinity gradient and under fluctuating environmental conditions. The analysis of estuarine fish core microbiota in relation to variable bacterial components indicated dysbiotic states under sustained hypoxia and high nutrient loads largely driven by increased prevalence of facultatively aerobic (Acinetobacter) and anaerobic heterotrophs (Shewanella, Aeromonas). By correlating bacterial abundances with environmental and physiological parameters in a co-occurrence network approach, we describe plasticity in microbiota composition, identify potential biomarkers for fish health monitoring and reconstruct movement patterns of the fish. Our results can help to shape future minimal-invasive and cost-effective monitoring programs, and identify factors that need to be controlled in the estuary to promote fish and stock health.

PMID:39536868 | DOI:10.1016/j.scitotenv.2024.177505

Dev Cell. 2024 Nov 6:S1534-5807(24)00632-4. doi: 10.1016/j.devcel.2024.10.013. Online ahead of print.

ABSTRACT

Mammalian spermatogenesis is a highly stereotyped and conserved developmental process that is essential for fitness. At the same time, gene expression in spermatogenic cells is rapidly evolving. This combination of features has been suggested to drive rapid fixation of new gene expression patterns. Using a high-resolution dataset comprising bulk and single-cell data from juvenile and adult testes of the opossum Monodelphis domestica, a model marsupial, we define the developmental timing of the spermatogenic first wave in opossum and delineate conserved and divergent gene expression programs across the placental-marsupial split by comparison to equivalent data from mouse, a model placental mammal. Epigenomic data confirmed divergent regulation at the level of transcription, and comparison to data from four additional amniote species identified hundreds of genes with evidence of rapid fixation of expression. This gene set encompasses known and previously undescribed regulators of spermatogenic development.

PMID:39536760 | DOI:10.1016/j.devcel.2024.10.013

Ecotoxicol Environ Saf. 2024 Nov 12;287:117290. doi: 10.1016/j.ecoenv.2024.117290. Online ahead of print.

ABSTRACT

BACKGROUND: Previous research has proposed that exposure to polycyclic aromatic hydrocarbons (PAHs) during pregnancy could potentially lead to a higher risk of adverse birth anthropometric outcomes. However, the current evidence on this connection remains inconclusive, as various studies have presented conflicting results.

OBJECTIVE: This systematic review and meta-analysis seeks to synthesize the available research on the potential link between maternal PAHs exposure and birth anthropometric outcomes.

METHODS: A comprehensive search of Scopus, PubMed/MEDLINE, Web of Science, and the Cochrane Library up to July 1, 2024, was conducted to identify studies investigating the impact of maternal PAHs exposure during pregnancy on birth anthropometric measures, including small gestational age (SGA), low birth weight (LBW), birth weight (BW), birth length (BL), birth head circumference (BHC), and birth chest circumference (BCC). Quality assessment was performed using the Newcastle-Ottawa Scale (NOS) and the GRADE framework, and a random-effects meta-analysis was conducted to consolidate association estimates.

RESULTS: Out of 5499 articles initially screened, 27 studies were included in the review. The meta-analysis revealed no significant association between maternal PAHs exposure and LBW (OR: 1.02, 95 % CI: 0.96-1.08), with moderate heterogeneity (I²: 25.8 %, P=0.37). Notably, PAHs exposure was significantly associated with BW (β: -9.79 g, 95 % CI: -16.71 to -2.87), along with high heterogeneity (I²: 99.9 %, P<0.001), and shorter BL (β: -0.04 cm, 95 % CI: -0.07 to -0.01), also with high heterogeneity (I²: 84.3 %, P<0.001). Additionally, a borderline significant decrease in BHC was observed (β: -0.01 cm, 95 % CI: -0.02 to -0.00) with no significant heterogeneity among studies. The results SGA were inconsistent across the studies.

CONCLUSION: Maternal exposure to PAHs was associated with adverse birth anthropometric outcomes, particularly lower BW and BL. The borderline significant reduction in BHC suggests a potential impact worth further investigation, although this finding remains inconclusive and not yet actionable. Results for SGA varied significantly among studies, underscoring the complexity of these associations. Collectively, these findings highlight the necessity for additional research to elucidate the effects of specific PAH metabolites on birth anthropometric outcomes and to explore potential interventions aimed at mitigating the identified risks.

PMID:39536563 | DOI:10.1016/j.ecoenv.2024.117290

Phys Biol. 2024 Nov 13. doi: 10.1088/1478-3975/ad9213. Online ahead of print.

ABSTRACT

Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more strongly to the receptors that it uses to enter human cells. Here, we compared two methods that estimate the fitness effects of viral mutations using the abundant sequence data gathered over the course of the pandemic. Both approaches are grounded in population genetics theory but with different assumptions. One approach, tQLE, features an epistatic fitness landscape and assumes that alleles are nearly in linkage equilibrium. Another approach, MPL, assumes a simple, additive fitness landscape, but allows for any level of correlation between alleles. We characterized differences in the distributions of fitness values inferred by each approach and in the ranks of fitness values that they assign to sequences across time. We find that in a large fraction of weeks the two methods are in good agreement as to their top-ranked sequences, \textit{i.e.} as to which sequences observed that week are most fit. We also find that agreement between the ranking of sequences varies with genetic unimodality in the population in a given week.&#xD.

PMID:39536448 | DOI:10.1088/1478-3975/ad9213

PLoS Pathog. 2024 Nov 13;20(11):e1012653. doi: 10.1371/journal.ppat.1012653. eCollection 2024 Nov.

ABSTRACT

The COVID-19 pandemic, caused by SARS-CoV-2, demonstrated that zoonotic transmission of animal sarbecoviruses threatens human health but the determinants of transmission are incompletely understood. Here, we show that most spike (S) proteins of horseshoe bat and Malayan pangolin sarbecoviruses employ ACE2 for entry, with human and raccoon dog ACE2 exhibiting broad receptor activity. The insertion of a multibasic cleavage site into the S proteins increased entry into human lung cells driven by most S proteins tested, suggesting that acquisition of a multibasic cleavage site might increase infectivity of diverse animal sarbecoviruses for the human respiratory tract. In contrast, two bat sarbecovirus S proteins drove cell entry in an ACE2-independent, trypsin-dependent fashion and several ACE2-dependent S proteins could switch to the ACE2-independent entry pathway when exposed to trypsin. Several TMPRSS2-related cellular proteases but not the insertion of a multibasic cleavage site into the S protein allowed for ACE2-independent entry in the absence of trypsin and may support viral spread in the respiratory tract. Finally, the pan-sarbecovirus antibody S2H97 enhanced cell entry driven by two S proteins and this effect was reversed by trypsin while trypsin protected entry driven by a third S protein from neutralization by S2H97. Similarly, plasma from quadruple vaccinated individuals neutralized entry driven by all S proteins studied, and availability of the ACE2-independent, trypsin-dependent pathway reduced neutralization sensitivity. In sum, our study reports a pathway for entry into human cells that is ACE2-independent, can be supported by TMPRSS2-related proteases and may be associated with antibody evasion.

PMID:39536058 | DOI:10.1371/journal.ppat.1012653

PLoS One. 2024 Nov 13;19(11):e0308873. doi: 10.1371/journal.pone.0308873. eCollection 2024.

ABSTRACT

Flow cytometry enables quantitative measurements of fluorescence in single cells. The technique was widely used for immunology to identify populations with different surface protein markers. More recently, the usage of flow cytometry has been extended to additional readouts, including intracellular proteins and fluorescent protein transgenes, and is widely utilized to study developmental biology, systems biology, microbiology, and many other fields. A common file format (FCS format, defined by the International Society for Advancement of Cytometry (ISAC)) has been universally adopted, facilitating data exchange between different machines. A diverse spectrum of software packages has been developed for the analysis of flow cytometry data. However, those are either 1) costly proprietary softwares, 2) open source packages with prerequisite installation of R or Python and sometimes require users to have experience in coding, or 3) online tools that are limiting for analysis of large data sets. Here, we present EasyFlow, an open-source flow cytometry analysis graphic user interface (GUI) based on Matlab or Python, that can be installed and run locally across platforms (Windows, MacOS, and Linux) without requiring previous coding knowledge. The Python version (EasyFlowQ) is also developed on a popular plotting framework (Matplotlib) and modern user interface toolkit (Qt), allowing more advanced users to customize and keep contributing to the software, as well as its tutorials. Overall, EasyFlow serves as a simple-to-use tool for inexperienced users with little coding experience to use locally, as well as a platform for advanced users to further customize for their own needs.

PMID:39536028 | DOI:10.1371/journal.pone.0308873

PLoS One. 2024 Nov 13;19(11):e0306402. doi: 10.1371/journal.pone.0306402. eCollection 2024.

ABSTRACT

Research on ancient adhesives from the South African Stone Age is expanding, driven by excellent preservation conditions of adhesives and the potential to address diverse archaeological questions. These adhesives are primarily characterized through microscopic and chemical analysis. Despite geographic variability, a consistently identified component is Podocarpus resin or tar. We challenge these identifications, considering another Podocarpaceae genus, Afrocarpus, and the Cupressaceae genus Widdringtonia. Gas Chromatography-Mass Spectrometry was employed to analyze molecular signatures of modern wood, tar, resin, and seed cones from these genera. The results form an extensive reference database and reveal challenges in distinguishing these genera based on the diterpenoid signature. While Podocarpus is frequently cited, we advocate for a broader classification as Podocarpaceae when phenolic diterpenoids are found in high abundances and pimaranes and abietanes in lower abundances, and Widdringtonia when the opposite is true. The study differentiates materials used in adhesive production, including leaves and wood, highlighting the significance of α,ω-dicarboxylic acids, hydroxy acids, n-alkanes, and alcohols. Tars produced from leaves are characterized by odd-numbered n-alkanes, while tars produced from twigs and branches are characterized by long-chain α,ω-dicarboxylic acids, hydroxy acids, and alcohols. Because the differences between these adhesives in terms of raw material procurement and production are great, a more nuanced and cautious approach that acknowledges the challenges in differentiating tree species on a molecular level and considers archaeological and environmental context is required.

PMID:39536024 | DOI:10.1371/journal.pone.0306402

STAR Protoc. 2024 Nov 12;5(4):103420. doi: 10.1016/j.xpro.2024.103420. Online ahead of print.

ABSTRACT

Here, we present a protocol for Xenium spatial transcriptomics studies using fixed frozen mouse brain sections. We describe steps for intracardiac perfusion, cryosectioning, and floating section mounting of brain sections, which enable runs on the Xenium analyzer and data delivery. We demonstrate that, in addition to the 10× Genomics-validated formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections, fixed frozen thin brain sections are compatible with the Xenium platform and provide excellent imaging and quantification results for spatially resolved gene expression. For complete details on the use and execution of this protocol, please refer to Ma et al.1.

PMID:39535916 | DOI:10.1016/j.xpro.2024.103420

Mol Biol Cell. 2024 Nov 13:mbcE24060254. doi: 10.1091/mbc.E24-06-0254. Online ahead of print.

ABSTRACT

Fluorescence microscopy has revolutionised biological research by enabling the visualisation of subcellular structures at high resolution. With the increasing complexity and volume of microscopy data, there is a growing need for automated image analysis to ensure efficient and consistent interpretation. In this study, we introduce PunctaFinder, a novel Python-based algorithm designed to detect puncta, small bright spots, in raw fluorescence microscopy images without image denoising or signal enhancement steps. Furthermore, unlike other available spot detectors, PunctaFinder not only detects puncta, but also defines the cytoplasmic region, making it a valuable tool to quantify target molecule localisation in cellular contexts. PunctaFinder is a widely applicable punctum detector and size estimator, as evidenced by its successful detection of Atg9-positive vesicles, lipid droplets, aggregates of a destabilised luciferase mutant, and the nuclear pore complex. Notably, PunctaFinder excels in detecting puncta in images with a relatively low resolution and signal-to-noise ratio, demonstrating its capability to identify dim puncta and puncta of dynamic target molecules. PunctaFinder reliably detects puncta in fluorescence microscopy images where automated analysis was not possible before, providing researchers with an efficient and robust method for punctum quantification in fluorescence microscopy images.

PMID:39535892 | DOI:10.1091/mbc.E24-06-0254

Methods Mol Biol. 2025;2863:297-317. doi: 10.1007/978-1-0716-4176-7_18.

ABSTRACT

The asymmetric distribution of RNA within a cell plays a pivotal biological role, ensuring the distinctive shapes and functionality of subcellular compartments. In neurons, these mechanisms are fundamental to cellular growth, synaptic plasticity, and information processing. To understand these mechanisms, diverse methods have been developed to analyze localized transcripts. Here, we outline our optimized method for measurement of mRNA half-lives in subcellular neuronal compartments-neurites, and cytoplasmic and nuclear fractions of cell bodies. We call this method spatial SLAMseq, as it combines SLAMseq with subcellular compartment separation techniques. Spatial SLAMseq facilitates the concurrent measurement of mRNA dynamics and steady-state RNA levels within neuronal subcellular compartments.

PMID:39535717 | DOI:10.1007/978-1-0716-4176-7_18

Pathologie (Heidelb). 2024 Nov 13. doi: 10.1007/s00292-024-01395-6. Online ahead of print.

ABSTRACT

The limited availability of suitable animal models and cell lines often impedes experimental cancer research. Wet-laboratory experiments are also time-consuming and cost-intensive. In this review, we present an in silico modeling strategy, namely, Boolean network (BN) models, and demonstrate how it could be applied to streamline experimental design and to focus the effort of experimental read-outs. Boolean network models allow for the dynamic analysis of large molecular signaling pathways and their crosstalks. After establishing and validating a specific tumor model, mechanistic insights into the tumor cell behavior can be gained by studying the trajectories of different tumor phenotypes. Also, tumor driver and drug target screenings can be performed. These automatic screenings can help to identify new intervention targets and putative biomarkers for tumor evolution, hence guiding new wet-laboratory experiments. The goal of this round-up is to demonstrate how to establish, validate, and use BN modeling and its crosstalks in classic wet-laboratory research using a chronic lymphocytic leukemia (CLL) BN model.

PMID:39535613 | DOI:10.1007/s00292-024-01395-6