Development. 2025 Feb 15;152(4):DEV204514. doi: 10.1242/dev.204514. Epub 2025 Mar 3.

ABSTRACT

The formation of a new head during Hydra regeneration involves the establishment of a head organizer that functions as a signaling center and contains an aster-shaped topological defect in the organization of the supracellular actomyosin fibers. Here, we show that the future head region in regenerating tissue fragments undergoes multiple instances of extensive stretching and rupture events from the onset of regeneration. These recurring localized tissue deformations arise due to transient contractions of the supracellular ectodermal actomyosin fibers that focus mechanical strain at defect sites. We further show that stabilization of aster-shaped defects is disrupted by perturbations of the Wnt signaling pathway. We propose a closed-loop feedback mechanism promoting head organizer formation, and develop a biophysical model of regenerating Hydra tissues that incorporates a morphogen source activated by mechanical strain and an alignment interaction directing fibers along morphogen gradients. We suggest that this positive-feedback loop leads to mechanical strain focusing at defect sites, enhancing local morphogen production and promoting robust organizer formation.

PMID:40026208 | DOI:10.1242/dev.204514

Small Methods. 2025 Mar 3:e2401416. doi: 10.1002/smtd.202401416. Online ahead of print.

ABSTRACT

Tandem repeats of a certain DNA sequence can be generated using rolling circle amplification (RCA), where a circular template is continuously amplified by a polymerase with strand displacement activity. In leveraging the linear repetition of the target sequence, enhanced accuracy is achievable by consensus calling in nanopore sequencing. However, traditional multiply-primed RCA produces branched products with limited length, which may not be optimal for nanopore sequencing. In this study, an enhanced RCA protocol is introduced using sequence-specific primers to produce longer and less branched amplicons. Taking advantage of the RCA amplicons of tandem repeats, custom-primed rolling circle amplification sequencing (CPRSeq) is developed, a highly accurate nanopore sequencing pipeline. Utilizing CPRSeq, this successfully sequence standard samples of tumor-associated single nucleotide variants at low mutation frequency and accomplished the whole-genome sequencing and assembly of E. coli.

PMID:40025906 | DOI:10.1002/smtd.202401416

J Cheminform. 2025 Mar 2;17(1):28. doi: 10.1186/s13321-025-00973-x.

ABSTRACT

Computer-aided drug design has the potential to significantly reduce the astronomical costs of drug development, and molecular docking plays a prominent role in this process. Molecular docking is an in silico technique that predicts the bound 3D conformations of two molecules, a necessary step for other structure-based methods. Here, we describe version 1.3 of the open-source molecular docking software GNINA. This release updates the underlying deep learning framework to PyTorch, resulting in more computationally efficient docking and paving the way for seamless integration of other deep learning methods into the docking pipeline. We retrained our CNN scoring functions on the updated CrossDocked2020 v1.3 dataset and introduce knowledge-distilled CNN scoring functions to facilitate high-throughput virtual screening with GNINA. Furthermore, we add functionality for covalent docking, where an atom of the ligand is covalently bound to an atom of the receptor. This update expands the scope of docking with GNINA and further positions GNINA as a user-friendly, open-source molecular docking framework. GNINA is available at https://github.com/gnina/gnina .Scientific contributions: GNINA 1.3 is an open source a molecular docking tool with enhanced support for covalent docking and updated deep learning models for more effective docking and screening.

PMID:40025560 | DOI:10.1186/s13321-025-00973-x

Plant Methods. 2025 Mar 2;21(1):29. doi: 10.1186/s13007-025-01348-x.

ABSTRACT

BACKGROUND: There is much interest in how roots can be manipulated to improve crop performance in a changing climate, yet root research is made difficult by the challenges of visualising the root system accurately, particularly when grown in natural environments such as soil. Scientists often resort to use of agar- or paper-based assays, which provide unnatural growing media, with the roots often exposed to light. Alternatives include rhizotrons or x-ray computed tomography, which require specialist and expensive pieces of equipment, not accessible to those in developing countries most affected by climate change. Another option is excavation of roots, however, this is time-consuming and near impossible to achieve without some degree of root damage. Therefore, new, affordable but reliable alternatives for root phenotyping are necessary.

RESULTS: This study reports a novel, low cost, Rootrainer-based system for root phenotyping. Rootrainers were tilted at an angle, in a rhizotron-like set-up. This encouraged root growth on the bottom plane of the Rootrainers, and since Rootrainers open (in a book-like fashion), root growth can be easily observed. This new technique was successfully used to uncover significant genotypic variance in rooting traits for a selection of lettuce (L. sativa) varieties across multiple timepoints.

CONCLUSION: This novel Rootrainertron method has many advantages over existing methods of phenotyping seedling roots. Rootrainers are cheap, and readily available from garden centres, unlike rhizotrons which are expensive and only available from specialist suppliers. Rootrainers allow the roots to grow in substrate medium, providing a significant advantage over agar and paper assays.This approach offers an affordable and relevant root phenotyping option and makes root phenotyping more accessible and applicable for researchers.

PMID:40025547 | DOI:10.1186/s13007-025-01348-x

Exp Mol Med. 2025 Mar 3. doi: 10.1038/s12276-025-01418-z. Online ahead of print.

ABSTRACT

The trapping of pathogenic ligands can potentially be used to prevent signal transduction mediated by catabolic factor expression in osteoarthritis (OA). Although vaspin is known to function as a pathogenic ligand and represents a novel adipokine, little is known about its function and the impact of its nebulization-based administration in OA. Here we provide a report on the function of vaspin in articular chondrocytes and OA model mice. RNA sequencing analysis and ingenuity pathway analysis demonstrated that vaspin upregulation in chondrocytes triggers OA development-related signaling. Vaspin is upregulated in the injured cartilage of patients with OA and DMM (Destabilization of the Medial Meniscus) mice, and its overexpression induces catabolic factor expression in vitro under OA-mimicked conditions. Col2a1-vaspin Tg (Transgenic) animals showed extensive cartilage degradation, whereas vaspin-/- (knockout) mice exhibited decreased OA development. Furthermore, in silico and biochemical analyses showed that vaspin activates the p38 and JNK signaling pathways to regulate AP-1-driven catabolic factor production and cartilage breakdown. Finally, we identified and characterized a vaspin-targeting nanobody, vas nanobody, and showed that intraarticularly injected vas nanobody could effectively block the vaspin-AP-1 axis to treat OA in DMM mice. Together, our results suggest that blockade of the vaspin-AP-1 axis could be an effective therapeutic approach for preventing OA development.

PMID:40025171 | DOI:10.1038/s12276-025-01418-z

Sci Rep. 2025 Mar 1;15(1):7314. doi: 10.1038/s41598-025-91546-3.

ABSTRACT

Lamin B1 (LMNB1) is an intermediate filament protein that is an integral component of the nuclear lamina, a structure that is critical for nuclear organization and function. Mutations involving the lamin B1 gene cause the adult-onset demyelinating disorder, Autosomal Dominant Leukodystrophy (ADLD) which is charactered by increased lamin B1 expression. Increased LMNB1 expression is also associated with poorer outcomes in multiple cancer subtypes. Reducing LMNB1 is thus an attractive therapeutic pathway for ADLD and potentially other diseases. Here we present the results of a high throughput / high content screen (HTS/HCS) to identify small molecules that reduce LMNB1 levels. Approximately 97,000 molecules were screened using an inducible mouse fibroblast model of LMNB1 overexpression that we have previously generated. Two small molecules, Pubchem CID 662896 and CID 5308648, were identified that reduced LMNB1 in a dose dependent manner without causing cellular toxicity and corrected nuclear abnormalities associated with LMNB1 overexpression, a hallmark of ADLD. CID 662896 also reduced LMNB1 levels in ADLD patient fibroblast samples, exhibited favorable "drug-like" physicochemical properties and crossed the blood brain barrier in mouse studies. While CID 662896 may be a promising candidate for ADLD therapy, further investigations are required to determine its mechanism of action and ability to target disease relevant cell types.

PMID:40025114 | DOI:10.1038/s41598-025-91546-3

Sci Rep. 2025 Mar 1;15(1):7283. doi: 10.1038/s41598-025-89684-9.

ABSTRACT

Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman's Rho = 0.58, p < 0.001), improving at the genus level (Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.

PMID:40025088 | DOI:10.1038/s41598-025-89684-9

Biotechnol Adv. 2025 Feb 28:108544. doi: 10.1016/j.biotechadv.2025.108544. Online ahead of print.

ABSTRACT

The persistent demand for plastic commodities, inadequate recycling infrastructure, and pervasive environmental contamination due to plastic waste present a formidable global challenge. Recycling, degradation and upcycling are the three most important ways to solve the problem of plastic pollution. Sequential enzymatic and microbial degradation of mechanically and chemically pre-treated plastic waste can be orchestrated, followed by microbial conversion into value-added chemicals and polymers through mixed culture systems. Furthermore, plastics-degrading enzymes can be optimized through protein engineering to enhance their specific binding capacities, stability, and catalytic efficiency across a broad spectrum of polymer substrates under challenging high salinity and temperature conditions. Also, the production and formulation of enzyme mixtures can be fine-tuned to suit specific waste compositions, facilitating their effective deployment both in vitro, in vivo and in combination with chemical technologies. Here, we emphasized the comprehensive strategy leveraging microbial processes to transform mixed plastics of fossil-derived polymers such as PP, PE, PU, PET, and PS, most notably polyesters, in conjunction with potential biodegradable alternatives such as PLA and PHA. Any residual material resistant to enzymatic degradation can be reintroduced into the process loop following appropriate physicochemical treatment.

PMID:40024585 | DOI:10.1016/j.biotechadv.2025.108544

Lab Invest. 2025 Feb 28:104123. doi: 10.1016/j.labinv.2025.104123. Online ahead of print.

ABSTRACT

Preferentially Expressed Antigen in Melanoma (PRAME) and Ten-Eleven Translocation (TET) dioxygenase-mediated 5-hydroxymethylcytosine (5hmC) are emerging melanoma biomarkers. We observed an inverse correlation between PRAME expression and 5hmC levels in benign nevi, melanoma in situ, primary invasive melanoma, and metastatic melanomas via immunohistochemistry and multiplex immunofluorescence: nevi exhibited high 5hmC and low PRAME, whereas melanomas showed the opposite pattern. Single-cell multiplex imaging of melanoma precursors revealed that diminished 5hmC coincides with PRAME upregulation in premalignant cells. Analysis of TCGA and GTEx databases confirmed a negative relationship between TET2 and PRAME mRNA expression in melanoma. Additionally, 5hmC levels were reduced at the PRAME 5' promoter in melanoma compared to nevi, suggesting a role for 5hmC in PRAME transcription. Restoring 5hmC levels via TET2 overexpression notably reduced PRAME expression in melanoma cell lines. These findings establish a function of TET2-mediated DNA hydroxymethylation in regulating PRAME expression and demonstrate epigenetic reprogramming as pivotal in melanoma tumorigenesis.

PMID:40024557 | DOI:10.1016/j.labinv.2025.104123

J Mol Biol. 2025 Feb 28:169054. doi: 10.1016/j.jmb.2025.169054. Online ahead of print.

ABSTRACT

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute's efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation and large transcriptomic and proteomic datasets - focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors -- that are well-used and appreciated by the community. A new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true "green yeast" and as a platform for engineering algae to produce useful bioproducts.

PMID:40024437 | DOI:10.1016/j.jmb.2025.169054

Biochem Pharmacol. 2025 Feb 28:116839. doi: 10.1016/j.bcp.2025.116839. Online ahead of print.

ABSTRACT

Dengue viruses (DENV) pose significant health threats, with no approved antiviral drugs currently available, creating an urgent need for new therapies. This study screened FDA-approved drugs for their antiviral ability against DENV and identified three promising candidates: darunavir (DRV), domperidone, and tetracycline. DRV demonstrated the highest efficacy against three DENV serotypes, with half-maximal effective concentrations (EC50) below 1 µM, surpassing the performance of tetracycline and domperidone. It effectively blocked DENV envelope (E) protein attachment to two type cells with EC50 values less than 0.2 μM. Domperidone reduced DENV-2 attachment to TE671 cells (EC50 = 3.08 μM) but was less effective in BHK-21 cells, while tetracycline inhibited NS3 protease (IC50 = 1.12 μM). Among DRV's structurally related drugs, fosamprenavir (FPV) significantly reduced DENV infectivity and virus yield, with EC50 values below 0.5 µM. In vivo, DRV at 1, 2, and 5 mg/kg achieved 100 % survival in suckling mice, compared to 83.5 % with FPV. Real-time RT-PCR showed DRV more effectively reduced DENV-2 RNA in mouse brains than FPV. Molecular docking showed DRV and FPV bind tightly to the DENV-2 E protein's N-octyl-β-D-glucoside (βOG) hydrophobic pocket, with DRV forming stronger interactions than FPV. Chimeric DENV-2 single-round infectious particle tests confirmed DRV's effective targeting of this pocket, though mutations at K128, L198, Q200, I270, and T280 reduced its efficacy. These findings highlight DRV as a potent antiviral agent against DENV, targeting the E protein's βOG hydrophobic pocket, with the potential for rapid deployment in treating and preventing infections.

PMID:40024350 | DOI:10.1016/j.bcp.2025.116839

Vaccine. 2025 Mar 1;53:126948. doi: 10.1016/j.vaccine.2025.126948. Online ahead of print.

ABSTRACT

In England, and many other countries, immunity to SARS-CoV-2 infection and COVID-19 disease is highly heterogeneous. Immunity has been acquired through natural infection, primary and booster vaccination, while protection has been lost through waning immunity and viral mutation. During the height of the pandemic in England, the main aim was to rapidly protect the population and large supplies of vaccine were pre-purchased, eliminating the need for cost-effective calculations. As we move to an era where for the majority of the population SARS-CoV-2 infections cause relatively mild disease, and vaccine stocks need to be re-purchased, it is important we consider the cost-effectiveness and economic value of COVID-19 vaccination programmes. Here using data from 2023 and 2024 in England on COVID-19 hospital admissions, ICU admissions and deaths, coupled with bespoke health economic costs, we consider the willingness to pay threshold for COVID-19 vaccines in different age and risk groups. Willingness to pay thresholds vary from less than £1 for younger age-groups without any risk factors, to over £100 for older age-groups with comorbidities that place them at risk. This extreme non-linear dependence on age, means that despite the different method of estimating vaccine effectiveness, there is considerable qualitative agreement on the willingness to pay threshold, and therefore which ages it is cost-effective to vaccinate. The historic offer of COVID-19 vaccination to those 65 and over for the autumn 2023 programme and those over 75 for the spring 2023 programme, aligns with our cost- effective threshold for pre-purchased vaccine when the only cost was administration. However, for future programmes, when vaccine costs are included, the age-thresholds slowly increase thereby demonstrating the continued importance of protecting the eldest and most vulnerable in the population.

PMID:40023905 | DOI:10.1016/j.vaccine.2025.126948

Bioresour Technol. 2025 Feb 27:132313. doi: 10.1016/j.biortech.2025.132313. Online ahead of print.

ABSTRACT

Lignocellulose is the most abundant terrestrial biomass type, and lignocellulose hydrolysate has the potential to replace glucose for microbial fermentation. Halomonas bluephagenesis has significant advantages in producing bioplastics polyhydroxyalkanoates (PHA), but there is relatively little research on the use of lignocellulose hydrolysate for this strain. In present study, H. bluephagenesis was engineered to use xylose and lignocellulose hydrolysate to produce PHB. Firstly, four xylose metabolism pathways were established. Secondly, several xfp genes were compared and genes in pathway I (xylA and xfp gene) were integrated into the genome. Thirdly, H. bluephagenesis was found to be able to utilize glucose and xylose simultaneously. H. bluephagenesis T39 containing xylA and xfp generated 15 g/L CDW containing 76 wt% PHB when cultured in lignocellulose hydrolysate, and it was grown to 62 g/L CDW containing 67 wt% PHB in a 7 L bioreactor. H. bluephagenesis T43 harboring xylA was found able to synthesize P(3HB-4HB-3HV) containing 3-hydroxybutyrate (3HB), 4-hydroxybutyrte (4HB) and 3-hydroxyvalerate (3HV) when grown on lignocellulose hydrolysate.

PMID:40023329 | DOI:10.1016/j.biortech.2025.132313

Brain Behav Immun. 2025 Feb 27:S0889-1591(25)00070-4. doi: 10.1016/j.bbi.2025.02.030. Online ahead of print.

ABSTRACT

Autism Spectrum Disorder (ASD) is a highly prevalent neurodevelopmental condition characterized by social communication deficits and repetitive/restricted behaviors. Several studies showed that oxidative stress and inflammation may contribute to ASD. Indeed, increased levels of oxygen radicals and pro-inflammatory molecules were described in the brain and peripheral blood of persons with ASD and mouse models. Despite this, a potential direct connection between oxidative stress and inflammation within specific brain areas and ASD-related behaviors has not been investigated in detail yet. Here, we used RT-qPCR, RNA sequencing, metabolomics, immunohistochemistry, and flow cytometry to show that pro-inflammatory molecules were increased in the cerebellum and periphery of mice lacking Cntnap2, a robust model of ASD. In parallel, oxidative stress was present in the cerebellum of mutant animals. Systemic treatment with N-acetyl-cysteine (NAC) rescued cerebellar oxidative stress, inflammation, as well as motor and social impairments in Cntnap2-/- mice, concomitant with enhanced function of microglia cells in NAC-treated mutants. Intriguingly, social deficits, cerebellar inflammation, and microglia dysfunction were induced by NAC in Cntnap2+/+ animals. Our findings suggest that the interplay between oxidative stress and inflammation accompanied by genetic vulnerability may underlie ASD-related behaviors in Cntnap2 mutant mice.

PMID:40023202 | DOI:10.1016/j.bbi.2025.02.030

Cell Syst. 2025 Feb 21:101202. doi: 10.1016/j.cels.2025.101202. Online ahead of print.

ABSTRACT

Regions on a host protein that interact with virus proteins (exogenous interfaces) frequently overlap with those that interact with other host proteins (endogenous interfaces), resulting in competition between hosts and viruses for these shared interfaces (mimic-targeted interfaces). Yet, the evolutionary consequences of this competitive relationship on the host are not well understood. Here, we integrate experimentally determined structures and homology-based templates of protein complexes with protein-protein interaction networks to construct a high-resolution human-virus structural interaction network. We perform site-specific evolutionary rate analyses on this structural interaction network and find that exogenous-specific interfaces evolve faster than endogenous-specific interfaces. Mimic-targeted interfaces evolve as fast as exogenous-specific interfaces, despite being targeted by both human and virus proteins. Our findings suggest that virus targeting plays a dominant role in host interfacial evolution within the context of domain-domain interactions and that mimic-targeted interfaces on human proteins are the key battleground for a mammalian-specific host-virus evolutionary arms race.

PMID:40023148 | DOI:10.1016/j.cels.2025.101202

Tissue Cell. 2025 Feb 28;94:102806. doi: 10.1016/j.tice.2025.102806. Online ahead of print.

ABSTRACT

BACKGROUND: Neurons, distributed throughout the body, regulate various bodily functions. The recovery of the nervous system is often slow and can be irreversible. Currently, the approach of using mesenchymal stem cells (MSCs) in conjunction with conventional treatments for nervous system injuries is being explored. Nanoemulsions are systems designed for the nanoscale delivery of drug cargoes. Foeniculum vulgare (F. vulgare), a medicinal plant long utilized in complementary medicine, is the focus of this study. The aim is to utilize nanoemulsions of fennel to induce the differentiation of MSCs into neural-like cells in vitro.

MATERIALS AND METHODS: Human adipose-derived mesenchymal stem cells (hADSCs) were commercially purchased. These cells were cultured in DMEM medium containing 10 % fetal bovine serum and 1 % penicillin-streptomycin antibiotic. Based on a sequential extraction method, n-hexane (Hex), ethyl acetate (EtAc), and ethanolic extracts were obtained from the seeds of F. vulgare. To prepare the F. vulgare extract nanoemulsion, the aqueous phase (distilled water), the oily part (F. vulgare extract), Span 80 and Tween 20 were used. The optimal dose of F. vulgare nanoemulsion was determined using the MTT assay and acridine orange/ethidium bromide (AO/EB) staining. Neural differentiation was induced using a specialized differentiation medium on the MSCs, with the prepared nanoemulsions acting as inducers. The neural differentiation of the human differentiated hADSCs was studied and evaluated through Real-time PCR and immunocytochemistry (ICC) techniques on days 7 and 14.

RESULTS: The results obtained from the MTT and AO/EB tests indicated that the optimal dose of F. vulgare nanoemulsions is 1 μg/ml. Analysis of neural differentiation index gene expression revealed a significant (P ≤ 0.05) upregulation of MAP-2, β-tubulin III, and NSE genes on days 7 and 14 following treatment with the nanoemulsions. It is noteworthy that the nanoemulsion prepared from the hexane extract of the plant showed a significant increase in the expression of marker genes in the process of neural differentiation. Protein expression analysis demonstrated an increase in MAP-2, β-tubulin III, and NSE (gamma enolase) proteins in response to the nanoemulsion inducers compared to the control group (TCPS).

DISCUSSION: Overall, our findings indicate that F. vulgare nanoemulsions have a positive effect on the expression of genes and proteins related to neural differentiation in hADSCs. The proposed protocol may serve as a potential therapeutic strategy in complementary medicine for patients seeking to improve injuries to the nervous system. However, further studies and performance measurements are necessary in future research to confirm these results.

PMID:40022910 | DOI:10.1016/j.tice.2025.102806

Virol J. 2025 Feb 28;22(1):52. doi: 10.1186/s12985-025-02669-y.

ABSTRACT

Viral hemorrhagic Lassa fever (LF), caused by Lassa virus (LASV), is a significant public health concern endemic in West Africa with high morbidity and mortality rates, limited treatment options, and potential for international spread. Despite advances in interrogating its epidemiology and clinical manifestations, the molecular mechanisms driving pathogenesis of LASV and other arenaviruses remain incompletely understood. This review synthesizes current knowledge regarding the role of LASV host-virus interactions in mediating the pathogenesis of LF, with emphasis on interactions between viral and host proteins. Through investigation of these critical protein-protein interactions, we identify potential therapeutic targets and discuss their implications for development of medical countermeasures including antiviral drugs. This review provides an update in recent literature of significant LASV host-virus interactions important in informing the development of targeted therapies and improving clinical outcomes for LF patients. Knowledge gaps are highlighted as opportunities for future research efforts that would advance the field of LASV and arenavirus pathogenesis.

PMID:40022100 | DOI:10.1186/s12985-025-02669-y

BMC Urol. 2025 Feb 28;25(1):41. doi: 10.1186/s12894-025-01723-9.

ABSTRACT

BACKGROUND: The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.

RESULTS: We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.

CONCLUSIONS: We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.

PMID:40022097 | DOI:10.1186/s12894-025-01723-9

Nat Metab. 2025 Feb 28. doi: 10.1038/s42255-025-01239-4. Online ahead of print.

NO ABSTRACT

PMID:40021935 | DOI:10.1038/s42255-025-01239-4

Nat Commun. 2025 Feb 28;16(1):2049. doi: 10.1038/s41467-025-57271-1.

ABSTRACT

Somatic mobilization of LINE-1 (L1) has been implicated in cancer etiology. We analyzed a recent TCGA data release comprised of nearly 5000 pan-cancer paired tumor-normal whole-genome sequencing (WGS) samples and ~9000 tumor RNA samples. We developed TotalReCall an improved algorithm and pipeline for detection of L1 retrotransposition (RT), finding high correlation between L1 expression and "RT burden" per sample. Furthermore, we mathematically model the dual regulatory roles of p53, where mutations in TP53 disrupt regulation of both L1 expression and retrotransposition. We found those with Li-Fraumeni Syndrome (LFS) heritable TP53 pathogenic and likely pathogenic variants bear similarly high L1 activity compared to matched cancers from patients without LFS, suggesting this population be considered in attempts to target L1 therapeutically. Due to improved sensitivity, we detect over 10 genes beyond TP53 whose mutations correlate with L1, including ATRX, suggesting other, potentially targetable, mechanisms underlying L1 regulation in cancer remain to be discovered.

PMID:40021663 | DOI:10.1038/s41467-025-57271-1