Table Of Contents Page, PNAS Volume 121, Number 10
This Week in PNAS
Retrospective
Commentaries
Brief Report
Bacterial spores have outstanding properties from the materials science perspective,
which allow them to survive extreme environmental conditions. Recent work by [S. G.
Harrellson et al., Nature 619, 500–505 (2023)] studied the mechanical properties of ...
Physical Sciences
Applied Physical Sciences
Real-time characterization of microresonator dynamics is important for many applications.
In particular, it is critical for near-field sensing and understanding light–matter
interactions. Here, we report camera-facilitated imaging and analysis of standing
...
Non-Newtonian fluids can be used for the protection of flexible laminates. Understanding
the coupling between the flow of the protecting fluid and the deformation of the protected
solids is necessary in order to optimize this functionality. We present a ...
The silica-based cell walls of diatoms are prime examples of genetically controlled,
species-specific mineral architectures. The physical principles underlying morphogenesis
of their hierarchically structured silica patterns are not understood, yet such ...
In a stack of atomically thin van der Waals layers, introducing interlayer twist creates
a moiré superlattice whose period is a function of twist angle. Changes in that twist
angle of even hundredths of a degree can dramatically transform the system’s ...
Biophysics and Computational Biology
Protein dynamics form a critical bridge between protein structure and function, yet
the impact of evolution on ultrafast processes inside proteins remains enigmatic.
This study delves deep into nanosecond-scale protein dynamics of a structurally and
...
The microtubule-associated protein tau aggregates into amyloid fibrils in Alzheimer’s
disease and other neurodegenerative diseases. In these tauopathies, tau is hyperphosphorylated,
suggesting that this posttranslational modification (PTM) may induce tau ...
Chemistry
Studying the pathways of ligand–receptor binding is essential to understand the mechanism
of target recognition by small molecules. The binding free energy and kinetics of
protein–ligand complexes can be computed using molecular dynamics (MD) simulations,
...
Atomically precise control over anisotropic nanoclusters constitutes a grand challenge
in nanoscience. In this work, we report our success in achieving a periodic series
of atomically precise gold quantum rods (abbrev. Au QRs) with unusual excitonic ...
Single-atom catalysts (SACs) with maximized metal atom utilization and intriguing
properties are of utmost importance for energy conversion and catalysis science. However,
the lack of a straightforward and scalable synthesis strategy of SACs on diverse ...
Earth, Atmospheric, and Planetary Sciences
Marine particulate organic carbon (POC) contributes to carbon export, food webs, and
sediments, but uncertainties remain in its origins. Globally, variations in stable
carbon isotope ratios (δ13C values) of POC between the upper and lower euphotic zones (...
Engineering
Micro-sized single-crystalline Ni-rich cathodes are emerging as prominent candidates
owing to their larger compact density and higher safety compared with poly-crystalline
counterparts, yet the uneven stress distribution and lattice oxygen loss result in
...
Physics
We demonstrate the importance of addressing the Γ vertex and thus going beyond the
GW approximation for achieving the energy levels of liquid water in many-body perturbation
theory. In particular, we consider an effective vertex function in both the ...
Electric currents have the intriguing ability to induce magnetization in nonmagnetic
crystals with sufficiently low crystallographic symmetry. Some associated phenomena
include the non-linear anomalous Hall effect in polar crystals and the nonreciprocal
...
Statistics
Single-cell data integration can provide a comprehensive molecular view of cells,
and many algorithms have been developed to remove unwanted technical or biological
variations and integrate heterogeneous single-cell datasets. Despite their wide usage,
...
Sustainability Science
China has committed to achieve net carbon neutrality by 2060 to combat global climate
change, which will require unprecedented deployment of negative emissions technologies,
renewable energies (RE), and complementary infrastructure. At terawatt-scale ...
Social Sciences
Anthropology
In the Stone Age, the collection of specific rocks was the first step in tool making.
Very little is known about the choices made during tool-stone acquisition. Were choices
governed by the knowledge of, and need for, specific properties of stones? Or ...
Since the early Holocene, western and central Europe was inhabited by a genetically
distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced
and assimilated by the incoming Neolithic farmers. The western Atlantic façade was
...
View related content:
Economic Sciences
Some scholars find that behavioral variation in the public goods game is explained
by variations in participants’ understanding of how to maximize payoff and that confusion
leads to cooperation. Their findings lead them to question the common assumption ...
We conducted a spatial and temporal analysis of housing patterns in Mexico City by
utilizing an extensive database of 16,000 prices for flats and houses, covering the
period from 2000 to 2022. Our findings reveal a striking trend: The average housing
...
Environmental Sciences
China has committed to achieve net carbon neutrality by 2060 to combat global climate
change, which will require unprecedented deployment of negative emissions technologies,
renewable energies (RE), and complementary infrastructure. At terawatt-scale ...
Marine protected areas (MPAs) are widely used for ocean conservation, yet the relative
impacts of various types of MPAs are poorly understood. We estimated impacts on fish
biomass from no-take and multiple-use (fished) MPAs, employing a rigorous matched
...
Psychological and Cognitive Sciences
Consolidating memories for long-term storage depends on reactivation. Reactivation
occurs both consciously, during wakefulness, and unconsciously, during wakefulness
and sleep. While considerable work has examined conscious awake and unconscious sleep
...
During real-time language comprehension, our minds rapidly decode complex meanings
from sequences of words. The difficulty of doing so is known to be related to words’
contextual predictability, but what cognitive processes do these predictability effects
...
Social Sciences
A great deal of empirical research has examined who falls for misinformation and why.
Here, we introduce a formal game-theoretic model of engagement with news stories that
captures the strategic interplay between (mis)information consumers and producers.
...
Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The
very logic of reciprocity, however, seems to require that individuals are symmetric,
and that everyone has the same means to influence each others’ payoffs. Yet in many
...
Biological Sciences
Anthropology
Since the early Holocene, western and central Europe was inhabited by a genetically
distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced
and assimilated by the incoming Neolithic farmers. The western Atlantic façade was
...
View related content:
Applied Biological Sciences
Tissue plasminogen activator (tPA) is the only FDA-approved treatment for ischemic
stroke but carries significant risks, including major hemorrhage. Additional options
are needed, especially in small vessel thrombi which account for ~25% of ischemic
...
Biochemistry
Protein dynamics form a critical bridge between protein structure and function, yet
the impact of evolution on ultrafast processes inside proteins remains enigmatic.
This study delves deep into nanosecond-scale protein dynamics of a structurally and
...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been detected
in almost all organs of coronavirus disease-19 patients, although some organs do not
express angiotensin-converting enzyme-2 (ACE2), a known receptor of SARS-CoV-2, ...
Metformin is the first-line treatment for type II diabetes patients and a pervasive
pollutant with more than 180 million kg ingested globally and entering wastewater.
The drug’s direct mode of action is currently unknown but is linked to effects on
gut ...
Mutations in PTEN-induced putative kinase 1 (PINK1) cause autosomal recessive early-onset
Parkinson’s disease (PD). PINK1 is a Ser/Thr kinase that regulates mitochondrial quality
control by triggering mitophagy mediated by the ubiquitin (Ub) ligase ...
Biophysics and Computational Biology
Studying the pathways of ligand–receptor binding is essential to understand the mechanism
of target recognition by small molecules. The binding free energy and kinetics of
protein–ligand complexes can be computed using molecular dynamics (MD) simulations,
...
Single-cell data integration can provide a comprehensive molecular view of cells,
and many algorithms have been developed to remove unwanted technical or biological
variations and integrate heterogeneous single-cell datasets. Despite their wide usage,
...
The microtubule-associated protein tau aggregates into amyloid fibrils in Alzheimer’s
disease and other neurodegenerative diseases. In these tauopathies, tau is hyperphosphorylated,
suggesting that this posttranslational modification (PTM) may induce tau ...
Oxysterol-binding protein-related proteins (ORPs) play key roles in the distribution
of lipids in eukaryotic cells by exchanging sterol or phosphatidylserine for PI4P
between the endoplasmic reticulum (ER) and other cell regions. However, it is unclear
...
Translocation of cytoplasmic molecules to the plasma membrane is commonplace in cell
signaling. Membrane localization has been hypothesized to increase intermolecular
association rates; however, it has also been argued that association should be faster
in ...
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel
that regulates electrolyte and fluid balance in epithelial tissues. While activation
of CFTR is vital to treating cystic fibrosis, selective inhibition of CFTR is a ...
View related content:
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured,
5′ genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure
of SL5 is predicted to contain a four-way junction of helical stems, some of ...
Cell Biology
Stress conditions can cause the relocalization of proteasomes to condensates in yeast
and mammalian cells. The interactions that facilitate the formation of proteasome
condensates, however, are unclear. Here, we show that the formation of proteasome
...
The late stages of Golgi maturation involve a series of sequential trafficking events
in which cargo-laden vesicles are produced and targeted to multiple distinct subcellular
destinations. Each of these vesicle biogenesis events requires activation of an ...
Well-controlled repair mechanisms are involved in the maintenance of genomic stability,
and their failure can precipitate DNA abnormalities and elevate tumor risk. In addition,
the tumor microenvironment, enriched with factors inducing oxidative stress ...
Developmental Biology
Basal progenitor cells serve as a stem cell pool to maintain the homeostasis of the
epithelium of the foregut, including the esophagus and the forestomach. Aberrant genetic
regulation in these cells can lead to carcinogenesis, such as squamous cell ...
Autophagy is essential for the turnover of damaged organelles and long-lived proteins.
It is responsible for many biological processes such as maintaining brain functions
and aging. Impaired autophagy is often linked to neurodevelopmental and ...
Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional
control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding
protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known
to ...
Ecology
The Saccharomycotina yeasts (“yeasts” hereafter) are a fungal clade of scientific,
economic, and medical significance. Yeasts are highly ecologically diverse, found
across a broad range of environments in every biome and continent on earth; however,
...
Environmental Sciences
Marine protected areas (MPAs) are widely used for ocean conservation, yet the relative
impacts of various types of MPAs are poorly understood. We estimated impacts on fish
biomass from no-take and multiple-use (fished) MPAs, employing a rigorous matched
...
Evolution
A great deal of empirical research has examined who falls for misinformation and why.
Here, we introduce a formal game-theoretic model of engagement with news stories that
captures the strategic interplay between (mis)information consumers and producers.
...
Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The
very logic of reciprocity, however, seems to require that individuals are symmetric,
and that everyone has the same means to influence each others’ payoffs. Yet in many
...
We used nuclear genomic data and statistical models to evaluate the ecological and
evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States ...
One of the drivers of life’s diversification has been the emergence of “evolutionary
innovations”: The evolution of traits that grant access to underused ecological niches.
Since ecological interactions can occur separately from mating, mating-related ...
Genetics
MicroRNAs (miRNA) associate with Argonaute (AGO) proteins and repress gene expression
by base pairing to sequences in the 3′ untranslated regions of target genes. De novo
coding variants in the human AGO genes AGO1 and AGO2 cause neurodevelopmental ...
Mutations in genes encoding transcription factors inactivate or generate ectopic activities
to instigate pathogenesis. By disrupting hematopoietic stem/progenitor cells, GATA2
germline variants create a bone marrow failure and leukemia predisposition, ...
Somatic mutations potentially play a role in plant evolution, but common expectations
pertaining to plant somatic mutations remain insufficiently tested. Unlike in most
animals, the plant germline is assumed to be set aside late in development, leading
to ...
Ovarian immature teratomas (OITs) are malignant tumors originating from the ovarian
germ cells that mainly occur during the first 30 y of a female’s life. Early age of
onset strongly suggests the presence of susceptibility gene mutations for the disease
...
Acute myeloid leukemia (AML) is an aging-related and heterogeneous hematopoietic malignancy.
In this study, a total of 1,474 newly diagnosed AML patients with RNA sequencing data
were enrolled, and targeted or whole exome sequencing data were obtained in ...
Immunology and Inflammation
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron strain has
evolved into highly divergent variants with several sub-lineages. These newly emerging
variants threaten the efficacy of available COVID-19 vaccines. To mitigate the ...
Hypoxia signaling influences tumor development through both cell-intrinsic and -extrinsic
pathways. Inhibiting hypoxia-inducible factor (HIF) function has recently been approved
as a cancer treatment strategy. Hence, it is important to understand how ...
Chimeric antigen receptor (CAR) T cell dysfunction is a major barrier to achieving
lasting remission in hematologic cancers, especially in chronic lymphocytic leukemia
(CLL). We have shown previously that Δ133p53α, an endogenous isoform of the human
TP53 ...
Medical Sciences
Intestinal epithelial expression of the tight junction protein claudin-2, which forms
paracellular cation and water channels, is precisely regulated during development
and in disease. Here, we show that small intestinal epithelial claudin-2 expression
is ...
NOVA1 is a neuronal RNA-binding protein identified as the target antigen of a rare
autoimmune disorder associated with cancer and neurological symptoms, termed paraneoplastic
opsoclonus-myoclonus ataxia. Despite the strong association between NOVA1 and ...
Microbiology
Since its introduction in the human population, SARS-CoV-2 has evolved into multiple
clades, but the events in its intrahost diversification are not well understood. Here,
we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of ...
Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms
interact with their extracellular world. EVs are able to traffic a diverse array of
molecules across different species and even domains, facilitating numerous ...
African swine fever, one of the major viral diseases of swine, poses an imminent threat
to the global pig industry. The high-efficient replication of the causative agent
African swine fever virus (ASFV) in various organs in pigs greatly contributes to
the ...
Enterococci are gut microbes of most land animals. Likely appearing first in the guts
of arthropods as they moved onto land, they diversified over hundreds of millions
of years adapting to evolving hosts and host diets. Over 60 enterococcal species are
...
Bacteroidota are abundant members of the human gut microbiota that shape the enteric
landscape by modulating host immunity and degrading dietary- and host-derived glycans.
These processes are mediated in part by Outer Membrane Vesicles (OMVs). Here, we ...
Human cytomegalovirus (HCMV) is a prevalent pathogen that establishes life-long latent
infection in hematopoietic cells. While this infection is usually asymptomatic, immune
dysregulation leads to viral reactivation, which can cause significant morbidity ...
Neuroscience
Consolidating memories for long-term storage depends on reactivation. Reactivation
occurs both consciously, during wakefulness, and unconsciously, during wakefulness
and sleep. While considerable work has examined conscious awake and unconscious sleep
...
Inner ear hair cells are characterized by the F-actin-based stereocilia that are arranged
into a staircase-like pattern on the apical surface of each hair cell. The tips of
shorter-row stereocilia are connected with the shafts of their neighboring taller-...
Connectomics research has made it more feasible to explore how neural circuits can
generate multiple outputs. Female sexual drive provides a good model for understanding
reversible, long-term functional changes in motivational circuits. After emerging,
...
Music is powerful in conveying emotions and triggering affective brain mechanisms.
Affective brain responses in previous studies were however rather inconsistent, potentially
because of the non-adaptive nature of recorded music used so far. Live music ...
Physiology
Motion is the basis of nearly all animal behavior. Evolution has led to some extraordinary
specializations of propulsion mechanisms among invertebrates, including the mandibles
of the dracula ant and the claw of the pistol shrimp. In contrast, vertebrate ...
Apical cilia on epithelial cells defend the lung by propelling pathogens and particulates
out of the respiratory airways. Ciliated cells produce ATP that powers cilia beating
by densely grouping mitochondria just beneath the apical membrane. However, this ...
Plant Biology
Pyrenoids are microcompartments that are universally found in the photosynthetic plastids
of various eukaryotic algae. They contain ribulose-1,5-bisphosphate carboxylase/oxygenase
(Rubisco) and play a pivotal role in facilitating CO2 assimilation via CO2-...
The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins
are conserved plant-specific Transcription Factors (TFs). They play critical roles
in the development of various plant organs (meristems, inflorescences, floral organs,
...
Nuclear and organellar genomes can evolve at vastly different rates despite occupying
the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster
than nuclear DNA, whereas this trend is generally reversed in plants. However, in
...
Psychological and Cognitive Sciences
Color naming in natural languages is not arbitrary: It reflects efficient partitions
of perceptual color space [T. Regier, P. Kay, N. Khetarpal, Proc. Natl. Acad. Sci. U.S.A. 104, 1436–1441 (2007)] modulated by the relative needs to communicate about ...
Corrections
Retraction
Cover image: Pictured is Calochortus tolmiei (Liliaceae). Nisa Karimi et al. used genomic, botanical, and environmental data to explore the drivers of species richness in Calochortus, which displays high diversity in the California Floristic Province. Six lineages diverged beginning around 10.3 million years ago, with several ensuing shifts in chromosome number and tolerance for serpentine soil. The authors found that ideal conditions for species coexistence include variation in topography, climate, and soil; plant dispersal routes from multiple physiographic provinces; and differing chromosome numbers that prevent hybridization among lineages. See the article by Karimi et al. e2305228121. Image credit: Ron Parsons.
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