Phys Rev Lett. 2025 Feb 14;134(6):068402. doi: 10.1103/PhysRevLett.134.068402.

ABSTRACT

The fuel-driven process of replication in living systems generates distributions of copied entities with varying degrees of copying accuracy. Here we introduce a thermodynamically consistent ensemble for investigating universal population features of template copying systems. In the context of copolymer copying, coarse-graining over molecular details, we establish a phase diagram of copying accuracy. We discover sharp non-equilibrium transitions between populations of random and accurate copies. Maintaining a population of accurate copies requires a minimum energy expenditure that depends on the configurational entropy of copolymer sequences.

PMID:40021163 | DOI:10.1103/PhysRevLett.134.068402

Cell Genom. 2025 Feb 20:100780. doi: 10.1016/j.xgen.2025.100780. Online ahead of print.

ABSTRACT

Deep learning models have advanced our ability to predict cell-type-specific chromatin patterns from transcription factor (TF) binding motifs, but their application to perturbed contexts remains limited. We applied transfer learning to predict how concentrations of the dosage-sensitive TFs TWIST1 and SOX9 affect regulatory element (RE) chromatin accessibility in facial progenitor cells, achieving near-experimental accuracy. High-affinity motifs that allow for heterotypic TF co-binding and are concentrated at the center of REs buffer against quantitative changes in TF dosage and predict unperturbed accessibility. Conversely, low-affinity or homotypic binding motifs distributed throughout REs drive sensitive responses with minimal impact on unperturbed accessibility. Both buffering and sensitizing features display purifying selection signatures. We validated these sequence features through reporter assays and demonstrated that TF-nucleosome competition can explain low-affinity motifs' sensitizing effects. This combination of transfer learning and quantitative chromatin response measurements provides a novel approach for uncovering additional layers of the cis-regulatory code.

PMID:40020686 | DOI:10.1016/j.xgen.2025.100780

Immunity. 2025 Feb 21:S1074-7613(25)00068-8. doi: 10.1016/j.immuni.2025.02.001. Online ahead of print.

ABSTRACT

Generating balanced populations of CD8+ effector and memory T cells is necessary for immediate and durable immunity to infections and cancer. Yet, a definitive understanding of how a diverse CD8+ T cell repertoire differentiates remains unclear. We identified several hundred T cell receptor (TCR) clonotypes that constitute the polyclonal response against a single antigen and found that a majority of TCR clonotypes were highly biased toward memory or effector fates. TCR-intrinsic biases were not stochastic and were dominant over environmental cues. Differential gene expression analysis of memory- or effector-biased TCR clonotypes showed bifurcation of differential fates at the early effector stage. Additionally, phylogenetic analysis revealed that memory-biased clonotypes retain their fate preferences in subclonal populations but effector-biased subclones can switch to a memory fate. Our study highlights that the polyclonal CD8+ T cell response is a composite of unbiased and biased clonotypes with varying capacity to incorporate environmental cues in their cell fate decisions.

PMID:40020673 | DOI:10.1016/j.immuni.2025.02.001

Cell. 2025 Feb 21:S0092-8674(25)00108-4. doi: 10.1016/j.cell.2025.01.039. Online ahead of print.

ABSTRACT

Space habitation provides unique challenges in built environments isolated from Earth. We produced a 3D map of the microbes and metabolites throughout the United States Orbital Segment (USOS) of the International Space Station (ISS) with 803 samples collected during space flight, including controls. We find that the use of each of the nine sampled modules within the ISS strongly drives the microbiology and chemistry of the habitat. Relating the microbiology to other Earth habitats, we find that, as with human microbiota, built environment microbiota also align naturally along an axis of industrialization, with the ISS providing an extreme example of an industrialized environment. We demonstrate the utility of culture-independent sequencing for microbial risk monitoring, especially as the location of sequencing moves to space. The resulting resource of chemistry and microbiology in the space-built environment will guide long-term efforts to maintain human health in space for longer durations.

PMID:40020666 | DOI:10.1016/j.cell.2025.01.039

Curr Opin Struct Biol. 2025 Feb 27;91:102994. doi: 10.1016/j.sbi.2025.102994. Online ahead of print.

ABSTRACT

Missense variants can affect the severity of disease, choice of treatment, and treatment outcomes. While the number of known variants has been increasing at a rapid pace, available evidence of their clinical effect has been lagging behind, constituting a challenge for clinicians and researchers. Multiplexed assays of variant effects (MAVEs) are important to close the gap; nonetheless, computational predictions of pathogenicity are still often the only available data for scoring variants. Such methods are not designed to provide a mechanistic explanation for the effect of amino acid substitutions. To this purpose, we propose structure-based frameworks as ensemble methodologies, with each method tailored to predict a different aspect among those exerted by amino acid substitutions to link predicted pathogenicity to mechanistic indicators. We review available frameworks, as well as advancements in underlying structure-based methods that predict variant effects on several protein features, such as protein stability, biomolecular interactions, allostery, post-translational modifications, and more.

PMID:40020537 | DOI:10.1016/j.sbi.2025.102994

Proc Natl Acad Sci U S A. 2025 Mar 4;122(9):e2406474122. doi: 10.1073/pnas.2406474122. Epub 2025 Feb 28.

ABSTRACT

B cells generate pathogen-specific antibodies and play an essential role in providing adaptive protection against infection. Antibody genes are modified in evolutionary processes acting on the B cell populations within an individual. These populations proliferate, differentiate, and migrate to long-term niches in the body. However, the dynamics of these processes in the human immune system are primarily inferred from mouse studies. We addressed this gap by sequencing the antibody repertoire and transcriptomes from single B cells in four immune-rich tissues from six individuals. We find that B cells descended from the same pre-B cell ("lineages") often colocalize within the same tissue, with the bone marrow harboring the largest excess of lineages without representation in other tissues. Within lineages, cells with different levels of somatic hypermutation are uniformly distributed among tissues and functional states. This suggests that the relative probabilities of localization and differentiation outcomes change negligibly during affinity maturation, and quantitatively agrees with a simple dynamical model of B cell differentiation. While lineages strongly colocalize, we find individual B cells nevertheless appear to make independent differentiation decisions. Proliferative antibody-secreting cells, however, deviate from these global patterns. These cells are often clonally expanded, their clones appear universally distributed among all sampled organs, and form lineages with an excess of cells of the same type. Collectively, our findings show the limits of peripheral blood monitoring of the immune repertoire, and provide a probabilistic model of the dynamics of antibody memory formation in humans.

PMID:40020190 | DOI:10.1073/pnas.2406474122

Sci Adv. 2025 Feb 28;11(9):eadr1938. doi: 10.1126/sciadv.adr1938. Epub 2025 Feb 28.

ABSTRACT

The Parkinson's disease-linked kinase, PINK1, is a short-lived protein that undergoes cleavage upon mitochondrial import leading to its proteasomal degradation. Under depolarizing conditions, it accumulates on mitochondria where it becomes activated, phosphorylating both ubiquitin and the ubiquitin E3 ligase Parkin, at Ser65. Our experiments reveal that in retinal pigment epithelial cells, only a fraction of PINK1 becomes stabilized after depolarization by electron transport chain inhibitors. Furthermore, the observed accrual of PINK1 cannot be completely accounted for without an accompanying increase in biosynthesis. We have used a ubiquitylation inhibitor TAK-243 to accumulate cleaved PINK1. Under these conditions, generation of unconjugated "free" phospho-ubiquitin serves as a proxy readout for PINK1 activity. This has enabled us to find a preconditioning phenomenon, whereby an initial depolarizing treatment leaves a residual pool of active PINK1 that remains competent to seed the activation of nascent cleaved PINK1 following a 16-hour recovery period.

PMID:40020067 | DOI:10.1126/sciadv.adr1938

Am J Primatol. 2025 Mar;87(3):e70013. doi: 10.1002/ajp.70013.

ABSTRACT

Facial gestures are a crucial component of primate multimodal communication. However, current methodologies for extracting facial data from video recordings are labor-intensive and prone to human subjectivity. Although automatic tools for this task are still in their infancy, deep learning techniques are revolutionizing animal behavior research. This study explores the distinctiveness of facial gestures in cotton-top tamarins, quantified using markerless pose estimation algorithms. From footage of captive individuals, we extracted and manually labeled frames to develop a model that can recognize a custom set of landmarks positioned on the face of the target species. The trained model predicted landmark positions and subsequently transformed them into distance matrices representing landmarks' spatial distributions within each frame. We employed three competitive machine learning classifiers to assess the ability to automatically discriminate facial configurations that cooccur with vocal emissions and are associated with different behavioral contexts. Initial analysis showed correct classification rates exceeding 80%, suggesting that voiced facial configurations are highly distinctive from unvoiced ones. Our findings also demonstrated varying context specificity of facial gestures, with the highest classification accuracy observed during yawning, social activity, and resting. This study highlights the potential of markerless pose estimation for advancing the study of primate multimodal communication, even in challenging species such as cotton-top tamarins. The ability to automatically distinguish facial gestures in different behavioral contexts represents a critical step in developing automated tools for extracting behavioral cues from raw video data.

PMID:40019116 | DOI:10.1002/ajp.70013

Am J Physiol Cell Physiol. 2025 Feb 28. doi: 10.1152/ajpcell.00308.2024. Online ahead of print.

ABSTRACT

Skeletal muscle microtissues are engineered to develop therapies for restoring muscle function in patients. However, optimal electrical field stimulation (EFS) parameters to evaluate the function of muscle microtissues remain unestablished. This study reports a protocol to optimize EFS parameters for eliciting contractile force of muscle microtissues cultured in micropost platforms. Muscle microtissues were produced across an opposing pair of microposts in polydimethylsiloxane and polymethyl methacrylate culture platforms using primary, immortalized, and induced pluripotent stem cell-derived myoblasts. In response to EFS between needle electrodes, contraction deflects microposts proportional to developed force. At 5 V, pulse durations used for native muscle (0.1-1 ms) failed to elicit contraction of microtissues; durations reported for engineered muscle (5-10 ms) failed to elicit peak force. Instead, pulse durations of 20-80 ms were required to elicit peak twitch force across microtissues derived from 5 myoblast lines. Similarly, while peak tetanic force occurs at 20-50 Hz for native human muscles, it varied across microtissues depending on the cell line type, ranging from 7-60 Hz. A new parameter, the dynamic oscillation of force, captured trends during rhythmic contractions, while quantifying the duration-at-peak force provides an extended kinetics parameter. Our findings indicate that muscle microtissues have cell line type-specific contractile properties, yet all contract and relax more slowly than native muscle, implicating underdeveloped excitation-contraction coupling. Failure to optimize EFS parameters can mask the functional potential of muscle microtissues by underestimating force production. Optimizing and reporting EFS parameters and metrics is necessary to leverage muscle microtissues for advancing skeletal muscle therapies.

PMID:40019026 | DOI:10.1152/ajpcell.00308.2024

J Integr Neurosci. 2025 Feb 19;24(2):36279. doi: 10.31083/JIN36279.

NO ABSTRACT

PMID:40018783 | DOI:10.31083/JIN36279

Chem Biomed Imaging. 2024 Dec 19;3(2):111-122. doi: 10.1021/cbmi.4c00077. eCollection 2025 Feb 24.

ABSTRACT

The COVID-19 pandemic has underscored the importance of in-depth research into the proteins encoded by coronaviruses (CoV), particularly the highly conserved nonstructural CoV proteins (nsp). Among these, the nsp13 helicase of severe pathogenic MERS-CoV, SARS-CoV-2, and SARS-CoV is one of the most preserved CoV nsp. Utilizing single-molecule FRET, we discovered that MERS-CoV nsp13 unwinds DNA in distinct steps of about 9 bp when ATP is employed. If a different nucleotide is introduced, these steps diminish to 3-4 bp. Dwell-time analysis revealed 3-4 concealed steps within each unwinding process, which suggests the hydrolysis of 3-4 dTTP. Combining our observations with previous studies, we propose an unwinding model of CoV nsp13 helicase. This model suggests that the elongated and adaptable 1B-stalk of nsp13 may enable the 1B remnants to engage with the unwound single-stranded DNA, even as the helicase core domain has advanced over 3-4 bp, thereby inducing accumulated strain on the nsp13-DNA complex. Our findings provide a foundational framework for determining the unwinding mechanism of this unique helicase family.

PMID:40018651 | PMC:PMC11863148 | DOI:10.1021/cbmi.4c00077

Front Mol Neurosci. 2025 Feb 13;18:1544971. doi: 10.3389/fnmol.2025.1544971. eCollection 2025.

ABSTRACT

INTRODUCTION: Growing recognition of microglia's role in neurodegenerative disorders has accentuated the need to characterize microglia profiles and their influence on pathogenesis. To understand changes observed in the microglial profile during the progression of synucleinopathies, microglial gene expression and DNA methylation were examined in the mThy1-α-synuclein mouse model.

METHODS: Disease progression was determined using behavioral tests evaluating locomotor deficits before DNA and RNA extraction at 7 and 10 months from isolated microglia for enzymatic methyl-sequencing and RNA-sequencing.

RESULTS: Pathway analysis of these changes at 7 months indicates a pro-inflammatory profile and changes in terms related to synaptic maintenance. Expression and methylation at both 7 and 10 months included terms regarding mitochondrial and metabolic stress. While behavior symptoms progressed at 10 months, we see many previously activated pathways being inhibited in microglia at a later stage, with only 8 of 53 shared pathways predicted to be directionally concordant. Despite the difference in pathway directionality, 21 of the 22 genes that were differentially expressed and annotated to differentially methylated regions at both 7 and 10 months had conserved directionality changes.

DISCUSSION: These results highlight a critical period in disease progression, during which the microglia respond to α-synuclein, suggesting a transition in the role of microglia from the early to late stages of the disease.

PMID:40018011 | PMC:PMC11865073 | DOI:10.3389/fnmol.2025.1544971

Front Oral Health. 2025 Feb 13;6:1543667. doi: 10.3389/froh.2025.1543667. eCollection 2025.

ABSTRACT

INTRODUCTION: Derivatives from Saccharomyces cerevisiae yeast including yeast extracts and yeast cell walls are sustainable sources of valuable nutrients, including dietary fibers and proteins. Previous studies have shown that certain components from these yeast derivatives can inhibit the growth of harmful intestinal bacteria and promote the growth of beneficial bacteria. However, the effects of yeast derivatives on oral health have not yet been investigated.

METHODS: An in vitro oral biofilm model was employed to examine the impacts of yeast derivatives on the oral microbiota and their potential benefits for maintaining oral homeostasis. The model incorporated dental plaque donor material from both healthy and periodontitis diagnosed individuals. Biofilm formation, density, and microbial composition were quantified. Additionally, the production of short-chain fatty acids in the biofilm supernatants was measured.

RESULTS: Yeast extracts had only minor effects on oral biofilm formation. In contrast, yeast cell wall derivatives, which are rich in polysaccharides such as beta-glucans and mannans, significantly reduced the density of the oral biofilms in vitro. This reduction in biofilm density was associated with an overall shift in the bacterial community composition, including an increase in beneficial bacteria and a decrease in the abundance of Tannerella forsythia, an important species involved in bacterial coaggregation and the development and maturation of the oral biofilm. Furthermore, the yeast cell wall derivatives decreased the production of short-chain fatty acids, including acetic and butyric acid. These findings were consistent across both healthy and periodontitis microbiomes.

CONCLUSION: This study has demonstrated the potential of yeast cell wall derivatives to positively impact oral health by significantly reducing biofilm density, modulating the oral microbial composition, and decreasing the production of short-chain fatty acids. The observed effects highlight the promising applications of these yeast-based compounds as an approach to managing oral diseases. Further research is needed to fully elucidate the mechanisms of action and explore the clinical potential of yeast cell wall derivatives in promoting and maintaining oral health.

PMID:40017617 | PMC:PMC11865069 | DOI:10.3389/froh.2025.1543667

Alzheimers Res Ther. 2025 Feb 27;17(1):52. doi: 10.1186/s13195-025-01697-8.

ABSTRACT

BACKGROUND: Recent studies have focused on improving our understanding of gut microbiome dysbiosis and its impact on cognitive function. However, the relationship between gut microbiome composition, accelerated brain atrophy, and cognitive function has not yet been fully explored.

METHODS: We recruited 292 participants from South Korean memory clinics to undergo brain magnetic resonance imaging, clinical assessments, and collected stool samples. We employed a pretrained brain age model- a measure associated with neurodegeneration. Using cluster analysis, we categorized individuals based on their microbiome profiles and examined the correlations with brain age, Mental State Examination (MMSE) scores, and the Clinical Dementia Rating Sum of Box (CDR-SB).

RESULTS: Two clusters were identified in the microbiota at the phylum level that showed significant differences on a few microbiotas phylum. Greater gut microbiome dysbiosis was associated with worse cognitive function including MMSE and CDR-SB; this effect was partially mediated by greater brain age even when accounting for chronological age, sex, and education.

CONCLUSIONS: Our findings indicate that brain age mediates the link between gut microbiome dysbiosis and cognitive performance. These insights suggest potential interventions targeting the gut microbiome to alleviate age-related cognitive decline.

PMID:40016766 | DOI:10.1186/s13195-025-01697-8

BMC Biol. 2025 Feb 27;23(1):62. doi: 10.1186/s12915-025-02168-0.

ABSTRACT

BACKGROUND: Melanin pigmentation in oocytes is a critical feature for both the esthetic and developmental aspects of oocytes, influencing their polarity and overall development. Despite substantial knowledge of melanogenesis in melanocytes and retinal pigment epithelium cells, the molecular mechanisms underlying oocyte melanogenesis remain largely unknown.

RESULTS: Here, we compare the oocytes of wild-type, tyr-/- and mitf-/- Xenopus tropicalis and found that mitf-/- oocytes exhibit normal melanin deposition at the animal pole, whereas tyr-/- oocytes show no melanin deposition at this site. Transmission electron microscopy confirmed that melanogenesis in mitf-/- oocytes proceeds normally, similar to wild-type oocytes. Transcriptomic analysis revealed that mitf-/- oocytes still express melanogenesis-related genes, enabling them to complete melanogenesis. Additionally, in Xenopus tropicalis oocytes, the expression of the MiT subfamily factor tfe3 is relatively high, while tfeb, mitf, and tfec levels are extremely low. The expression pattern of tfe3 is similar to that of tyr and other melanogenesis-related genes. Thus, melanogenesis in Xenopus tropicalis oocytes is independent of Mitf and may be regulated by other MiT subfamily factors such as Tfe3, which control the expression of genes like tyr, dct, and tyrp1. Furthermore, transcriptomic data revealed that changes in the expression of genes related to mitochondrial cloud formation represent the most significant molecular changes during oocyte development.

CONCLUSIONS: Overall, these findings suggest that further elucidation of Tyr-dependent and Mitf-independent mechanisms of melanin deposition at the animal pole will enhance our understanding of melanogenesis and Oogenesis.

PMID:40016733 | DOI:10.1186/s12915-025-02168-0

Cell Res. 2025 Feb 28. doi: 10.1038/s41422-025-01084-w. Online ahead of print.

ABSTRACT

The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights into the step-wise assembly, catalytic splicing and final disassembly of the spliceosome. However, the molecular details of how the spliceosome recognizes and rejects suboptimal splicing substrates remained unclear. Here, we show cryo-electron microscopy structures of spliceosomal quality control complexes from a thermophilic eukaryote, Chaetomium thermophilum. The spliceosomes, henceforth termed B*Q, are stalled at a catalytically activated state but prior to the first splicing reaction due to an aberrant 5' splice site conformation. This state is recognized by G-patch protein GPATCH1, which is docked onto PRP8-EN and -RH domains and has recruited the cognate DHX35 helicase to its U2 snRNA substrate. In B*Q, DHX35 has dissociated the U2/branch site helix, while the disassembly helicase DHX15 is docked close to its U6 RNA 3'-end substrate. Our work thus provides mechanistic insights into the concerted action of two spliceosomal helicases in maintaining splicing fidelity by priming spliceosomes that are bound to aberrant splice substrates for disassembly.

PMID:40016598 | DOI:10.1038/s41422-025-01084-w

Commun Med (Lond). 2025 Feb 27;5(1):49. doi: 10.1038/s43856-025-00764-3.

ABSTRACT

BACKGROUND: Accurately recognizing that a person may be dying is central to improving their experience of care at the end-of-life. However, predicting dying is frequently inaccurate and often occurs only hours or a few days before death.

METHODS: We performed urinary metabolomics analysis on patients with lung cancer to create a metabolite model to predict dying over the last 30 days of life.

RESULTS: Here we show a model, using only 7 metabolites, has excellent accuracy in the Training cohort n = 112 (AUC = 0·85, 0·85, 0·88 and 0·86 on days 5, 10, 20 and 30) and Validation cohort n = 49 (AUC = 0·86, 0·83, 0·90, 0·86 on days 5, 10, 20 and 30). These results are more accurate than existing validated prognostic tools, and uniquely give accurate predictions over a range of time points in the last 30 days of life. Additionally, we present changes in 125 metabolites during the final four weeks of life, with the majority exhibiting statistically significant changes within the last week before death.

CONCLUSIONS: These metabolites identified offer insights into previously undocumented pathways involved in or affected by the dying process. They not only imply cancer's influence on the body but also illustrate the dying process. Given the similar dying trajectory observed in individuals with cancer, our findings likely apply to other cancer types. Prognostic tests, based on the metabolites we identified, could aid clinicians in the early recognition of people who may be dying and thereby influence clinical practice and improve the care of dying patients.

PMID:40016594 | DOI:10.1038/s43856-025-00764-3

Lab Anim (NY). 2025 Feb 27. doi: 10.1038/s41684-025-01506-7. Online ahead of print.

ABSTRACT

HSALR mice are the most broadly used animal model for studying myotonic dystrophy type I (DM1). However, so far, HSALR preclinical studies have often excluded female mice or failed to document the biological sex of the animals. This leaves an unwanted knowledge gap concerning the differential development of DM1 in males and females, particularly considering that the disease has a different clinical presentation in men and women. Here we compared typical functional measurements, histological features, molecular phenotypes and biochemical plasma profiles in the muscles of male and female HSALR mice in search of any significant between-sex differences that could justify this exclusion of female mice in HSALR studies and, critically, in candidate therapy assays performed with this model. We found no fundamental differences between HSALR males and females during disease development. Both sexes presented comparable functional and tissue phenotypes, with similar molecular muscle profiles. The only sex differences and significant interactions observed were in plasma biochemical parameters, which are also intrinsically variable in patients with DM1. In addition, we tested the influence of age on these measurements. We therefore suggest including female HSALR mice in regular DM1 studies, and recommend documenting the sex of animals, especially in studies focusing on metabolic alterations. This will allow researchers to detect and report any potential differences between male and female HSALR mice, especially regarding the efficacy of experimental treatments that could be relevant to patients with DM1.

PMID:40016516 | DOI:10.1038/s41684-025-01506-7

Nat Med. 2025 Feb 27. doi: 10.1038/s41591-025-03530-z. Online ahead of print.

ABSTRACT

Brain metastases frequently develop in patients with non-small cell lung cancer (NSCLC) and are a common cause of cancer-related deaths, yet our understanding of the underlying human biology is limited. Here we performed multimodal single-nucleus RNA and T cell receptor, single-cell spatial and whole-genome sequencing of brain metastases and primary tumors of patients with treatment-naive NSCLC. Chromosomal instability (CIN) is a distinguishing genomic feature of brain metastases compared with primary tumors, which we validated through integrated analysis of molecular profiling and clinical data in 4,869 independent patients, and a new cohort of 12,275 patients with NSCLC. Unbiased analyses revealed transcriptional neural-like programs that strongly enriched in cancer cells from brain metastases, including a recurring, CINhigh cell subpopulation that preexists in primary tumors but strongly enriched in brain metastases, which was also recovered in matched single-cell spatial transcriptomics. Using multiplexed immunofluorescence in an independent cohort of treatment-naive pairs of primary tumors and brain metastases from the same patients with NSCLC, we validated genomic and tumor-microenvironmental findings and identified a cancer cell population characterized by neural features strongly enriched in brain metastases. This comprehensive analysis provides insights into human NSCLC brain metastasis biology and serves as an important resource for additional discovery.

PMID:40016452 | DOI:10.1038/s41591-025-03530-z

EMBO Rep. 2025 Feb 27. doi: 10.1038/s44319-025-00389-6. Online ahead of print.

NO ABSTRACT

PMID:40016427 | DOI:10.1038/s44319-025-00389-6