Table Of Contents Page, PNAS Volume 123, Number 14
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Core Concepts
Commentaries
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Perspective
Quantum biology is the field at the intersection of quantum-related physics and the
biology of living systems. The goal of the field is to determine if quantum phenomena
underpin biological function at the macroscale. Such results, supported by compelling
...
Letters
This article has a reply:
Reply to MacColl: Repeated evolution from standing genetic variation
View the original article:A species interaction kick-starts ecological speciation in allopatry
Brief Report
The acidic microenvironment of the stratum corneum is crucial for epidermal desquamation
and barrier homeostasis, yet the primary proton sensor that triggers this process
remains unknown. Here, we report that the proton-activated chloride channel PACC1
is ...
Physical Sciences
Applied Mathematics
A core tenet underpinning the conception of contemporary information networks, such
as social media platforms, is that users should not be constrained in the amount of
information they can freely and willingly exchange with one another about a given
...
Developing physics-based models for molecular simulation requires fitting many unknown
parameters to diverse experimental datasets. Traditionally, this process is piecemeal
and difficult to reproduce, leading to a fragmented landscape of models. Here, we
...
Applied Physical Sciences
Several theoretical models predict that spatial patterning increases ecosystem resilience.
However, these predictions rely on simplifying assumptions, such as assuming isotropic
and infinitely large ecosystems, and empirical evidence directly linking ...
Moiré superlattices of transition-metal dichalcogenide bilayers host strong Coulomb
interactions residing in narrow electron bands, leading to correlated insulating states
at fractional carrier doping densities, known as generalized Wigner crystals. In ...
The jamming transition between flow and amorphous-solid states exhibits paradoxical
properties characterized by hyperuniformity (suppressed spatial fluctuations) and
criticality (hyperfluctuations), whose origin remains unclear. Here, we model the
jamming ...
Biophysics and Computational Biology
The directed motility of unicellular organisms is critical for their survival and
ecological success, yet the mechanisms that enable rigid-walled diatoms to dynamically
reorient and alter the shape of their trajectories remain poorly understood. Here,
we ...
Understanding how viral mutant spectra organize and explore genotype space is essential
for elucidating the mechanisms that drive molecular evolution. Here, we use deep-sequencing
data of an amplicon in the A2 protein of the RNA bacteriophage Q
Chemistry
Spirocyclic β-lactones (SβLs) are ring-strain activated natural products produced
by actinomycetota, possessing potent and selective cytotoxicity, and with an unknown
pharmacological mechanism. To further the understanding of their mechanism of action
and ...
Singlet oxygen (1O2) is a short-lived, highly reactive oxidant driving natural element cycles, yet its
spatial distribution in complex multiphase systems remains poorly understood. Here,
we show that irradiation of organic carbon (OC)-containing aqueous ...
Earth, Atmospheric, and Planetary Sciences
Asteroid Bennu preserves primitive material from the early solar system, and returned
samples allow direct examination of how organics and minerals were assembled and altered.
We applied nanoscale infrared spectroscopy together with Raman spectroscopy to ...
Tropical Instability Waves (TIWs) dominate intraseasonal variability in the tropical
Pacific Ocean, strongly impacting climate variability and marine ecosystems. However,
their response to greenhouse warming remains uncertain because most current climate
...
Model evidence for distinct origins of glacial–interglacial and millennial signals in Greenland dust
Greenland ice-core records show that the mineral dust flux during the last glacial
maximum was twenty times greater than present and it responded rapidly during North
Atlantic abrupt climate events. Both glacial–interglacial and rapid modes of dust
...
Antarctic sea ice extent (SIE) has experienced unprecedented variability in recent
decades, with record expansion through 2015, followed by an abrupt transition to sustained
decline. Using over two decades of under-ice Argo float observations, we show ...
Engineering
Extracorporeal life support, such as hemodialysis, often face the risk of blood coagulation,
where systemic anticoagulation with heparin is routinely administered. However, this
strategy is contraindicated in patients at high risk of bleeding. Inspired by ...
Physics
Stochasticity plays an important role in all biological systems. The standard way
to deal with stochasticity involves averaging over an ensemble of independent realizations.
However, such mean statistics need not accurately reflect the typical outcomes in
...
We show how to adjust the parameters of a thermodynamic computer by gradient descent
in order to perform a desired computation at a specified observation time. Within
a digital simulation of a thermodynamic computer, training proceeds by maximizing
the ...
Statistics
Polygenic risk scores can be used to model the individual genetic liability for human
traits. Current methods primarily focus on modeling the mean of a phenotype while
neglecting the variance. However, genetic variants associated with phenotypic variance
...
Quantitative genetics is essential for genetic dissection of complex traits, yet the
existing theory fails to illustrate a comprehensive landscape of genetic control mechanisms
driving phenotypic variation and evolution. Here, we develop a statistical ...
Social Sciences
Political Sciences
The global decline in satisfaction with democracy, as measured in surveys, is sometimes
used as evidence of democracy’s precarious health. However, existing evidence on the
link between democratic attitudes and behaviors is mostly based on self-reported ...
Governments face persistent challenges in integrating refugees into the local labor
market, and many past interventions have shown limited impact. This study examines
the Job-Turbo program, a large-scale initiative launched by the German government
in ...
Psychological and Cognitive Sciences
Successful collective action on issues from climate change to the maintenance of democracy
depends on societal properties such as cultural tightness and social cohesion. How
these properties evolve is not well understood because they emerge from a complex
...
How the human brain flexibly adapts social perception by recategorizing out-group
(them) to in-group (us) remains unclear. Using functional MRI in Singapore’s multicultural
population, we investigated how priming subordinate (ethnic) versus superordinate
(...
Social Sciences
A core tenet underpinning the conception of contemporary information networks, such
as social media platforms, is that users should not be constrained in the amount of
information they can freely and willingly exchange with one another about a given
...
Sustainability Science
Given well-known credibility issues in project-based avoided-deforestation credits
and over $3 billion in committed credit purchases under ART TREES, the voluntary carbon
market is increasingly moving toward jurisdictional approaches to Reducing Emissions
...
Biological Sciences
Applied Biological Sciences
Spirocyclic β-lactones (SβLs) are ring-strain activated natural products produced
by actinomycetota, possessing potent and selective cytotoxicity, and with an unknown
pharmacological mechanism. To further the understanding of their mechanism of action
and ...
Biochemistry
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are structurally
diverse natural products that possess a range of bioactivities, often acting as antibiotics,
antifungals, or metallophores. In RiPP biosynthesis, different ...
Cystic fibrosis is a lethal genetic disorder caused by misfolding of the cystic fibrosis
transmembrane conductance regulator (CFTR) protein, most commonly due to the ΔF508
mutation. Despite extensive study, CFTR’s folding process has remained inaccessible
...
The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain
β-barrel membrane proteins that are assembled by conserved multisubunit machines.
In bacteria, the β-barrel assembly machine (BAM) folds over a hundred compositionally
...
Biophysics and Computational Biology
Developing physics-based models for molecular simulation requires fitting many unknown
parameters to diverse experimental datasets. Traditionally, this process is piecemeal
and difficult to reproduce, leading to a fragmented landscape of models. Here, we
...
The directed motility of unicellular organisms is critical for their survival and
ecological success, yet the mechanisms that enable rigid-walled diatoms to dynamically
reorient and alter the shape of their trajectories remain poorly understood. Here,
we ...
Understanding how viral mutant spectra organize and explore genotype space is essential
for elucidating the mechanisms that drive molecular evolution. Here, we use deep-sequencing
data of an amplicon in the A2 protein of the RNA bacteriophage Q
Cell Biology
Altered cell-surface glycans are established cancer biomarkers, yet no oncogenes have
been identified within glycan biosynthesis machinery. This represents a critical gap,
as defining a gene as a true oncogene, rather than merely a component of an ...
Developmental Biology
Paligenosis is a conserved cellular plasticity program that allows mature cells to
reenter the cell cycle in response to tissue injury. Paligenosis progresses via three
stages: autodegradation (with dramatic increase in autophagy and lysosomes), induction
...
Differentiation programs actively lock neurons into a terminally differentiated state.
How differentiation programs operate in distinct neuronal lineages remains obscure.
Here, we found that previously well-characterized Drosophila neuronal ...
Mammals are constantly exposed to various stressors of internal and external origin.
Though hair follicles (HFs) are exquisitely sensitive to stress, it remains largely
unknown how stress-induced responses are linked with the intrinsic regulators of HF
...
Transforming growth factor β (TGFβ) signaling pathways are integral for a plethora
of biological processes. SMAD2 and SMAD3 are the principal transcriptional effectors
of TGFβ superfamily ligands, yet quantitative, genome-wide mapping of their DNA-...
Ecology
Several theoretical models predict that spatial patterning increases ecosystem resilience.
However, these predictions rely on simplifying assumptions, such as assuming isotropic
and infinitely large ecosystems, and empirical evidence directly linking ...
The species–area relationship (SAR) has long been used to predict extirpation rates
from habitat loss, but these rates depend not only on habitat area but also on the
surrounding landscape and species’ habitat specialization. We collated global data
from ...
Anticipating how species distributions will shift with climate change is key for biodiversity
conservation and management. Commonly, species’ range shifts are observed by analyzing
changes in occurrence or abundance data through time, or predicted across ...
Environmental Sciences
While the ocean’s photosynthetic production of organic matter rivals that on land,
a combination of heterotrophy and sinking prevents significant accumulation of particulate
organic matter (POM) in open ocean surface waters. The origins and fates of POM ...
Evolution
Stochasticity plays an important role in all biological systems. The standard way
to deal with stochasticity involves averaging over an ensemble of independent realizations.
However, such mean statistics need not accurately reflect the typical outcomes in
...
Successful collective action on issues from climate change to the maintenance of democracy
depends on societal properties such as cultural tightness and social cohesion. How
these properties evolve is not well understood because they emerge from a complex
...
The availability of trophic niches is a key driver of biodiversity, promoting adaptive
radiation through evolutionary processes. However, most research has focused on how
species adapt to trophic niches as adults, largely overlooking the fact that many
...
How functional protein sequences are distributed in sequence space is fundamentally
important for evolutionary theory and protein design, particularly if a large diversity
of protein functions are hidden in evolutionarily unexplored areas of the sequence
...
Genetics
Polygenic risk scores can be used to model the individual genetic liability for human
traits. Current methods primarily focus on modeling the mean of a phenotype while
neglecting the variance. However, genetic variants associated with phenotypic variance
...
Quantitative genetics is essential for genetic dissection of complex traits, yet the
existing theory fails to illustrate a comprehensive landscape of genetic control mechanisms
driving phenotypic variation and evolution. Here, we develop a statistical ...
During spermiogenesis, nuclear remodeling occurs where histones are sequentially replaced
by transition proteins (TNPs) and protamines, a process essential for sperm maturation.
Although the degradation of histones and TNPs is thought to be essential for ...
Background selection (BGS)—the reduction of linked neutral diversity via the purging
of deleterious mutations—is a pervasive force in genomic evolution. However, its impact
on complex phenotypes remains poorly understood because classical theory treats ...
Immunology and Inflammation
A key function of the germinal center (GC) reaction consists in the preferential expansion
and enrichment of high-affinity B cell clones. Whether and how persistent viral infection
thwarts this purpose remains ill-defined. Here, we transferred monoclonal ...
Multiple system atrophy (MSA) is a progressive neurologic disease, known as an α-synucleinopathy.
There are currently no effective disease-modifying therapies for MSA. While neuroinflammation
is a hallmark of MSA, the contribution of adaptive immune ...
Class switch recombination (CSR) and somatic hypermutation are essential mechanisms
of effective antibody production, dependent on the enzyme activation-induced cytidine
deaminase (AID). Since AID lacks the intrinsic ability to cleave DNA, topoisomerase
1 ...
Medical Sciences
Deciphering the mechanisms underlying antitumor immunity is critical for improving
cancer immunotherapy efficacy. Here, we identify WFDC21P (lnc-DC) as a positive regulator
of antitumor immunity through promoting the activation of the RNA-sensing retinoic
...
Facilitating endogenous cardiomyocyte proliferation has emerged as an important strategy
for cardiac repair. Conserved retinol saturase (Retsat) functions in producing all-trans
13,14-dihydroretinol in the endoplasmic reticulum (ER). However, Retsat’s ...
Loss of skeletal muscle mass and strength are common manifestations of frailty in
older people and are linked to reduced quality of life. However, whether mitochondria
are mechanistically linked to frailty and how physical activity, or lack thereof,
is ...
Extrachromosomal circular DNA (eccDNA) are molecules that originate from chromosomal
DNA but exist independently. While large eccDNA (ecDNA) contributes to tumorigenesis,
the role of smaller eccDNA (<100,000 base pairs) in cancer remains unclear. Our ...
Despite the high incidence of influenza virus infections, one-fifth of people infected
with influenza remain asymptomatic. The mechanisms associated with this immune resilience
are, however, unknown. Here, we show that the human antimicrobial peptide ...
Microbiology
Hepatitis A virus (HAV) is an unusual picornavirus with two types of extracellular
virions: nonenveloped particles (nHAV) shed in feces and quasi-enveloped particles
(eHAV) circulating in blood. Both enter cells by clathrin-dependent endocytic pathways
...
CRISPR screening is a powerful approach to identify genetic perturbations that impact
viral infection. However, most virus-focused CRISPR screens utilize selection strategies
that limit the ability to identify genes important for infection. Here, we ...
The HIV-1 genome [genomic RNA (gRNA)] has an unusually biased nucleotide content and
is rich in adenosines. Selective packaging of the gRNA is thought to be driven by
specific binding of the nucleocapsid (NC) domain of the viral Gag protein to the ...
In the opportunistic pathogen Pseudomonas aeruginosa (Pa), ClpXP proteases selectively degrade key transcriptional regulators (TRs), enabling
dynamic control over phenotypes that promote pathogenesis and virulence. Here, we
report that a natural Pa ...
Middle East Respiratory Syndrome coronavirus (MERS-CoV) is a lethal pathogen with
pandemic potential. Clade A and B MERS-CoV viruses have caused outbreaks in the Middle
East since 2012 when they initially spilled over from camels to humans. Clade C ...
Neuroscience
How the human brain flexibly adapts social perception by recategorizing out-group
(them) to in-group (us) remains unclear. Using functional MRI in Singapore’s multicultural
population, we investigated how priming subordinate (ethnic) versus superordinate
(...
The shift from glycolysis to oxidative phosphorylation is a key step in neural differentiation.
Yet, the timing of metabolic rewiring in the development from progenitors to neurons
remains elusive, especially in human corticogenesis. To bridge this gap, ...
Nonmammalian vertebrates possess photosensitive pineal organs. We previously found
that in the zebrafish pineal organ, photoreceptor cells expressing parapinopsin 1
(PP1), a bistable opsin, exhibit “chromatic” responses to ultraviolet (UV) and visible
...
Electrocorticography (ECoG) provides a high-spatiotemporal-resolution measure of cortical
activity (cortical surface electrical potentials, CSEPs) in humans and animals. The
CSEP high-gamma band (Hγ, 65 to 170 Hz) correlates with neuronal firing rates at ...
Traumatic brain injury (TBI) is a leading cause of morbidity and mortality, with closed-head
mild TBI (mTBI) accounting for nearly 90% of all cases. Early pathological events
include microglial activation and neuronal mitochondrial dysfunction; however, ...
Physiology
Regulation of food intake in mammals is complex and controlled by an interplay between
hedonic and homeostatic signals, including hormones like leptin, which senses fat
storage and suppresses food intake. Caenorhabditis elegans lack leptin and leptin ...
Psychological and Cognitive Sciences
The honey bee waggle dance, which encodes food location, is often thought to involve
only one-way information transfer from dancers to signal receivers. Here, we show
that the information content of the dance is influenced by the presence of followers
and ...
Systems Biology
Understanding and manipulating the spread of mobile genetic elements represents a
great challenge with potential benefits across synthetic biology, agriculture, and
medicine. A key part of this challenge is the multiple scales in play, from the molecular
...
Corrections
Cover image: Pictured are robust woodpeckers (Campephilus robustus) in the Brazilian Atlantic Forest. Anderson S. Bueno, Chase D. Mendenhall et al. analyzed the impact of surrounding landscapes on 1,954 bird species living in 1,005 tropical and subtropical forest remnants created by deforestation. Bird extirpation rates were lower in forest remnants surrounded by terrestrial landscapes compared to forest remnants surrounded by water from dammed rivers, with increasing tree cover within 300 meters of forest remnants further reducing species losses. The findings highlight the potential of improving landscapes around forest remnants to enhance biodiversity conservation. See the article by Bueno, Mendenhall et al. e2521783123. Image credit: Gabriel Brutti (photographer).
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