Table Of Contents Page, PNAS Volume 122, Number 7
This Week in PNAS
Opinion
Profile
Commentaries
Letters
Physical Sciences
Applied Mathematics
Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g.,
bacteria, baker’s yeast) can actively kill each other and avoid mixing. How do such
antagonistic interactions impact the growth and survival of competing strains, while
...
The unsupervised and principled diagnosis of multiscale data is a fundamental obstacle
in modern scientific problems from, for instance, weather and climate prediction,
neurology, epidemiology, and turbulence. Multiscale data are characterized by a ...
Applied Physical Sciences
Knitting can turn a one-dimensional yarn into a highly ramified three-dimensional
structure. As a method of additive manufacturing, it holds promise for a class of
lightweight, ultrastrong materials. Here, we present a purely geometric model to predict
...
Understanding the complex temporal and spatial correlations of ions in disordered
perovskite oxides is critical to rationalize their functional properties. Here, we
provide insights into the longstanding controversy regarding the off-centering of
...
In wearable smart systems, continuous monitoring and accurate classification of different
sleep-related conditions are critical for enhancing sleep quality and preventing sleep-related
chronic conditions. However, the requirements for device–skin coupling ...
The immune system exploits a wide range of strategies to combine sensitivity with
selectivity for optimal response. We propose a generic physical mechanism that allows
tuning the location and steepness of the response threshold of cellular processes
...
Enhancing thermoelectric conversion efficiency (TCE) is pivotal for advancing global
energy conservation and emission reduction initiatives. Traditional approaches primarily
focus on microscopic strategies such as bandgap engineering, chemical potential ...
The discovery of ferroelectric phases in HfO2 offers insights into ferroelectricity. Its unique fluorite structure and complex
polarization switching pathways exhibit distinct characteristics, challenging conventional
analysis methods. Combining group ...
Biophysics and Computational Biology
Fluid flows are dominant features of many bacterial environments, and flow can often
impact bacterial behaviors in unexpected ways. For example, the most common type of
cardiovascular infection is heart valve colonization by gram-positive bacteria like
...
Samaras are known for their elegant and robust autorotation, a resilience that persists
in the adverse conditions imposed by high-speed raindrops. Like flying insects, samaras
descending from tall trees are likely to be struck by raindrops in an intense ...
Chemistry
The detection and identification of polycyclic aromatic hydrocarbons (PAHs) and their
derivatives, polycyclic aromatic compounds (PACs), are essential for environmental
and health monitoring, for assessing toxicological exposure and their associated ...
Calcium ions (Ca2+) play central roles in cellular physiology. Fluorescent indicators for Ca2+ ions revolutionized our ability to make rapid, accurate, and highly parallel measurement
of Ca2+ concentrations in living cells. The use of ratio-based imaging ...
Adaptive crystals have attracted significant attention from solid-state chemists and
crystal engineers for their promising applications in memories, capacitors, sensors,
and actuators. Among them, thermosalient crystals are particularly favored thanks
to ...
Understanding the dynamic evolution of protein structures is crucial for uncovering
their biological functions. Yet, real-time prediction of these dynamic structures
remains a significant challenge. Two-dimensional infrared (2DIR) spectroscopy is a
...
Affinity proteins based on a three-helix bundle (affibodies, alphabodies, and computationally
de novo designed ones) have been shown to be a general platform to discover binders
with properties reminiscent of antibodies, combining high target specificity ...
Earth, Atmospheric, and Planetary Sciences
The tectonic evolution of the Tibetan Plateau has been influenced by continental collision
and postcollisional convergence of Indian and Eurasian plates, both of which have
undoubtedly imposed their imprints on the lithosphere and upper-mantle structures
...
Engineering
Primary progressive multiple sclerosis (MS) is a demyelinating autoimmune disease
with only a single class of FDA-approved treatment, B cell depletion. Novel treatments
could emerge from a deeper understanding of the interplay between multiple cell types
...
Quantifying viral load, a key indicator required to achieve control and elimination
of the HIV epidemic, requires cell-free plasma or serum to ensure measurements are
not biased by proviral DNA contained in infected CD4 T lymphocytes. Plasma separation
...
Physics
We have studied the magnetic moments of artificial spin ice arrays of nanomagnets
in both undistorted square arrays and in arrays with a topological defect induced
by a single disclination. We confirm that the disclination induces global, macroscopic
...
We implement a variant of the quantum pigeonhole paradox thought experiment to study
whether classical counting principles survive in the quantum domain. We observe strong
measurements significantly violate the pigeonhole principle (that among three ...
Nonanalytic Bloch eigenstates at isolated band degeneracy points exhibit singular
behavior in the quantum metric. Here, a description of superfluid weight for zero-energy
flat bands in proximity to other high-energy bands is presented, where they together
...
Statistics
Modern machine learning has achieved impressive prediction performance, but often
sacrifices interpretability, a critical consideration in high-stakes domains such
as medicine. In such settings, practitioners often use highly interpretable decision
tree ...
Social Sciences
Anthropology
The evolution of stone tool technology marks a significant milestone in hominin development,
enabling early humans to manipulate their environments. The oldest known evidence,
dating to 3.3 Ma, indicates a combination of percussive and flake production ...
Psychological and Cognitive Sciences
A standard assumption in game theory is that decision-makers have preplanned strategies
telling them what actions to take for every contingency. In contrast, nonstrategic
decisions often involve an on-the-spot comparison process, with longer response ...
Job advertisements for jobs in male-dominated fields tend to contain more masculine
language, and a commonly proposed intervention to increase gender diversity in applicant
pools is to remove this language. In our research, we offer predictions about the
...
Based on the seminal minimal group experiment, the widely influential social identity
theory has, in the last 45 y, led to the belief that discrimination follows from intergroup
relations and social identity. A large body of research evidenced that people ...
Social Sciences
Children from families across the income distribution attend public schools, making
schools and classrooms potential sites for interaction between more- and less-affluent
children. However, limited information exists regarding the extent of economic ...
Biological Sciences
Anthropology
The evolution of stone tool technology marks a significant milestone in hominin development,
enabling early humans to manipulate their environments. The oldest known evidence,
dating to 3.3 Ma, indicates a combination of percussive and flake production ...
Applied Biological Sciences
Hepatitis B virus (HBV) poses a significant global health challenge, necessitating
the urgent development of curative therapeutics. However, this progress is impeded
by the lack of robust, immunocompetent preclinical animal models due to HBV’s strict
...
Biochemistry
The detection and identification of polycyclic aromatic hydrocarbons (PAHs) and their
derivatives, polycyclic aromatic compounds (PACs), are essential for environmental
and health monitoring, for assessing toxicological exposure and their associated ...
Affinity proteins based on a three-helix bundle (affibodies, alphabodies, and computationally
de novo designed ones) have been shown to be a general platform to discover binders
with properties reminiscent of antibodies, combining high target specificity ...
According to classical Anfinsen’s dogma, a protein folds into a single unique conformation
with minimal Gibbs energy under physiological conditions. However, certain proteins
may fold into two or more conformations from single amino acid sequences. Here, ...
Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize
them, microbial life including symbionts and pathogens has evolved polysaccharide
lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism.
PL ...
Fungal infections represent a significant global health concern, with a growing prevalence
of antifungal drug resistance. Targeting glucosylceramides (GlcCer), which are functionally
important glycosphingolipids (GSL) present in fungal membranes, ...
Biophysics and Computational Biology
Positive-strand RNA viruses of the order Nidovirales have the largest known RNA genomes of vertebrate and invertebrate viruses with 36.7
and 41.1 kb, respectively. The acquisition of a proofreading exoribonuclease (ExoN)
by an ancestral nidovirus enabled ...
Despite the rising challenge of antibiotic resistance, current approaches to eradicate
nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal
bacteria, i.e., ...
Structural characterization of influenza group 1 chimeric hemagglutinins as broad vaccine immunogens
Chimeric hemagglutinins (cHA) appear to be promising for the design and development
of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1,
comprising an H1 stem attached to either an H5, H8, or H11 globular head, have been
...
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion channel that
plays an important role in neuronal signaling throughout the nervous system. Its implication
in neurological disorders and inflammation has spurred the development of ...
Cell Biology
Calcium ions (Ca2+) play central roles in cellular physiology. Fluorescent indicators for Ca2+ ions revolutionized our ability to make rapid, accurate, and highly parallel measurement
of Ca2+ concentrations in living cells. The use of ratio-based imaging ...
The introns of the gene encoding the long noncoding RNA (lncRNA) GAS5 host up to 10
C/D box small nucleolar RNAs (snoRNAs). However, whether there is a regulatory and
functional relationship between these snoRNAs and GAS5 is unknown. Here, we show that
...
Functions of RNAs are associated with their abundance and unique subcellular localizations.
RNA imaging methods for spatiotemporal monitoring of RNA dynamics would facilitate
the discovery of unknown functions of RNA, yet improving RNA imaging is ...
Urate provides ~50% of the reducing potential in human and primate plasma which is
key to detoxifying reactive oxygen by-products of cellular metabolism. Urate is the
endpoint of purine metabolism in primates, and its concentration in plasma is a balance
...
COP1 and DET1 are components of an E3 ubiquitin ligase that is conserved from plants
to humans. Mammalian COP1 binds to DET1 and is a substrate adaptor for the CUL4A-DDB1-RBX1
RING E3 ligase. Transcription factor substrates, including c-Jun, ETV4, and ...
Developmental Biology
Male germ cells, which are responsible for producing millions of genetically diverse
sperm through meiosis in the testis, rely on lactate as their central energy metabolite.
Recent study has revealed that lactate induces epigenetic modification in cells ...
Hemolysis induces tissue damage by releasing cellular contents into the plasma. It
is widely accepted that hemolysis-derived toxic molecules are cleared by macrophages
or metabolized in hepatocytes. In zebrafish, we found that scavenger endothelial cells
(...
Double assurance in the induction of axial development by egg dorsal determinants in Xenopus embryos
We recently reported that microinjection of Xenopus nodal-related (xnr) mRNAs into β-catenin-depleted Xenopus embryos rescued a complete dorsal axis. Xnrs mediate the signal of the Nieuwkoop
center that induces the Spemann–Mangold organizer in the ...
Ecology
Species-level networks emerge as the combination of interactions spanning multiple
individuals, and their study has received considerable attention over the past 30
y. However, less is known about the structure of interaction configurations within
species,...
Habitat fragmentation is causing the collapse of seed dispersal interactions and ecosystem
functioning. When management and conservation strategies aim to sustain ecosystem
functioning of fragmented forests, species’ traits and functional performance are
...
Bacteria frequently inhabit surface-attached communities where rich “social” interactions
can significantly alter their population-level behavior, including their response
to antibiotics. Understanding these collective effects in spatially heterogeneous
...
Litter decomposition is a fundamental biogeochemical process for carbon flux and nutrient
cycling in terrestrial ecosystems, yet the global variation in decomposition rates
and their covariations with climate and substrate are not fully understood. Here,
...
Experimental studies have shown that symbiotic relationships between arbuscular mycorrhizal
(AM) fungi and host plants can regulate soil organic carbon (SOC) storage. Although
the impacts of mycorrhiza are highly context-dependent, it remains unclear how ...
Evolution
The average long-term impact of Darwinian evolution on Earth’s habitability remains
extremely uncertain. Recent attempts to reconcile this uncertainty by “Darwinizing”
nonreplicating biogeochemical processes subject to persistence-based selection conform
...
Zymocin is a well-characterized killer toxin secreted by some strains of the yeast
Kluyveromyces lactis. It acts by cleaving a specific tRNA in sensitive recipient cells. Zymocin is encoded
by a killer plasmid or virus-like element (VLE), which is a ...
Genetics
In most eukaryotic organisms, cells that rely on continuous cell division employ the
enzyme telomerase which replenishes chromosome termini through the addition of telomeric
repeats. In budding yeast, the telomerase holoenzyme is composed of a catalytic ...
The house mouse X and Y chromosomes have recently acquired multicopy, rapidly evolving
gene families representing an evolutionary arms race. This arms race between proteins
encoded by X-linked Slxl1/Slx and Y-linked Sly gene families can distort offspring ...
Alzheimer’s disease (AD) affects more than 10% of the population ≥65 y of age, but
the underlying biological risks of most AD cases are unclear. We show anti-poly-glycine-arginine
(a-polyGR) positive aggregates frequently accumulate in sporadic AD autopsy ...
Immunology and Inflammation
Primary progressive multiple sclerosis (MS) is a demyelinating autoimmune disease
with only a single class of FDA-approved treatment, B cell depletion. Novel treatments
could emerge from a deeper understanding of the interplay between multiple cell types
...
All glioblastoma (GBM) molecular subsets share the common trait of accelerated progression
following necrosis, which cannot be adequately explained by cellular proliferation
arising from accumulated genetic alterations. Counter to dogma that “cancer ...
Immune responses in the intestine are intricately balanced to prevent pathogen entry
without inducing immunopathology. The nervous system is well established to interface
with the immune system to fine-tune immunity in various organ systems including the
...
Multiple cell death and inflammatory signaling pathways converge on two critical factors:
receptor-interacting serine/threonine kinase 1 (RIPK1) and caspase-8. Careful regulation
of these molecules is critical to control apoptosis, pyroptosis, and ...
Medical Sciences
Modern machine learning has achieved impressive prediction performance, but often
sacrifices interpretability, a critical consideration in high-stakes domains such
as medicine. In such settings, practitioners often use highly interpretable decision
tree ...
Clear cell renal cell carcinoma (ccRCC) is the predominant human renal cancer with
surging incidence and fatality lately. Hyperactivation of hypoxia-inducible factor
(HIF) and mammalian target of rapamycin (mTOR) signaling are the common signatures
in ...
In this study, we used an inhibitor of phosphodiesterase 6 (PDE6) to examine the impact
of changes in the conformation of the PDE6 protein on the light-induced process responsible
for altering the length of the outer segments of photoreceptor cells in ...
Microbiology
Fluid flows are dominant features of many bacterial environments, and flow can often
impact bacterial behaviors in unexpected ways. For example, the most common type of
cardiovascular infection is heart valve colonization by gram-positive bacteria like
...
Quantifying viral load, a key indicator required to achieve control and elimination
of the HIV epidemic, requires cell-free plasma or serum to ensure measurements are
not biased by proviral DNA contained in infected CD4 T lymphocytes. Plasma separation
...
Microbes use quorum-sensing systems to respond to ecological and environmental changes.
In the oral microbiome, the pathogenic bacterium Streptococcus mutans uses quorum-sensing to control the production of bacteriocins. These antimicrobial
peptides kill ...
Systemic infections caused by Cryptococcus claim over 161,000 lives annually, with global mortality rate close to 70% despite
antifungal therapies. Currently, no vaccine is available. To develop an effective
multivalent vaccine against this free-living ...
Neuroscience
Poststroke inflammation critically influences functional outcomes following ischemic
stroke. Arginase-1 (Arg1) is considered a marker for anti-inflammatory macrophages,
associated with the resolution of inflammation and promotion of tissue repair in ...
Aminoglycosides (AGs) are highly potent, broad-spectrum antibiotics frequently used
as first-line treatments for multiple life-threatening infections. Despite their severe
ototoxicity, causing irreversible hearing loss in millions of people annually, no
...
Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4),
are important in regulating hippocampal synapse loss, which is the key driver of memory
decline in Alzheimer’s disease (AD). However, the cell-specific roles and ...
How early sensory experience during “critical periods” of postnatal life affects the
organization of the mammalian neocortex at the resolution of neuronal cell types is
poorly understood. We previously reported that the functional and molecular profiles
...
Physiology
Identification of FSH-regulated and estrous stage–specific transcriptional networks in mouse ovaries
Follicle-stimulating hormone (FSH) acts by binding to FSHRs expressed on ovarian granulosa
cells and produces estradiol. FSH is essential for female fertility because mice lacking
FSH (Fshb KO) are anestrous and infertile. Although several in vitro cell ...
Bone is a dynamic organ constantly undergoing remodeling with both bone formation
and resorption. Bone formation is mediated by osteoblasts originating from the differentiation
of bone marrow (BM) mesenchymal stem and progenitor cells (BM-MSPCs). However, ...
Plant Biology
Ripening is crucial for the development of fleshy fruits that release their seeds
following consumption by frugivores and are important contributors to human health
and nutritional security. Many genetic ripening regulators have been identified, ...
Photosynthesis, the fundamental process using light energy to convert carbon dioxide
to organic matter, is vital for life on Earth. It relies on capturing light through
light-harvesting complexes (LHC) in photosystem I (PSI) and PSII and on the conversion
...
Population Biology
Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g.,
bacteria, baker’s yeast) can actively kill each other and avoid mixing. How do such
antagonistic interactions impact the growth and survival of competing strains, while
...
Psychological and Cognitive Sciences
A standard assumption in game theory is that decision-makers have preplanned strategies
telling them what actions to take for every contingency. In contrast, nonstrategic
decisions often involve an on-the-spot comparison process, with longer response ...
Systems Biology
Acute lymphoblastic leukemia (ALL) poses challenges in adult patients, considering
its heterogeneous nature and often suboptimal treatment outcomes. Here, we performed
a study on 201 newly diagnosed adult ALL cases (age ≥ 15 y) to generate intracellular
...
Corrections
SI Correction
Retraction
Cover image: Pictured is a colony containing antibiotic-resistant (green) and antibiotic-sensitive (magenta) subpopulations of pathogenic Enterococcus faecalis bacteria. Marlis K. Denk-Lobnig and Kevin Wood combined experiments and mathematical modeling to characterize the impact of antibiotic exposure on a randomly distributed community of antibiotic-resistant and antibiotic-sensitive E. faecalis. Local competition and long-range cooperation between bacteria resulted in a variety of complex spatial arrangements following exposure, depending on initial conditions. The results provide insight into the role of spatial structure in the antibiotic resistance of bacterial communities. See the article by Denk-Lobnig and Wood e2417065122. Image credit: Marlis K. Denk-Lobnig.
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