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Table of Contents — June 17, 2025, 122 (24) | PNAS

Table Of Contents Page, PNAS Volume 122, Number 24

PNAS June 17, 2025

This Week in PNAS

Opinion

QnAs

Commentaries

Perspective

Through the industrial era, pollutants have been unevenly distributed in the environment, disproportionately impacting disenfranchised communities. Redressing the unequal distribution of environmental pollution is thus a question of environmental justice ...

Letters

Brief Reports

Recognition of epitopic peptide antigens presented on class I major histocompatibility complex (MHC-I) proteins by T cell receptors (TCRs) forms the cornerstone of immune surveillance, leading to a plethora of adaptive immune responses. Characterization ...
The union of two or more different nuclear genomes with maternally inherited organellar genomes may lead to cytonuclear incompatibilities in plant allopolyploids. These incompatibilities may be reconciled by coevolutionary responses at the genomic and ...
The Mitochondrial Antiviral Signaling Protein (MAVS) is a key adaptor in antiviral immunity, mediating type I interferon responses downstream of RIG1 and TLR3. While MAVS regulation is essential for antiviral defense, its modulation in keratinocytes is ...
Efficient targeted integration (TI) of homologous donor DNA is crucial for precise genome editing. Although mismatch repair (MMR) is known to suppress TI as well as homologous recombination (HR) when sequence divergence is present, it remains ...

Physical Sciences

Applied Physical Sciences

The wave-like behavior of matter in quantum physics has spurred insightful analogies between the dynamics of particles and waves in classical systems. In this study, drawing inspiration from synchrotrons that resonate to accelerate ions along a closed ...
Reflection and refraction are ubiquitous phenomena with extensive applications, yet minimizing energy loss and information distortion during these processes remains a significant challenge. This study examines the behavior of structurally stable solitons, ...

Biophysics and Computational Biology

Ryanodine receptors (RyRs) are intracellular Ca2+ channels essential for muscle contraction. Caffeine, a xanthine derivative, has been known for decades to increase muscle contraction and enhance activation of RyRs by increasing the sensitivity to Ca2+. ...
Biological microswimmers exhibit intricate taxis behaviors in response to environmental stimuli and swim in complex trajectories to navigate their environment. How microswimmers respond to stimulus instantaneously, and how adaptation to stimulus ...
Intermediate filaments are key regulators of cell mechanics. Vimentin, a type of intermediate filament expressed in mesenchymal cells and involved in migration, forms a dense network in the cytoplasm that is constantly remodeling through filament ...
A hallmark feature of active matter systems is the ability of individual elements to interact and organize over length scales exceeding that of the constituent molecular players. However, the nature of internal redistribution that occurs in the bulk of ...
The early detection of high-fitness viral variants is critical for pandemic response, yet limited experimental resources at the onset of variant emergence hinder effective identification. To address this, we introduce an active learning framework, VIRAL (...
Effector-Triggered Immunity (ETI) is an important part of the plant immune system, allowing plants to sense and respond to harmful pathogen proteins known as “effectors.” Effectors can be sensed directly or indirectly by NLR (Nucleotide-binding Leucine-...

Chemistry

The breaking of translational symmetry at oxide surfaces gives rise to coordinatively unsaturated cations/anions and surface restructuring—key factors that govern surface reactivity. Using direct in situ environmental transmission electron microscopy (TEM)...
The FeMo cofactor (FeMoco), the key active site in the Mo-based nitrogenase, is one of the most complicated metalloenzyme molecules. Synthesis of the FeMoco model cluster ([MoFe7S9C]) is essential to understanding its function in dinitrogen binding, ...
Breast cancer has now overtaken lung cancer as the “world’s leading cancer,” yet detecting and implementing effective therapies remains a significant challenge. Substantial advances have been made in photothermal therapy (PTT), where photosensitizers use ...
Emergent patterns in biological systems arise through dissipative processes that balance reaction and transport phenomena, producing highly functional properties from self-regulating mechanisms. Synthetic fabrication, by contrast, often relies on user-...

Computer Sciences

For biomedical applications, new link prediction algorithms are continuously being developed. These algorithms are typically evaluated computationally, using test sets generated by sampling the edges uniformly at random. However, as we demonstrate, this ...

Earth, Atmospheric, and Planetary Sciences

Reduction of China’s SO2 emissions has been found to nonlinearly decrease the atmospheric sulfate (SO42−) aerosol concentrations in East Asia. Compared to Europe and North America, the lower effectiveness of SO42− reduction in East Asia suggested much ...
Macromolecular organic solids found in primitive meteorites were the main source of carbon delivered to forming planets in the early Solar System. However, the conditions under which this material formed and its subsequent incorporation into growing ...
Mass-independent isotope fractionation (MIF) enables powerful geochemical tracers for various geological and planetary problems, yet the mechanisms driving MIF for tin (Sn) remain ambiguous. Here, we demonstrate that distinct Sn isotope fractionation ...
Human emissions continue to influence Earth’s climate. Effective radiative forcing quantifies the effect of such anthropogenic emissions together with natural factors on Earth’s energy balance. Evaluating the exact rate of effective radiative forcing is ...

Engineering

The anomalous Hall effect (AHE), a hallmark of time-reversal symmetry breaking, has been reported in rutile RuO2, a debated metallic altermagnetic candidate. Previously, AHE in RuO2 was observed only in strain-relaxed thick films under extremely high ...
Spatial ordering of matter elicits exotic properties sometimes absent from a material’s constituents. A few highly mineralized natural materials achieve high toughness through delocalized damage, whereas synthetic particulate composites must trade ...
Grain growth in polycrystals is traditionally considered a capillarity-driven process, where grain boundaries (GBs) migrate toward their centers of curvature (i.e., mean curvature flow) with a velocity proportional to the local curvature (including ...
Hydrogen embrittlement (HE) remains a critical scientific challenge in building reliable infrastructure for a carbon-free hydrogen economy. Predictive models for hydrogen-induced material failure are still lacking, largely due to an incomplete ...
Injuries affecting the central nervous system may disrupt neural pathways to muscles causing motor deficits. Yet the brain exhibits sensorimotor rhythms (SMRs) during movement intents, and brain–computer interfaces (BCIs) can decode SMRs to control ...

Environmental Sciences

Reduction of China’s SO2 emissions has been found to nonlinearly decrease the atmospheric sulfate (SO42−) aerosol concentrations in East Asia. Compared to Europe and North America, the lower effectiveness of SO42− reduction in East Asia suggested much ...
The β-N-methylamino-L-alanine (BMAA) is an emerging neurotoxin associated with human neurodegenerative diseases such as Alzheimer’s disease. Here, we report the prevalence of BMAA synthesis in protein forms by marine diatoms and reconstruct its tentative ...

Mathematics

We give an explicit counterexample to the bunkbed conjecture introduced by Kasteleyn in 1985. The counterexample is given by a planar graph on 7,222 vertices and is built on the recent work of Hollom (2024).

Statistics

The correlation between synonymous codon usage and secondary structure in translated proteins has been widely demonstrated. This usage plays a capital role in tuning translational rates and protein folding kinetics, indirectly influencing multiple ...
Characterizing the feedback linking human behavior and the transmission of infectious diseases (i.e., behavioral changes) remains a significant challenge in computational and mathematical epidemiology. Existing behavioral epidemic models often lack real-...

Sustainability Science

Sub-Saharan Africa (SSA) has the world’s largest projected increase in demand for food. Increased dependence on imports makes SSA vulnerable to geopolitical and economic risks, while further expansion of agricultural land is environmentally harmful. ...

Social Sciences

Anthropology

The domestication of pigs (Sus scrofa) has had profound socioeconomic and ecological consequences. Although pigs are believed to have been independently domesticated in South China, the timing and initial mechanisms of this process remain debated. This ...

Demography

Though racial disparities in shortened life expectancy have been well established, racial disparities in the burden of bereavement after such premature deaths are severely understudied. This is, in part, due to a lack of measurement tools for ...
In vitro fertilization (IVF) affects human fertility by 1) increasing the probability of multiple births through the transfer of multiple embryos, 2) raising the proportion of dizygotic twins, which leads to a higher occurrence of one-boy-one-girl twins, ...

Economic Sciences

As the renewable energy transition continues into less receptive communities, local opposition is expected to intensify, potentially slowing the process. Since the local impacts are neither well quantified nor widely recognized, we lack policies and ...

Psychological and Cognitive Sciences

AI systems, particularly large language models (LLMs), are increasingly being employed in high-stakes decisions that impact both individuals and society at large, often without adequate safeguards to ensure safety, quality, and equity. Yet LLMs ...
Sporting events are powerful social phenomena that extend beyond the game itself, offering a unique lens to study collective emotional dynamics. We examine emotional alignment among football fans during a high-stakes match in Brazil, focusing on both the ...

Social Sciences

Recent studies suggest large language models (LLMs) can generate human-like responses, aligning with human behavior in economic experiments, surveys, and political discourse. This has led many to propose that LLMs can be used as surrogates or simulations ...
Evolution of complexity in human languages has been vigorously debated, including the proposal that complexity can build in small, isolated populations but is often lost in situations of language contact. If it is generally true that small, isolated ...

Sustainability Science

We use a globally consistent dataset—Google Environmental Insights Explorer—to quantify how urban form and transport infrastructure affect walking and cycling rates in 11,587 cities from 121 countries across six continents. At the city level, population ...

Biological Sciences

Agricultural Sciences

Sub-Saharan Africa (SSA) has the world’s largest projected increase in demand for food. Increased dependence on imports makes SSA vulnerable to geopolitical and economic risks, while further expansion of agricultural land is environmentally harmful. ...

Applied Biological Sciences

In utero gene editing has the potential to modify disease-causing genes in multiple developing tissues before birth, possibly allowing for normal organ development, disease improvement, and conceivably, cure. In cystic fibrosis (CF), a disease that arises ...

Biochemistry

Subcellular compartmentalization is integral to the spatial regulation of mechanistic target of rapamycin (mTOR) signaling. However, the biological outputs associated with location-specific mTOR signaling events are poorly understood and challenging to ...
PARP7 is an enzyme that uses donor substrate NAD+ to attach a single ADP-ribose moiety onto proteins related to immunity, transcription, and cell growth and motility. Despite the importance of PARP7 in these processes, PARP7 signaling networks remain ...
The endopeptidase activity of ADAM (a disintegrin and metalloproteinase)-17, the primary processor of several EGFR ligands and tumor necrosis factor-alpha (TNF-α), is essential for proper embryonic development and immune regulation. Dysregulated ADAM17 ...
GCN5-related N-acetyltransferases (GNATs) are essential for regulating bacterial metabolism by acetylating specific target proteins. Despite their importance in bacterial physiology, the mechanisms behind their enzymatic and regulatory functions remain ...
Cancer therapy is limited by resistance to standard-of-care chemotherapeutic and/or by treatment-associated toxicity. Identifying molecular mechanisms that modulate cellular toxicity is crucial for enhancing treatment efficacy. We characterize CDADC1, a ...
Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated ...
The limited doubling capacity of human cells, known as replicative senescence or cellular senescence, is a major factor in cellular aging. This process is triggered by telomere erosion, which activates a p53-mediated DNA damage response (DDR) that halts ...

Biophysics and Computational Biology

Biological microswimmers exhibit intricate taxis behaviors in response to environmental stimuli and swim in complex trajectories to navigate their environment. How microswimmers respond to stimulus instantaneously, and how adaptation to stimulus ...
Intermediate filaments are key regulators of cell mechanics. Vimentin, a type of intermediate filament expressed in mesenchymal cells and involved in migration, forms a dense network in the cytoplasm that is constantly remodeling through filament ...
For biomedical applications, new link prediction algorithms are continuously being developed. These algorithms are typically evaluated computationally, using test sets generated by sampling the edges uniformly at random. However, as we demonstrate, this ...
The correlation between synonymous codon usage and secondary structure in translated proteins has been widely demonstrated. This usage plays a capital role in tuning translational rates and protein folding kinetics, indirectly influencing multiple ...
The early detection of high-fitness viral variants is critical for pandemic response, yet limited experimental resources at the onset of variant emergence hinder effective identification. To address this, we introduce an active learning framework, VIRAL (...
Munc13 family proteins are crucial for the secretion of neurotransmitters and hormones necessary for cell communication. They share a conserved C-terminal region that includes C2 and the MUN domains, which facilitate membrane interactions and the assembly ...
PKD2 is a member of the polycystin subfamily of transient receptor potential (TRP) ion channel subunits which traffic and function in primary cilia organelle membranes. Millions of individuals carry pathogenic genetic variants in PKD2 that cause a life-...
The relationship between genotype and phenotype remains an outstanding question for organism-level traits because these traits are generally complex. The challenge arises from complex traits being determined by a combination of multiple genes (or loci), ...
Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pretrained on large-scale biological sequences can capture evolutionary conservation and offer cross-species prediction better than ...
Cushing’s syndrome (CS) is an abnormal condition characterized by elevated cortisol levels, often resulting from genetic alterations in the PRKACA gene, which encodes the catalytic subunit of cAMP-dependent protein kinase A (PKA-C). The most common CS ...

Cell Biology

Necroptosis and apoptosis are two alternatively regulated cell death pathways. Activation of RIPK1 upon engagement of TNFR1 by TNFα may promote necroptosis by interacting with RIPK3 or apoptosis by activating caspases. RIPK1 is extensively regulated by a ...
Tumor-infiltrating nerves play a critical role in cancer progression and treatment resistance. Our recent work identified ALKAL2, a ligand for the Anaplastic Lymphoma Kinase (ALK) receptor, as a key mediator of inflammatory pain, with its expression ...
Cellular senescence, a major contributor to aging and age-related pathologies, is characterized by irreversible proliferative arrest and a disease-linked, proinflammatory profile known as the Senescence Associated Secretory Phenotype (SASP). A critical ...

Developmental Biology

Germ cells transmit genetic information to offspring and maintain the genome of the species. In many animals including Drosophila, germ cell formation relies on maternal determinants in the germ plasm. Several proteins present in the germ plasm of oocytes ...
Antlers, a male deer secondary sex characteristic, are unique mammalian appendages that fully regenerate annually, under androgen regulation. Stem cells located in the antlerogenic periosteum (AP), a tissue overlaying the frontal crest of both male and ...

Ecology

The β-N-methylamino-L-alanine (BMAA) is an emerging neurotoxin associated with human neurodegenerative diseases such as Alzheimer’s disease. Here, we report the prevalence of BMAA synthesis in protein forms by marine diatoms and reconstruct its tentative ...
Bald cypress (Taxodium distichum) is the longest-lived tree species in Eastern North America, but coastal cypress forests are vulnerable to a range of environmental factors [D. W. Stahle et al., Q. Sci. Rev. 34, 1–15 (2012)]. Here, we present analyses of ...
Many dynamical systems can exist in alternative regimes for which small changes in an environmental driver can cause sudden jumps between regimes. In ecology, predicting the regime of population fluctuations under unobserved levels of an environmental ...
Resource fluctuations are ubiquitous in nature and yet are generally assumed to play a limited role in the maintenance of biodiversity. We challenge this assumption by analyzing resource competition dynamics under conditions where prevailing theory does ...
The growth of populations and organisms often depends on their previous history of environmental exposure: a phenomenon referred to as “phenotypic memory.” The field of ecology presently lacks a mechanistic theory describing phenotypic memory and, as such,...
The discovery of transgenerational epigenetic inheritance and the unraveling of its molecular mechanisms are currently solving previously puzzling challenges that Mendelian genetics based solely on DNA could not explain, leading to significant paradigm ...

Evolution

Evolution of complexity in human languages has been vigorously debated, including the proposal that complexity can build in small, isolated populations but is often lost in situations of language contact. If it is generally true that small, isolated ...
Species invasions spur costly and labor-intensive control efforts, yet even local eradication is seldom achieved. When control measures are initially effective, they may drive evolutionary adaptation that prevents full eradication, as has been documented ...
Although it is widely recognized that nutritional symbionts can manipulate host reproduction, the underlying molecular and cellular mechanisms are largely unclear. The facultative symbiont Hamiltonella in bacteriocyte induces female-biased sex ratio of ...
Many eukaryotic species undergo programmed elimination of specific chromosomes during embryogenesis, typically retaining these chromosomes only in their germ cells. In some species, programmatic elimination of GRCs, or sex chromosomes, also occurs in a ...
Polyploidization (whole-genome duplication, WGD) is a widespread large-effect macromutation with far-reaching genomic, phenotypic, and evolutionary consequences. Yet, we do not know whether the consistent phenotypic changes that are associated with ...
Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is ...

Genetics

Polygenic risk scores (PRS) are essential tools for estimating individual susceptibility to complex diseases by aggregating the effects of many genetic variants. With the advent of whole-genome sequencing (WGS), rare and de novo variants can now be ...

Immunology and Inflammation

Periodontitis, a prevalent chronic inflammatory disease, profoundly impacts both quality of life and overall health. Clinical studies have suggested a correlation between periodontitis and sleep deficiency, but the underlying mechanisms involved remain ...
Alveolar macrophages (AMs) are indispensable to prevent pulmonary alveolar proteinosis and clear inhaled pathogens. Receptor for activated C kinase 1 (RACK1) is a versatile adaptor protein that regulates multiple signaling pathways. Whether RACK1 is ...

Medical Sciences

AI systems, particularly large language models (LLMs), are increasingly being employed in high-stakes decisions that impact both individuals and society at large, often without adequate safeguards to ensure safety, quality, and equity. Yet LLMs ...
Lipoprotein retention in Bruch’s membrane is a key event in the pathobiology of early and intermediate age-related macular degeneration (AMD). However, the mechanism of lipoprotein retention in BrM is unknown. Given the established role of ...
Age-related macular degeneration (AMD) is a leading cause of blindness among the elderly. It is characterized by degeneration of the retinal pigment epithelium (RPE), which can develop into choroidal neovascularization (CNV) to cause severe and rapid ...
In situ T cell transfection methods overcome the complexity and high costs associated with conventional chimeric antigen receptor (CAR)-T therapy. However, the in situ CAR-T cell approach operates within the patient’s complex immune environment and ...

Microbiology

The OXA β-lactamases in Acinetobacter baumannii represent a primary mechanism for resistance to the carbapenems, a class of antibiotics that represent a last line for treatment. In a screen of an U.S. Food and Drug Administration (FDA)-approved drug ...
Human cytomegalovirus (HCMV) is a prevalent pathogen that chronically infects the majority of human population. Among the many features that allow such widespread HCMV infection, one is its ability to maintain a transcriptionally dormant immune-evasive ...
The α-hemolysin (HlyA) of uropathogenic Escherichia coli (UPEC) is a pore-forming toxin (PFT) that is thought to function by disrupting the host cell plasma membrane. Although CD18 (LFA-1) has been implicated as a receptor on myeloid cells, the mechanisms ...
A cure for chronic hepatitis B requires eliminating or permanently silencing covalently closed circular DNA (cccDNA). A pivotal target of this approach is the hepatitis B virus (HBV) X protein (HBx), which is a key factor that promotes transcription from ...
Positive-strand RNA viruses are important pathogens of humans and plants. These viruses built viral replication organelles (VROs) with the help of co-opted host proteins and intracellular membranes to support robust virus replication in infected cells. ...
In recent years, the number of newly discovered systems that bacteria use to combat bacteriophages is increasing at an impressive rate. To obtain mechanistic insights into several antiphage systems identified in previous studies, we isolated 66 phage ...
Mycobacterium leprae, the causative agent of leprosy, has never been cultured in vitro, posing significant challenges for genetic manipulation and drug discovery. Current antileprosy drug screening methods relying on microscopic count, radiorespirometry, ...

Neuroscience

Injuries affecting the central nervous system may disrupt neural pathways to muscles causing motor deficits. Yet the brain exhibits sensorimotor rhythms (SMRs) during movement intents, and brain–computer interfaces (BCIs) can decode SMRs to control ...
Reading is one of the most complex skills that we utilize daily, and it involves the early development and interaction of various lower-level subskills, including phonological processing and oral language. These subskills recruit brain structures, which ...
Our understanding of neural circuits that respond to skin dysfunction, triggering itch, and pathophysiological scratching remains incomplete. Here, we describe a profound chronic itch phenotype in transgenic mice expressing the tetracycline transactivator ...
To decide how to move around the world, we must determine which locomotive actions (e.g., walking, swimming, or climbing) are afforded by the immediate visual environment. The neural basis of our ability to recognize locomotive affordances is unknown. ...

Pharmacology

Ryanodine receptors (RyRs) are intracellular Ca2+ channels essential for muscle contraction. Caffeine, a xanthine derivative, has been known for decades to increase muscle contraction and enhance activation of RyRs by increasing the sensitivity to Ca2+. ...
The chemokine receptor CXCR4 is overexpressed in many cancers and contributes to pathogenesis, disease progression, and resistance to therapies. CXCR4 is known to form oligomers, but the potential functional relevance in malignancies remains elusive. ...

Physiology

Liver biology is functionally linked to lactation, as liver size and metabolic output increase during lactation to support synthesis of breast milk. Upon weaning, the rodent liver returns to baseline homeostasis via hepatocyte cell death, in a process ...

Plant Biology

Effector-Triggered Immunity (ETI) is an important part of the plant immune system, allowing plants to sense and respond to harmful pathogen proteins known as “effectors.” Effectors can be sensed directly or indirectly by NLR (Nucleotide-binding Leucine-...
SMAX1-LIKE (SMXL) proteins in plants are cellular signaling hubs, many of which are posttranslationally regulated by karrikins from smoke, the plant hormones strigolactones (SLs), and/or cues such as light and nutrients. SMXL proteins control diverse ...
21-nt phasiRNAs are abundantly expressed in anthers and play crucial roles in anther development and male reproduction in grasses. In maize, the target genes that 21-nt phasiRNAs regulate remain largely unknown. Here, we show that 21-nt phasiRNAs direct ...
Arbuscular mycorrhiza (AM) with soilborne Glomeromycota fungi was pivotal in the conquest of land by plants almost half a billion years ago. In flowering plants, it is hypothesized that AM is initiated by the perception of AM fungi-derived chito- and ...
Isoprene is the most abundant nonmethane biogenic hydrocarbon emitted by some plants, mostly trees. It plays critical roles in atmospheric chemistry by contributing to ozone and aerosol formation. Isoprene also benefits plants, particularly under stress, ...
Herbivore attack elicits jasmonate (JA) signaling which in turn elicits both anti-herbivore plant defenses and growth inhibitions. The resulting growth–defense trade-offs constrain the utility of JA-based plant defense inducers to enhance endogenous pest ...
Improving fruit growth and quality without compromising yield is a highly sought-after goal in crop breeding. Here, we report that an EAR motif-containing transcription factor SlPLT6 controls the onset of fruit ripening and quality traits in tomato. ...

Population Biology

Characterizing the feedback linking human behavior and the transmission of infectious diseases (i.e., behavioral changes) remains a significant challenge in computational and mathematical epidemiology. Existing behavioral epidemic models often lack real-...
Plague continues to pose a public health problem in multiple regions of the world, including Madagascar, where it is characterized by a pronounced seasonal pattern. The drivers of plague seasonality remain poorly understood. Using a deterministic ...

Systems Biology

Fungal pathogens infect billions and kill millions of people each year. Many of these pathogens have evolved strategies to evade our antifungal immune defenses. Candida albicans, for example, masks the proinflammatory pathogen-associated molecular pattern ...

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