Table Of Contents Page, PNAS Volume 122, Number 12
This Week in PNAS
Retrospective
Commentaries
Perspective
Metamorphic proteins switch reversibly between two differently folded states under
a variety of environmental conditions. Their identification and prediction are gaining
attention, but the fundamental physicochemical basis for fold switching remains ...
Letters
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Reply to Fiscella: Why study erosion now? And why these risk factors?
View the original article:Income inequality and the erosion of democracy in the twenty-first century
Brief Reports
Epithelial cells (human keratinocyte cells and the canine MDCK cell line), traditionally
viewed as electrically non-self-excitable and involved primarily in physiological
functions such as barrier presentation, absorption, secretion, and protection, are
...
The file drawer problem—often operationalized in terms of statistically significant
results being published and statistically insignificant not being published—is widely
documented in the social sciences. We extend Franco’s et al. [Science 345, 1502–1505(...
Physical Sciences
Applied Physical Sciences
The high resource intensity of industrial beef in high-income economies has prompted
growing interest in alternative, potentially lower environmental impact beef production
pathways. Of those, grass feeding is promoted by some as one such alternative, but
...
Diatoms, a highly successful group of photosynthetic algae, contribute to a quarter
of global primary production. Many species are motile, despite having no appendages
and a completely rigid cell body. Cells move to seek out nutrients, locate mating
...
Delivering audible content to a targeted listener without disturbing others is paramount
in audio engineering. However, achieving this goal has long been challenging due to
the diffraction of low-frequency (long-wavelength) audio waves in linear ...
Thermally induced ripples are intrinsic features of nanometer-thick films, atomically
thin materials, and cell membranes, significantly affecting their elastic properties.
Despite decades of theoretical studies on the mechanics of suspended thermalized ...
Biophysics and Computational Biology
Mechanical stretch can activate long-lived changes in fibroblasts, increasing their
contractility and initiating phenotypic transformations. This activation, critical
to wound healing and procedures such as skin grafting, increases with mechanical ...
Bacterial motility in spatially structured environments impacts a variety of natural
and engineering processes. Constructing models to predict, control, and design bacterial
motility for these processes remains challenging because bacteria and active ...
During mitosis, there are significant structural changes in chromosomes. We used a
maximum entropy approach to invert experimental Hi-C data to generate effective energy
landscapes for chromosomal structures at different stages during the cell cycle. ...
Chemistry
Simultaneous profiling of multiple molecules trafficking at a single organelle and
the surrounding cytosol within a living cell is crucial for elucidating their functions,
necessitating advanced techniques that provide high spatial–temporal resolution and
...
Photosystem II (PSII) can achieve near-unity quantum efficiency of light harvesting
in ideal conditions and can dissipate excess light energy as heat to prevent the formation
of reactive oxygen species (ROS) under light stress. Understanding how this ...
Integrating the optoelectronic properties of quantum dots (QDs) with biological enzymatic
systems to form microbe-semiconductor biohybrids offers promising prospects for both
solar-to-chemical conversion and light-modulated biochemical processes. ...
Single-walled carbon nanotubes (SWCNTs) exhibit nonphotobleaching, near-infrared (NIR)
fluorescence suitable for bioimaging applications. In particular, SWCNT fluorescence
quenching induced by biopolymer dispersants facilitates flexible design of ...
Peptides and proteins, essential components of living organisms, are composed of amino
acids linked by peptide bonds. However, the mechanism of peptide bond formation during
the prebiotic era remains unclear. In this study, advanced Born–Oppenheimer ...
The slime of velvet worms (Onychophora) is a protein-based bioadhesive that undergoes
rapid, yet reversible transition from a fluid into stiff fibers used for prey capture
and defense, but the mechanism by which this phase transition functions is largely
...
Computer Sciences
Quantum hardware is inherently fragile and noisy. We find that the accuracy of traditional
quantum error correction algorithms can be improved depending on the hardware. Given
different hardware specifications, we automatically synthesize hardware-optimal ...
Earth, Atmospheric, and Planetary Sciences
Türkiye’s geographic position between Europe, Asia, and Africa gives it pivotal importance
for understanding the local, interregional, and intercontinental dynamics of Neogene
vertebrate evolution. Although rich in vertebrate fossil deposits spanning the ...
Forested wetlands such as mangroves are considered highly valuable for nature-based
mitigation of coastal flooding. However, their wave attenuation capacity during extreme
storms, when risks are highest, is rarely measured and remains challenging to ...
Conventional computational models of climate adaptation frameworks inadequately consider
decision-makers’ capacity to learn, update, and improve decisions. Here, we investigate
the potential of reinforcement learning (RL), a machine learning technique ...
The global sulfur cycle plays a critical role in the redox evolution of Earth’s surface
and upper mantle, yet the distribution and origin of sulfur in the mantle remains
largely unconstrained. El Hierro is a volcanic island in the Canary archipelago that
...
Engineering
Sponges, the basalmost members of the animal kingdom, exhibit a range of complex architectures
in which microfluidic channels connect multitudes of spherical chambers lined with
choanocytes, flagellated filter-feeding cells. Choanocyte chambers can ...
Interaction of electric fields with biological cells is indispensable for many physiological
processes. Thermal electrical noise in the cellular environment has long been considered
as the minimum threshold for detection of electrical signals by cells. ...
Environmental Sciences
Agriculture is a cornerstone of global food production, accounting for a substantial
portion of water withdrawals worldwide. As the world’s population grows, so does the
demand for water in agriculture, leading to alterations in regional water–energy ...
The co-occurrence of arsenic and uranium in groundwater has been found in many countries,
posing a significant challenge to human health. Here, we have demonstrated the efficient
simultaneous removal of arsenic and uranyl-carbonate complexes from ...
Mathematics
In 2005, Britto, Cachazo, Feng, and Witten gave a recurrence (now known as the BCFW
recurrence) for computing scattering amplitudes in N = 4 super Yang–Mills theory. Arkani-Hamed and Trnka subsequently introduced the amplituhedron
to give a geometric ...
We show that there exist closed three-dimensional Riemannian manifolds where the incompressible
Euler equations exhibit smooth steady solutions that are isolated in the C1-topology. The proof of this fact combines ideas from dynamical systems, which ...
Physics
In nature, there are significant relationships known between microorganisms from two
kingdoms of life, as in the supply of vitamin B12 by bacteria to algae. Such interactions motivate general investigations into the
spatiotemporal dynamics of metabolite ...
Introducing the concept of topology into material science has sparked a revolution
from classic electronic and optoelectronic devices to topological quantum devices.
The latter has potential for transferring energy and information with unprecedented
...
The Hubbard and closely related t-J models are exciting platforms for unconventional superconductivity (SC). Through
state-of-the-art density matrix renormalization group calculations using the grand
canonical ensemble, we address open issues regarding ...
An emerging concept for identification of different types of spin liquids [C. Broholm
et al., Science 367, eaay0668 (2020)] is through the use of spontaneous spin noise [S. Chatterjee, J.
F. Rodriguez-Nieva, E. Demler, Phys. Rev. B 99, 104425 (2019)]. ...
Sustainability Science
Agriculture is a cornerstone of global food production, accounting for a substantial
portion of water withdrawals worldwide. As the world’s population grows, so does the
demand for water in agriculture, leading to alterations in regional water–energy ...
Social Sciences
Economic Sciences
An effective way to foster cooperation is to monitor behavior and sanction freeriding.
Yet, previous studies have shown that cooperation quickly declines when sanctioning
mechanisms are removed. We test whether explicitly expressing trust in players’ ...
Psychological and Cognitive Sciences
What constitutes a language? Natural languages share features with other domains:
from math, to music, to gesture. However, the brain mechanisms that process linguistic
input are highly specialized, showing little response to diverse nonlinguistic tasks.
...
Biological Sciences
Anthropology
Türkiye’s geographic position between Europe, Asia, and Africa gives it pivotal importance
for understanding the local, interregional, and intercontinental dynamics of Neogene
vertebrate evolution. Although rich in vertebrate fossil deposits spanning the ...
The relationship between humans and pigs has changed dramatically since their domestication
in southwest Asia and subsequent human-induced introduction into Europe. Introgression
between incoming southwest Asian pigs and European boar resulted in the ...
Applied Biological Sciences
The high resource intensity of industrial beef in high-income economies has prompted
growing interest in alternative, potentially lower environmental impact beef production
pathways. Of those, grass feeding is promoted by some as one such alternative, but
...
The slime of velvet worms (Onychophora) is a protein-based bioadhesive that undergoes
rapid, yet reversible transition from a fluid into stiff fibers used for prey capture
and defense, but the mechanism by which this phase transition functions is largely
...
Biochemistry
Simultaneous profiling of multiple molecules trafficking at a single organelle and
the surrounding cytosol within a living cell is crucial for elucidating their functions,
necessitating advanced techniques that provide high spatial–temporal resolution and
...
Deciphering metabolic enzyme catalysis in living cells remains a formidable challenge
due to the limitations of in vivo assays, which focus on enzymes isolated from respiration.
This study introduces an innovative whole-cell electrochemical assay to ...
Mitochondrial respiratory complexes I to IV and the F1Fo-ATP synthase (complex V) are large protein assemblies producing the universal cellular
energy currency adenosine triphosphate (ATP). Individual complexes have been extensively
studied in vitro, but ...
PAS domains are ubiquitous sensory modules that transduce environmental signals into
cellular responses through tandem PAS folds and PAS-associated C-terminal (PAC) motifs.
While this conserved architecture underpins their regulatory roles, here we ...
The continuing discovery of new peptide-aminoacyl-tRNA ligases (PEARLs) has unveiled
a diverse array of enzymes with the unique potential to append amino acids to the
C terminus of substrate peptides in an aminoacyl-tRNA-dependent manner. To date, PEARLs
...
α-hydroxy acids (αHAs), simple and prebiotically plausible organic monomers, were
likely present in various environments on and off Earth and could have played a role
in directing the emergence of the first homochiral living systems. Some αHAs, which
...
Highly reducing iterative polyketide synthases (HR-iPKSs) are huge enzyme complexes
with multiple catalytic domains that biosynthesize polyketides by intrinsically programmed
iterative carbon chain extensions and reductions. Unlike most HR-iPKSs, which ...
Biophysics and Computational Biology
Photosystem II (PSII) can achieve near-unity quantum efficiency of light harvesting
in ideal conditions and can dissipate excess light energy as heat to prevent the formation
of reactive oxygen species (ROS) under light stress. Understanding how this ...
In nature, there are significant relationships known between microorganisms from two
kingdoms of life, as in the supply of vitamin B12 by bacteria to algae. Such interactions motivate general investigations into the
spatiotemporal dynamics of metabolite ...
During cell division in animal cells, a bipolar spindle assembles to segregate the
chromosomes. Various motor proteins with different properties are essential for spindle
self-organization. The minimal set of components required to organize dynamic ...
ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission
through a direct ability to tubulate membrane. We have pursued cryoelectron microscopy
(EM) to reveal at 3.9 Å resolution how ARF6 assembles into a protein lattice on ...
NuA4 is the only essential acetyltransferase in yeast that can catalyze the acetylation
of the histones H2A, H2A.Z, and H4, thereby affecting gene transcription. However,
the acetylation process of NuA4, such as how NuA4 acetylates H4 and H2A.Z ...
Cell Biology
Mechanical stretch can activate long-lived changes in fibroblasts, increasing their
contractility and initiating phenotypic transformations. This activation, critical
to wound healing and procedures such as skin grafting, increases with mechanical ...
Motile cilia are organelles found on many eukaryotic cells that play critical roles
in development and fertility. Human CFAP298 has been implicated in the transport/assembly
of ciliary dyneins, and defects in this protein cause primary ciliary dyskinesia.
...
Developmental Biology
During fetal stage, hematopoietic stem and progenitor cells (HSPCs) undergo rapid
proliferation with a tight control of genomic stability. Although histone H3 lysine
4 (H3K4) methylation has been reported to stabilize the genome in proliferating cells,
...
The mandible, also known as the lower jaw, is the only bone in the skull that can
move and is essential for speaking and chewing. Meckel’s cartilage (MC) is a temporary
structure that supports the formation of the mandible, but how MC is involved in the
...
Ecology
The phenological timing of leaf out in temperate forests is a critical transition
point each year that alters the global climate system, which in turn, feeds back to
plants, driving leaf out to occur nearly 3 d earlier per decade as temperatures rise.
To ...
Individual heterogeneity shapes ecoevolutionary processes at multiple scales. Yet,
the scarcity of long-term life-history data and limitations in classic statistical
tools hinder our capacity to uncover and understand individual heterogeneity in wildlife
...
Evolution
Founder-event speciation can occur when one or more organisms colonize a distant,
unoccupied area via long-distance dispersal, leading to the evolution of a new species
lineage. Species radiations established by long-distance, and especially transoceanic,
...
To understand infectious disease dynamics, we need to understand the inextricably
intertwined nature of the ecology and evolution of pathogens and hosts. Epidemiological
dynamics of many infectious diseases have highlighted the importance of considering
...
How organisms evolve under extreme environmental changes is a critical question in
the face of global climate change. Genetic accommodation is an evolutionary process
by which natural selection acts on novel phenotypes generated through repeated ...
Genetics
Seed size is one of the important yield traits, and size control is also a fundamental
developmental question. The knowledge about the genetic and molecular mechanisms that
govern seed size is crucial for improving crop yield. Here, we report that the ...
Meiotic recombination is a prominent force shaping genome evolution, and understanding
why recombination rates vary within and between species has remained a central, though
challenging, question. Variation in recombination is widely thought to influence ...
Immunology and Inflammation
Platelets, known for maintaining blood balance, also participate in antimicrobial
defense. Upon severeacute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection,
platelets become hyperactivated, releasing molecules such as cytokines, granule contents,...
The nasal mucosa is the first immunologically active site that respiratory viruses
encounter and establishing immunity at the initial point of pathogen contact is essential
for preventing viral spread. Influenza A virus (IAV) in humans preferentially ...
Maternal–fetal immune tolerance guarantees a successful pregnancy throughout gestation.
HLA-G, a nonclassical human leukocyte antigen (HLA) molecule exclusively expressed
in extravillous trophoblasts (EVT), is a crucial factor in establishing maternal–...
Aging is associated with increased variability and dysregulation of the immune system.
We performed a system-level analysis of serum cytokines in a longitudinal cohort of
133 healthy individuals over 9 y. We found that cancer incidence is a major ...
Sexual dimorphism in immune responses is well documented, but the underlying mechanisms
remain incompletely understood. Here, we identified a subset of corticotropin-releasing
hormone (CRH) neurons that express androgen receptors (ARs) as key mediators of ...
Medical Sciences
The mandible, also known as the lower jaw, is the only bone in the skull that can
move and is essential for speaking and chewing. Meckel’s cartilage (MC) is a temporary
structure that supports the formation of the mandible, but how MC is involved in the
...
A sustained blood supply is critical for tumor growth, as it delivers the nutrients
and oxygen required for development. Targeting of blood vessel formation via immunotherapies
is an area of great importance. Knowing that certain embryonic genes, such as ...
Redox imbalance contributes to aberrant osteoclastogenesis and osteoporotic bone loss.
In this study, we observed lower Forkhead box protein O3 (FoxO3), a transcription
factor associated with cellular oxidative stress, enhanced osteoclastogenesis in ...
Poly-ADP-ribose polymerase (PARP) inhibitors are vital therapeutic agents that exploit
synthetic lethality, particularly effective in tumors with homologous recombination
(HR) defects. However, broadening their clinical utility remains a significant ...
Neuroendocrine prostate cancer (NEPC), an aggressive subtype induced by hormone therapy,
lacks effective treatments. This study explored the role of E26 transformation-specific
variant 5 (ETV5) in NEPC development. Analysis of multiple prostate cancer ...
Lipoprotein lipase (LPL) carries out the lipolytic processing of triglyceride-rich
lipoproteins (TRL) along the luminal surface of capillaries. LPL activity is regulated
by the angiopoietin-like proteins (ANGPTL3, ANGPTL4, ANGPTL8), which control the ...
Microbiology
Staphylococcus aureus is a Gram-positive pathogen responsible for numerous antibiotic-resistant infections.
Identifying vulnerabilities in S. aureus is crucial for developing new antibiotics to treat these infections. With this in
mind, we probed the ...
Cyanobacteria are the oldest form of photosynthetic life on Earth and contribute to
primary production in nearly every habitat, from permafrost to hot springs. Despite
longstanding interest in the acclimation of these microbes, it remains poorly ...
West Nile virus (WNV) and Usutu virus (USUV) are closely related mosquito-borne neurotropic
flaviviruses that share common transmission cycle and can infect humans. However,
while human infections by WNV are widespread, infections by USUV are ...
Desiccation-tolerant cyanobacteria are able to survive frequent cycles of hydration
and dehydration, which are closely linked to diurnal light oscillations. Previous
studies have shown that light serves as a crucial anticipatory cue, activating desert
...
The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic
diversity and metabolic novelty, and the metabolic capabilities and ecological roles
of these communities remain largely unknown. We observed a widespread and ...
Mycobacterium tuberculosis (Mtb) primarily infects macrophages. In vitro without antibiotics, wild-type Mtb
hastens death of the macrophages, but the processes leading to rapid cell death are
not well understood. Our earlier work indicated that the death ...
Neuroscience
The human cerebral cortex exhibits intricate interareal functional synchronization
at the macroscale, with substantial individual variability in these functional connections.
However, the spatial organization of functional connectivity (FC) variability ...
Opioids trigger structural and functional neural adaptations of the reward circuit
that lead to dependence. Synaptic cell adhesion molecules (CAMs) play a pivotal role
in circuit organization and present prime candidates for orchestrating remodeling
of ...
Transmembrane channel-like protein 1 (TMC1), a pore-forming component of the mechano-electrical
transducer (MET) channel in cochlear outer hair cells, is subject to numerous mutations
causing deafness and hair cell death. We studied mice harboring ...
Pharmacology
Protein therapeutics such as antibodies require in-depth in vivo characterization
during development and consequently account for a large proportion of laboratory animal
consumption in the pharmaceutical industry. Currently, antibody candidates are ...
Physiology
Diapause, a developmental arrest mechanism, helps animals to survive seasonal changes
via endocrine regulation. While obligate diapause is genetically programmed, facultative
diapause is typically triggered by environmental cues such as photoperiod. In ...
Plant Biology
Plants produce diverse specialized metabolites with important ecological functions.
It has recently become apparent that the genes for many of these pathways are not
dispersed in plant genomes, but rather are arranged like beads on a string in ...
Psychological and Cognitive Sciences
What constitutes a language? Natural languages share features with other domains:
from math, to music, to gesture. However, the brain mechanisms that process linguistic
input are highly specialized, showing little response to diverse nonlinguistic tasks.
...
Internal states like motivation fluctuate substantially over time. However, studies
of the neurocomputational mechanims of motivated behavior have failed to capture this.
Here, we examined how naturalistic ups and downs in state motivation influence the
...
Systems Biology
Bacterial motility in spatially structured environments impacts a variety of natural
and engineering processes. Constructing models to predict, control, and design bacterial
motility for these processes remains challenging because bacteria and active ...
Endothelial cells (ECs) are constantly exposed to hemodynamic forces, which play a
crucial role in regulating EC functions. Pulsatile laminar shear stress (PS), representing
atheroprotective flow, maintains the anti-inflammation and homeostatic phenotype ...
Corrections
SI Correction
Cover image: Pictured is a female iguana (Brachylophus fasciatus) from the southern Lau Islands in Fiji. Simon G. Scarpetta et al. examined evolutionary relationships to determine how iguanas colonized Fiji. Iguanas inhabiting oceanic islands were previously known to travel long distances via overwater rafting on floating debris, including to the Galápagos Islands. Genetic data suggested that Fijian iguanas diverged from their closest relatives, North American desert iguanas, in the late Paleogene Period and rafted more than 8,000 kilometers to reach the Fijian archipelago. According to the authors, the finding represents the longest known transoceanic dispersal among terrestrial vertebrates. See the article by Scarpetta et al. e2318622122. Image credit: Robert Fisher.
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