Plant Genome. 2025 Mar;18(1):e20536. doi: 10.1002/tpg2.20536.

ABSTRACT

The organization of subcellular components in a cell is critical for its function and studying cellular processes, protein-protein interactions, identifying potential drug targets, network analysis, and other systems biology mechanisms. Determining protein localization experimentally is time-consuming and expensive. Due to the need for meticulous experimentation, validation, and data analysis, computational methods provide a quick and accurate alternative. Arabidopsis thaliana, a beneficial model organism in plant biology, facilitates experimentation and applies to other plants. Predicting its proteins' subcellular localization can improve our understanding of cellular processes and have applications in crop improvement and biotechnology. We propose AtSubP-2.0, an extension of our previously developed and widely used AtSubP v1.0 tool for annotating the Arabidopsis proteome. For precise protein subcellular localization prediction, AtSubP-2.0 employs a four-phase strategy. The first phase differentiates between single and dual localization with accuracy (97.66% in fivefold training/testing, 98.10% on independent data) and high Matthews correlation coefficient (0.88 training, 0.90 independent). Single localized proteins are classified into 12 locations at the second phase, with accuracy (98.37% in fivefold training/testing, 97.43% on independent data) and Matthews correlation coefficient (0.94 training, 0.91 independent). The third phase categorizes dual location proteins into nine classes with accuracy (99.65% in fivefold training/testing, 98.16% on independent data) and Matthews correlation coefficient (0.92 training, 0.87 independent). We also employed a fourth phase that classifies the membrane type proteins predicted in phase I into single-pass and multi-pass membrane with accuracy (98% in fivefold training/testing, 98.55% on independent data) and a high Matthews correlation coefficient (0.95 training, 0.97 independent). A web-based prediction server has been implemented for community use and is freely available at https://kaabil.net/AtSubP2/, including a standalone version. AtSubP2 will help researchers to better understand organelle-specific functions, cellular processes, and regulatory mechanisms important for plant growth, development, and response to environmental stimuli.

PMID:39924294 | DOI:10.1002/tpg2.20536

Biochim Biophys Acta Biomembr. 2025 Feb 7:184416. doi: 10.1016/j.bbamem.2025.184416. Online ahead of print.

NO ABSTRACT

PMID:39924097 | DOI:10.1016/j.bbamem.2025.184416

Kidney Int. 2025 Feb 7:S0085-2538(25)00087-0. doi: 10.1016/j.kint.2025.01.024. Online ahead of print.

ABSTRACT

Chronic kidney disease (CKD) is a global health epidemic that greatly increases mortality due to cardiovascular disease. Left ventricular hypertrophy (LVH) is an important mechanism of cardiac injury in CKD. High serum levels of fibroblast growth factor (FGF) 23 in patients with CKD may contribute mechanistically to the pathogenesis of LVH by activating FGF receptor (FGFR) 4 signaling in cardiac myocytes. Mitochondrial dysfunction and cardiac metabolic remodeling are early features of cardiac injury that predate development of hypertrophy, but these mechanisms have been insufficiently studied in models of CKD. We found in wild-type mice with CKD induced by adenine diet, that morphological changes occurred in mitochondrial structure and cardiac mitochondrial and that metabolic dysfunction preceded the development of LVH. In bioengineered cardio-bundles and neonatal rat ventricular myocytes grown in vitro, FGF23-mediated activation of FGFR4 caused mitochondrial pathology, characterized by increased bioenergetic stress and increased glycolysis that preceded the development of cellular hypertrophy. The cardiac metabolic changes and associated mitochondrial alterations in mice with CKD were prevented by global and cardiac-specific deletion of FGFR4. Our findings indicate that metabolic remodeling and mitochondrial dysfunction are early cardiac complications of CKD that precede structural remodeling of the heart. Mechanistically, FGF23-mediated activation of FGFR4 causes mitochondrial dysfunction, suggesting that early pharmacologic inhibition of FGFR4 might serve as novel therapeutic intervention to prevent development of LVH and heart failure in patients with CKD.

PMID:39923962 | DOI:10.1016/j.kint.2025.01.024

Int J Biol Macromol. 2025 Feb 8;304(Pt 1):140766. doi: 10.1016/j.ijbiomac.2025.140766. Online ahead of print.

NO ABSTRACT

PMID:39923600 | DOI:10.1016/j.ijbiomac.2025.140766

STAR Protoc. 2025 Feb 8;6(1):103628. doi: 10.1016/j.xpro.2025.103628. Online ahead of print.

ABSTRACT

Inhibitory synaptic transmission mediated by the neurotransmitter γ-aminobutyric acid (GABA) is dependent on the concentration of chloride ions (Cl-) in neurons, which can be assessed by making patch-clamp recordings of the reversal potential for GABA (EGABA). Here, we present a protocol to study the regulation of cation-chloride cotransporters and the strength of synaptic inhibition in cultured mouse cortical neurons using electrophysiology. We describe steps for culturing neurons isolated from postnatal pups and electrophysiological measurement of EGABA. For complete details on the use and execution of this protocol, please refer to Raveendran et al.1.

PMID:39923240 | DOI:10.1016/j.xpro.2025.103628

Nat Commun. 2025 Feb 8;16(1):1469. doi: 10.1038/s41467-025-56749-2.

ABSTRACT

Enhancers serve as pivotal regulators of gene expression throughout various biological processes by interacting with transcription factors (TFs). While transcription factor binding sites (TFBSs) are widely acknowledged as key determinants of TF binding and enhancer activity, the significant role of their surrounding context sequences remains to be quantitatively characterized. Here we propose the concept of transcription factor binding unit (TFBU) to modularly model enhancers by quantifying the impact of context sequences surrounding TFBSs using deep learning models. Based on this concept, we develop DeepTFBU, a comprehensive toolkit for enhancer design. We demonstrate that designing TFBS context sequences can significantly modulate enhancer activities and produce cell type-specific responses. DeepTFBU is also highly efficient in the de novo design of enhancers containing multiple TFBSs. Furthermore, DeepTFBU enables flexible decoupling and optimization of generalized enhancers. We prove that TFBU is a crucial concept, and DeepTFBU is highly effective for rational enhancer design.

PMID:39922842 | DOI:10.1038/s41467-025-56749-2

Sci Rep. 2025 Feb 8;15(1):4695. doi: 10.1038/s41598-024-84367-3.

ABSTRACT

Understanding how the traits of lineages are related to diversification is key for elucidating the origin of variation in species richness. Here, we test whether traits are related to species richness among lineages of trees from all major biogeographical settings of the lowland wet tropics. We explore whether variation in mortality rate, breeding system and maximum diameter are related to species richness, either directly or via associations with range size, among 463 genera that contain wet tropical forest trees. For Amazonian genera, we also explore whether traits are related to species richness via variation among genera in mean species-level range size. Lineages with higher mortality rates-faster life-history strategies-have larger ranges in all biogeographic settings and have higher mean species-level range sizes in Amazonia. These lineages also have smaller maximum diameters and, in the Americas, contain dioecious species. In turn, lineages with greater overall range size have higher species richness. Our results show that fast life-history strategies influence species richness in all biogeographic settings because lineages with these ecological strategies have greater range sizes. These links suggest that dispersal has been a key process in the evolution of the tropical forest flora.

PMID:39922807 | DOI:10.1038/s41598-024-84367-3

Trends Cell Biol. 2025 Feb 7:S0962-8924(25)00003-0. doi: 10.1016/j.tcb.2025.01.003. Online ahead of print.

ABSTRACT

The selective removal of mitochondria by mitophagy proceeds via multiple mechanisms and is essential for human well-being. The PINK1/Parkin and NIX/BNIP3 pathways are strongly linked to mitochondrial dysfunction and hypoxia, respectively. Both are regulated by ubiquitylation and mitochondrial import. Recent studies have elucidated how the ubiquitin kinase PINK1 acts as a sensor of mitochondrial import stress through stable interaction with a mitochondrial import supercomplex. The stability of BNIP3 and NIX is regulated by the SCFFBXL4 ubiquitin ligase complex. Substrate recognition requires an adaptor molecule, PPTC7, whose availability is limited by mitochondrial import. Unravelling the functional implications of each mode of mitophagy remains a critical challenge. We propose that mitochondrial import stress prompts a switch between these two pathways.

PMID:39922712 | DOI:10.1016/j.tcb.2025.01.003

Arch Biochem Biophys. 2025 Feb 6:110330. doi: 10.1016/j.abb.2025.110330. Online ahead of print.

ABSTRACT

Glucose provides substrate for the predominant anaplerotic pathway which involves the activity of pyruvate carboxylase (PC). PC-mediated anaplerosis has been extensively studied as a metabolic regulator in glycolytic cells during tumorigenesis and metastasis. Herein, inaccuracies in established methods to measure relative intracellular flux through PC are highlighted and a compartmentalized condensed metabolic network (CCMN) is used to resolve the total malate pool into relative contributions from PC and other sources by metabolic flux analysis (MFA) with [U-13C6]glucose tracing. Performance of the CCMN method is evaluated in breast cancer cell lines that are exposed to small molecules targeting metabolism. Across conditions and cell lines, the CCMN approach yields results nearest to an accepted gold-standard methodology, using [3-13C]glucose, or even exposes the gold standard's limitations. The CCMN method does not require a separate experiment with a much more costly and generally less informative metabolic tracer, such as [3-13C]glucose, and in some cases, may outperform its application.

PMID:39922407 | DOI:10.1016/j.abb.2025.110330

Cell Syst. 2025 Feb 5:101168. doi: 10.1016/j.cels.2025.101168. Online ahead of print.

ABSTRACT

Biomolecular condensates have been proposed to buffer intracellular concentrations and reduce noise. However, concentrations need not be buffered in multicomponent systems, leading to a non-constant saturation concentration (csat) when individual components are varied. Simplified equilibrium considerations suggest that noise reduction might be closely related to concentration buffering and that a fixed saturation concentration is required for noise reduction to be effective. Here, we present a theoretical analysis to demonstrate that these suggestions do not apply to mesoscopic fluctuating systems. We show that concentration buffering and noise reduction are distinct concepts, which cannot be used interchangeably. We further demonstrate that concentration buffering and a constant csat are neither necessary nor sufficient for noise reduction to be effective. Clarity about these concepts is important for studying the role of condensates in controlling cellular noise and for the interpretation of concentration relationships in cells. A record of this paper's transparent peer review process is included in the supplemental information.

PMID:39922189 | DOI:10.1016/j.cels.2025.101168

J Exp Bot. 2025 Feb 8:eraf053. doi: 10.1093/jxb/eraf053. Online ahead of print.

ABSTRACT

Arbuscular mycorrhizal (AM) symbiosis can prime plant defenses, leading to mycorrhiza-induced resistance (MIR) against different attackers, including insect herbivores. Still, our knowledge of the complex molecular regulation leading to MIR is very limited. Here, we show that the AM fungus Funneliformis mosseae protects tomato plants against two different chewing herbivores, Spodoptera exigua and Manduca sexta. We explore the underlying molecular mechanism through genome-wide transcriptional profiling, bioinformatics network analyses, and functional bioassays. Herbivore-triggered JA-regulated defenses were primed in leaves of mycorrhizal plants, while ET biosynthesis and signaling were also higher both before and after herbivory. We hypothesized that fine-tuned ET signaling is required for the primed defensive response leading to MIR. ET is a complex regulator of plant responses to stress and is generally considered a negative regulator of plant defenses against herbivory. However, ET-deficient or insensitive lines did not show AM-primed JA biosynthesis or defense response, and were unable to develop MIR against any of the herbivores. Thus, we demonstrate that hormone crosstalk is central to the priming of plant immunity by beneficial microbes, with ET fine-tuning being essential for the primed JA biosynthesis and boosted defenses leading to MIR in tomato.

PMID:39921876 | DOI:10.1093/jxb/eraf053

STAR Protoc. 2025 Feb 7;6(1):103614. doi: 10.1016/j.xpro.2025.103614. Online ahead of print.

ABSTRACT

Owing to inconsistencies in human B cell classification and the difficulty in distinguishing heterogeneous subpopulations, we present a protocol to construct gene regulatory networks and gene activity landscapes for human B cell developmental stages. We describe steps for acquiring bone marrow data; conducting single-cell downstream analysis; and leveraging the St. Jude Algorithm for the Reconstruction of Accurate Cellular Networks (SJARACNe), Network-based Bayesian Inference of Drivers (NetBID2), and single-cell Mutual Information-based Network Engineering Ranger (scMINER) algorithms for network-based analysis. Our protocol elucidates the biological characteristics of developmental stages in human B cells. For complete details on the use and execution of this protocol, please refer to Huang et al.1.

PMID:39921864 | DOI:10.1016/j.xpro.2025.103614

STAR Protoc. 2025 Feb 6;6(1):103618. doi: 10.1016/j.xpro.2025.103618. Online ahead of print.

ABSTRACT

Network analysis is a powerful tool for investigating complex interactions between different microbial taxa within a community. We present a protocol to study the gut microbial community in a mouse model of breast cancer using a network-based approach. Here, we describe the procedures for tumor cell production and inoculation and 16S rRNA data processing. We then detail steps for constructing co-occurrence networks based on correlations between microbial abundances. For complete details on the use and execution of this protocol, please refer to Wu-Chuang et al.1.

PMID:39921860 | DOI:10.1016/j.xpro.2025.103618

Nucleic Acids Res. 2025 Feb 8;53(4):gkaf058. doi: 10.1093/nar/gkaf058.

ABSTRACT

Transcription factors (TFs) are often classified as activators or repressors, yet these context-dependent labels are inadequate to predict quantitative profiles that emerge across different promoters. A mechanistic understanding of how different regulatory sequences shape TF function is challenging due to the lack of systematic genetic control in endogenous genes. To address this, we use a library of Escherichia coli strains with precise control of TF copy number, measuring the quantitative regulatory input-output function of 90 TFs on synthetic promoters that isolate the contributions of TF binding sequence, location, and basal promoter strength to gene expression. We interpret the measured regulation of these TFs using a thermodynamic model of gene expression and uncover stabilization of RNA polymerase as a pervasive regulatory mechanism, common to both activating and repressing TFs. This property suggests ways to tune the dynamic range of gene expression through the interplay of stabilizing TF function and RNA polymerase basal occupancy, a phenomenon we confirm by measuring fold change for stabilizing TFs across synthetic promoter sequences spanning over 100-fold basal expression. Our work deconstructs TF function at a mechanistic level, providing foundational principles on how gene expression is realized across different promoter contexts, with implications for decoding the relationship between sequence and gene expression.

PMID:39921566 | DOI:10.1093/nar/gkaf058

Adv Sci (Weinh). 2025 Feb 8:e2411459. doi: 10.1002/advs.202411459. Online ahead of print.

ABSTRACT

Tailored droplet generation is crucial for droplet microfluidics that involve samples of varying sizes. However, the absence of precise predictive models forces droplet platforms to rely on empiricism derived from extensive experiments, underscoring the need for comprehensive modeling analysis. To address this, a novel customized assembled centrifugal step emulsifier (CASE) is presented by incorporating a "jigsaw puzzles" design to efficiently acquire large-scale experimental data. Numerical simulations are utilized to analyze fluid configurations during step emulsification, identifying a key connection tube that determines droplet size. By training and verifying with the experimental and simulation datasets, a comprehensive theoretical model is established that allows for the preliminary design of the droplet size and generation frequency with an average error rate of 4.8%, successfully filling a critical gap in existing field. This predictive model empowers the CASE to achieve all-in-one functionality, including droplet pre-design, generation, manipulation, and on-site detection. As a proof of concept, multiscale sample analysis ranging from nanoscale nucleic acids to microscale bacteria and 3D cell spheroids is realized in the CASE. In summary, this platform offers valuable guidance for customized droplet generation by centrifugal step emulsifiers and promotes the adoption of droplet microfluidics in biochemical assays.

PMID:39921431 | DOI:10.1002/advs.202411459

Adv Sci (Weinh). 2025 Feb 7:e2406021. doi: 10.1002/advs.202406021. Online ahead of print.

ABSTRACT

Re-epithelialization constitutes a critical stage in the intricate process of wound healing, yet its mechanisms in the context of diabetic wounds remain elusive. In this study, the role of the mesenchymal-epithelial transition (MET) vis-à-vis the epithelial-mesenchymal transition (EMT) of keratinocytes in diabetic wound re-epithelialization is investigated. The findings reveal an impediment in the MET process, rather than EMT, which significantly compromised re-epithelialization in diabetic wounds. Furthermore, Desmoplakin (DSP) gene expression, encoding a key desmosome protein, is down-regulated in diabetic rats. This down-regulation coincided with aberrant hypo-demethylation of the DSP promoter. The inhibition of DSP expression is linked to reduced occupancy of Ten-eleven translocation 3 (TET3) at the DSP promoter, consequently suppressing TET3-dependent DNA demethylation. Additionally, a novel lncRNA termed DSP-AS1is identified, which is antisense to DSP. Notably, DSP-AS1 expression is down-regulated in diabetic skin wounds, and it interacted with TET3, a DNA demethylase. Notably, DSP-AS1 is found to form R-loops, triple-stranded DNA:RNA hybrids, at the DSP promoter, facilitating TET3 localization to the DSP promoter. Collectively, the findings suggest that reduced R-loop formation by DSP-AS1 impairs DSP gene transcription by repressing TET3-mediated DNA demethylation. This disruption of the orchestrated re-epithelialization process contributes to refractory diabetic wound healing.

PMID:39921255 | DOI:10.1002/advs.202406021

Microbiome. 2025 Feb 7;13(1):46. doi: 10.1186/s40168-025-02043-8.

ABSTRACT

BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.

RESULTS: The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14 days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.

CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstract.

PMID:39920864 | DOI:10.1186/s40168-025-02043-8

Genome Med. 2025 Feb 7;17(1):11. doi: 10.1186/s13073-025-01435-7.

ABSTRACT

Ineffective medication is a major healthcare problem causing significant patient suffering and economic costs. This issue stems from the complex nature of diseases, which involve altered interactions among thousands of genes across multiple cell types and organs. Disease progression can vary between patients and over time, influenced by genetic and environmental factors. To address this challenge, digital twins have emerged as a promising approach, which have led to international initiatives aiming at clinical implementations. Digital twins are virtual representations of health and disease processes that can integrate real-time data and simulations to predict, prevent, and personalize treatments. Early clinical applications of DTs have shown potential in areas like artificial organs, cancer, cardiology, and hospital workflow optimization. However, widespread implementation faces several challenges: (1) characterizing dynamic molecular changes across multiple biological scales; (2) developing computational methods to integrate data into DTs; (3) prioritizing disease mechanisms and therapeutic targets; (4) creating interoperable DT systems that can learn from each other; (5) designing user-friendly interfaces for patients and clinicians; (6) scaling DT technology globally for equitable healthcare access; (7) addressing ethical, regulatory, and financial considerations. Overcoming these hurdles could pave the way for more predictive, preventive, and personalized medicine, potentially transforming healthcare delivery and improving patient outcomes.

PMID:39920778 | DOI:10.1186/s13073-025-01435-7

J Transl Med. 2025 Feb 7;23(1):166. doi: 10.1186/s12967-025-06180-4.

ABSTRACT

Prostate cancer (PCa) is a kind of malignant solid tumor commonly observed among males worldwide. The dilemma of increasing incidence with therapeutic resistance has become the leading issue in PCa clinical management. Ferroptosis is a new form of regulatory cell death caused by iron-dependent lipid peroxidation, which has a dual role in PCa evolution and treatment due to the multi-omics cascade of interactions among pathways and environmental stimuli. Hence deciphering the role of ferroptosis in carcinogenesis would provide novel insights and strategies for precision medicine and personalized healthcare against PCa. In this study, the mechanisms of ferroptosis during cancer development were summarized both at the molecular and tumor microenvironment level. Then literature-reported ferroptosis-related signatures in PCa, e.g., genes, non-coding RNAs, metabolites, natural products and drug components, were manually collected and functionally compared as drivers/inducers, suppressors/inhibitors, and biomarkers according to their regulatory patterns in PCa ferroptosis and pathogenesis. The state-of-the-art techniques for ferroptosis-related data integration, knowledge identification, and translational application to PCa theranostics were discussed from a combinative perspective of artificial intelligence-powered modelling and advanced material-oriented therapeutic scheme design. The prospects and challenges in ferroptosis-based PCa researches were finally highlighted to light up future wisdoms for the flourishing of current findings from bench to bedside.

PMID:39920771 | DOI:10.1186/s12967-025-06180-4

BMC Cancer. 2025 Feb 7;25(1):217. doi: 10.1186/s12885-025-13616-z.

ABSTRACT

BACKGROUND: The relationship between cancer development and alterations in IgG N-glycosylation has been well-established. However, comprehensive profiling of the N-glycome and N-glycoproteome in gastric cancer (GC) remains limited. Furthermore, the prognostic potential of IgG N-glycan patterns in identifying precursors to GC has yet to be fully elucidated.

METHODS: The IgG N-glycome in GC was characterized using a custom high-throughput orthogonal mass spectrometry approach. Multivariate analysis was employed to identify and assess glycomic alterations. A comprehensive bioinformatics analysis was also conducted to investigate the differential expression of N-glycosylation-related genes and their potential roles in GC pathogenesis. Additionally, interleukin-11 (IL-11) levels were quantified using a standardized enzyme-linked immunosorbent assay (ELISA).

RESULTS: Galactosylation and sialylation of IgG decreased mainly in the IgG1 and IgG2 subclasses in GC, with subclass-specific changes in IgG3 and IgG4 galactosylation. These glycan modifications were represented by unique glycopeptides (IgG1_H5N5, IgG2_H4N3F1, IgG2_H4N4, IgG2_H4N4F1S1, IgG3/4_H4N4F1, IgG3/4_H4N4F1S1), which outperformed CA72-4 for GC diagnosis. Analysis of key glycogenes revealed differential expression patterns, implicating a functional role for IgG N-glycosylation in GC. Notably, the abundance of specific IgG glycosylation exhibited a significant correlation with serum level of IL-11.

CONCLUSIONS: Alterations in subclass-specific IgG N-glycosylation represent promising biomarkers for the detection and monitoring of GC progression, potentially influenced by cytokine-driven inflammation. Understanding these changes could improve our knowledge of molecular mechanisms, aiding in diagnostic improvements and therapeutic development.

PMID:39920693 | DOI:10.1186/s12885-025-13616-z