Table Of Contents Page, PNAS Volume 121, Number 33
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Brief Reports
Tracking biodiversity and its dynamics at scale is essential if we are to solve global
environmental challenges. Detecting animal vocalizations in passively recorded audio
data offers an automatable, inexpensive, and taxonomically broad way to monitor ...
The persistence and size of the Greenland Ice Sheet (GrIS) through the Pleistocene
is uncertain. This is important because reconstructing changes in the GrIS determines
its contribution to sea level rise during prior warm climate periods and informs ...
The mammalian mitochondrial genome (mtDNA) is multicopy and its copy number (mtCN)
varies widely across tissues, in development and in disease. Here, we systematically
catalog this variation by assaying mtCN in 52 human tissues across 952 donors (10,499
...
Physical Sciences
Applied Mathematics
An increasingly common viewpoint is that protein dynamics datasets reside in a nonlinear
subspace of low conformational energy. Ideal data analysis tools should therefore
account for such nonlinear geometry. The Riemannian geometry setting can be suitable
...
Applied Physical Sciences
Microbial interactions in the rhizosphere contribute to soil health, making understanding
these interactions crucial for sustainable agriculture and ecosystem management. Yet
it is difficult to understand what we cannot see; among the limitations in ...
We study the coupled charge density wave (CDW) and insulator-to-metal transitions
in the 2D quantum material 1T-TaS2. By applying in situ cryogenic 4D scanning transmission electron microscopy with
in situ electrical resistance measurements, we directly ...
CMOS-compatible reconstructive spectrometers with self-referencing integrated Fabry–Perot resonators
Miniaturized reconstructive spectrometers play a pivotal role in on-chip and portable
devices, offering high-resolution spectral measurement through precalibrated spectral
responses and AI–driven reconstruction. However, two key challenges persist for ...
Amorphous materials undergo a transition from liquid-like to solid-like states through
processes like rapid quenching or densification. Under external loads, they exhibit
yielding, with minimal structural changes compared to crystals. However, these ...
The laws of thermodynamics apply to biophysical systems on the nanoscale as described
by the framework of stochastic thermodynamics. This theory provides universal, exact
relations for quantities like work, which have been verified in experiments where
a ...
How does social complexity depend on population size and cultural transmission? Kinship
structures in traditional societies provide a fundamental illustration, where cultural
rules between clans determine people’s marriage possibilities. Here, we propose ...
Biophysics and Computational Biology
Blood plasma viscosity (PV) is an established biomarker for numerous diseases. Measurement
of the shear PV using conventional rheological techniques is, however, time consuming
and requires significant plasma volumes. Here, we show that Brillouin light ...
Investigating a long-standing conceptual question in bacterial physiology, we examine
why DnaA, the bacterial master replication initiator protein, exists in both ATP and
ADP forms, despite only the ATP form being essential for initiation. We engineered
...
Chemistry
The formation of macrophage–derived foam cells has been recognized as the pathological
hallmark of atherosclerotic diseases. However, the pathological evolution dynamics
and underlying regulatory mechanisms remain largely unknown. Herein, we introduce
a ...
The 2011 discovery of the first rare earth–dependent enzyme in methylotrophic Methylobacterium extorquens AM1 prompted intensive research toward understanding the unique chemistry at play
in these systems. This enzyme, an alcohol dehydrogenase (ADH), ...
The fundamental question of “what is the transport path of electrons through proteins?”
initially introduced while studying long-range electron transfer between localized
redox centers in proteins in vivo is also highly relevant to the transport ...
Protein therapeutics play a critical role in treating a large variety of diseases,
ranging from infections to genetic disorders. However, their delivery to target tissues
beyond the liver, such as the lungs, remains a great challenge. Here, we report a
...
Na5YSi4O12 (NYSO) is demonstrated as a promising electrolyte with high ionic conductivity and
low activation energy for practical use in solid Na-ion batteries. Solid-state NMR
was employed to identify the six types of coordination of Na+ ions and ...
Earth, Atmospheric, and Planetary Sciences
Biomass burning plays an important role in climate-forcing and atmospheric chemistry.
The drivers of fire activity over the past two centuries, however, are hotly debated
and fueled by poor constraints on the magnitude and trends of preindustrial fire ...
The Earth’s rotation has been decelerating throughout its history due to tidal dissipation,
but the variation of the rate of this deceleration through time has not been established.
We present a detailed analysis of eight geological datasets to constrain ...
Engineering
Microvortices are emerging components that impart functionality to microchannels by
exploiting inertia effects such as high shear stress, effective fluid diffusion, and
large pressure loss. Exploring the dynamic generation of vortices further expands
the ...
Artificial neuromorphic devices can emulate dendric integration, axonal parallel transmission,
along with superior energy efficiency in facilitating efficient information processing,
offering enormous potential for wearable electronics. However, ...
Transparent solar cells (TSCs) hold substantial potential as continuous energy generators,
enabling their use in situations where conventional devices may not be feasible. However,
research aimed at modularizing TSCs for the purpose of regulating the ...
Environmental Sciences
Water resources are indispensable basic resources and important environmental carriers;
the presence of organic contaminants in wastewater poses considerable risks to the
health of both humans and ecosystems. Although the Fenton-like reactions using H2O2 ...
Physics
Complex systems are typically characterized by intricate internal dynamics that are
often hard to elucidate. Ideally, this requires methods that allow to detect and classify
in an unsupervised way the microscopic dynamical events occurring in the system. ...
Statistics
Polygenic risk scores (PRS) enhance population risk stratification and advance personalized
medicine, but existing methods face several limitations, encompassing issues related
to computational burden, predictive accuracy, and adaptability to a wide range ...
Sustainability Science
Biomass burning plays an important role in climate-forcing and atmospheric chemistry.
The drivers of fire activity over the past two centuries, however, are hotly debated
and fueled by poor constraints on the magnitude and trends of preindustrial fire ...
Social Sciences
Economic Sciences
While studies have examined the effects of schools offering in-person learning during
the pandemic, this study provides analysis of student enrollment decisions (remote
versus in-person) in response to schools providing in-person learning opportunities.
...
Psychological and Cognitive Sciences
In the pursuit of mental and physical health, effective pain management stands as
a cornerstone. Here, we examine a potential sex bias in pain management. Leveraging
insights from psychological research showing that females’ pain is stereotypically
judged ...
Moral values guide consequential attitudes and actions. Here, we report evidence of
seasonal variation in Americans’ endorsement of some—but not all—moral values. Studies
1 and 2 examined a decade of data from the United States (total N = 232,975) and ...
AI is now an integral part of everyday decision-making, assisting us in both routine
and high-stakes choices. These AI models often learn from human behavior, assuming
this training data is unbiased. However, we report five studies that show that people
...
Social Sciences
Violence is a key mechanism in the reproduction of community disadvantage. The existing
evidence indicates that violence in a community impacts the intergenerational mobility
of its residents. The current study explores the possibility of a reverse ...
Models of indirect reciprocity study how social norms promote cooperation. In these
models, cooperative individuals build up a positive reputation, which in turn helps
them in their future interactions. The exact reputational benefits of cooperation
...
Sustainability Science
Satellite-based land use monitoring and farm-level traceability offer opportunities
for targeted zero-deforestation interventions on private lands. Brazil’s Rural Environmental
Registry (Cadastro Ambiental Rural, or “CAR”), a land cadaster based on self-...
Biological Sciences
Agricultural Sciences
Insects and their gut bacteria form a tight and beneficial relationship, especially
in utilization of host nutrients. The red turpentine beetle (RTB), a destructive and
invasive pine pest, employs mutualistic microbes to facilitate its invasion success.
...
Applied Biological Sciences
Regeneration of hyaline cartilage in human-sized joints remains a clinical challenge,
and it is a critical unmet need that would contribute to longer healthspans. Injectable
scaffolds for cartilage repair that integrate both bioactivity and sufficiently ...
Biochemistry
The formation of macrophage–derived foam cells has been recognized as the pathological
hallmark of atherosclerotic diseases. However, the pathological evolution dynamics
and underlying regulatory mechanisms remain largely unknown. Herein, we introduce
a ...
The 2011 discovery of the first rare earth–dependent enzyme in methylotrophic Methylobacterium extorquens AM1 prompted intensive research toward understanding the unique chemistry at play
in these systems. This enzyme, an alcohol dehydrogenase (ADH), ...
Serial capture affinity purification (SCAP) is a powerful method to isolate a specific
protein complex. When combined with cross-linking mass spectrometry and computational
approaches, one can build an integrated structural model of the isolated complex.
...
Ubiquitination is one of the most common posttranslational modifications in eukaryotic
cells. Depending on the architecture of polyubiquitin chains, substrate proteins can
meet different cellular fates, but our understanding of how chain linkage controls
...
Secreted signaling peptides are central regulators of growth, development, and stress
responses, but specific steps in the evolution of these peptides and their receptors
are not well understood. Also, the molecular mechanisms of peptide–receptor binding
...
Endosomal membrane trafficking is mediated by specific protein coats and formation
of actin-rich membrane domains. The Retromer complex coordinates with sorting nexin
(SNX) cargo adaptors including SNX27, and the SNX27–Retromer assembly interacts with
the ...
DNA recognition is critical for assembly of double-stranded DNA viruses, particularly
for the initiation of packaging the viral genome into the capsid. The key component
that recognizes viral DNA is the small terminase protein. Despite prior studies, the
...
HIV-1 transcript function is controlled in part by twinned transcriptional start site
usage, where 5′ capped RNAs beginning with a single guanosine (1G) are preferentially
packaged into progeny virions as genomic RNA (gRNA) whereas those beginning with ...
Biophysics and Computational Biology
Blood plasma viscosity (PV) is an established biomarker for numerous diseases. Measurement
of the shear PV using conventional rheological techniques is, however, time consuming
and requires significant plasma volumes. Here, we show that Brillouin light ...
The hierarchic assembly of fibrillar collagen into an extensive and ordered supramolecular
protein fibril is critical for extracellular matrix function and tissue mechanics.
Despite decades of study, we still know very little about the complex process of ...
Biofilm-protected pathogenic Staphylococcus aureus causes chronic infections that are difficult to treat. An essential building block
of these biofilms are functional amyloid fibrils that assemble from phenol-soluble
modulins (PSMs). PSMα1 cross-seeds ...
Phase separation in aqueous solutions of macromolecules underlies the generation of
biomolecular condensates in cells. Condensates are membraneless bodies, representing
dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient
...
Protein phase transitions (PPTs) from the soluble state to a dense liquid phase (forming
droplets via liquid–liquid phase separation) or to solid aggregates (such as amyloids)
play key roles in pathological processes associated with age-related diseases ...
Linker histones play an essential role in chromatin packaging by facilitating compaction
of the 11-nm fiber of nucleosomal “beads on a string.” The result is a heterogeneous
condensed state with local properties that range from dynamic, irregular, and ...
Cell Biology
Upstream frameshift 1 (UPF1) is an RNA helicase involved in a number of mRNA regulatory
processes including nonsense-mediated decay. Mutations in the UPF1 locus that reduce its expression have been associated with adenosquamous carcinoma
of the pancreas, ...
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum
(ER)-resident secretory protein that reduces inflammation and promotes proliferation
in pancreatic β cells. Numerous studies have highlighted the potential of MANF as
a ...
Many cytoskeletal networks consist of individual filaments that are organized into
elaborate higher-order structures. While it is appreciated that the size and architecture
of these networks are critical for their biological functions, much of the work ...
The ring-shaped Cohesin complex, consisting of core subunits Smc1, Smc3, Scc1, and
SA2 (or its paralog SA1), topologically entraps two duplicated sister DNA molecules
to establish sister chromatid cohesion in S-phase. It remains largely elusive how
the ...
Developmental Biology
Chromosomal abnormalities are a common cause of human miscarriage but rarely reported
in any other species. As a result, there are currently inadequate animal models available
to study this condition. Horses present one potential model since mares receive ...
Constitutive heterochromatin, a fundamental feature of eukaryotic nucleus essential
for transposon silencing and genome stability, is rebuilt on various types of repetitive
DNA in the zygotic genome during early embryogenesis. However, the molecular ...
Ecology
The Amazon forest contains globally important carbon stocks, but in recent years,
atmospheric measurements suggest that it has been releasing more carbon than it has
absorbed because of deforestation and forest degradation. Accurately attributing the
...
Evolution
How does social complexity depend on population size and cultural transmission? Kinship
structures in traditional societies provide a fundamental illustration, where cultural
rules between clans determine people’s marriage possibilities. Here, we propose ...
Models of indirect reciprocity study how social norms promote cooperation. In these
models, cooperative individuals build up a positive reputation, which in turn helps
them in their future interactions. The exact reputational benefits of cooperation
...
Van Valen’s law of constant extinction postulates that in comparable ecological contexts,
the probability for a taxon to survive to the next time interval is independent of
how long it has already existed. The law implies that species do not age, that is,
...
Eusocial organisms typically live in colonies with one reproductive queen supported
by thousands of sterile workers. It is widely believed that monogamous mating is a
precondition for the evolution of eusociality. Here, we present a theoretical model
that ...
Genetics
Polygenic risk scores (PRS) enhance population risk stratification and advance personalized
medicine, but existing methods face several limitations, encompassing issues related
to computational burden, predictive accuracy, and adaptability to a wide range ...
Linking genetic diversity to extinction is a common goal in genomic studies. Recently,
a debate has arisen regarding the importance of genetic variation in conservation
as some studies have failed to find associations between genome-wide genetic diversity
...
Immunology and Inflammation
Immune checkpoint therapy has limited efficacy for patients with bone-metastatic castration-resistant
prostate cancer (bmCRPC). To improve immunotherapy for bmCRPC, we aimed to identify
the mechanism of bmCRPC-induced changes in the immune ...
Oxysterol binding protein regulates the resolution of TLR-induced cytokine production in macrophages
Toll-like receptors (TLRs) on macrophages sense microbial components and trigger the
production of numerous cytokines and chemokines that mediate the inflammatory response
to infection. Although many of the components required for the activation of the ...
We developed a highly sensitive assay for detecting protein–protein interaction using
chimeric receptors comprising two molecules of interest in the extracellular domain
and interferon alpha and beta receptor subunit 1 or 2 (IFNAR1/2) in the intracellular
...
Nuclear factor kappa B (NFκB) is a pathogenic factor in chronic lymphocytic leukemia
(CLL) that is not addressed specifically by current therapies. NFκB is activated by
inflammatory factors that stimulate toll-like receptors (TLRs) and receptors for ...
Medical Sciences
In the pursuit of mental and physical health, effective pain management stands as
a cornerstone. Here, we examine a potential sex bias in pain management. Leveraging
insights from psychological research showing that females’ pain is stereotypically
judged ...
Deleterious accumulation of R-loops, a DNA–RNA hybrid structure, contributes to genome
instability. They are associated with BRCA1 mutation-related breast cancer, an estrogen receptor α negative (ERα−) tumor type originating from luminal progenitor cells. ...
Microbiology
Microbial interactions in the rhizosphere contribute to soil health, making understanding
these interactions crucial for sustainable agriculture and ecosystem management. Yet
it is difficult to understand what we cannot see; among the limitations in ...
Investigating a long-standing conceptual question in bacterial physiology, we examine
why DnaA, the bacterial master replication initiator protein, exists in both ATP and
ADP forms, despite only the ATP form being essential for initiation. We engineered
...
Sustained community spread of influenza viruses relies on efficient person-to-person
transmission. Current experimental transmission systems do not mimic environmental
conditions (e.g., air exchange rates, flow patterns), host behaviors, or exposure
...
Johne’s disease (JD), a chronic, infectious enteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP), affects wild and domestic ruminants. There is no cure or effective prevention,
and current vaccines have substantial limitations, leaving ...
Laboratory models are central to microbiology research, advancing the understanding
of bacterial physiology by mimicking natural environments, from soil to the human
microbiome. When studying host–bacteria interactions, animal models enable investigators
...
The obligatory intracellular bacterium Anaplasma phagocytophilum causes human granulocytic anaplasmosis, an emerging zoonosis. Anaplasma has limited biosynthetic and metabolic capacities, yet it effectively replicates
inside of inclusions/vacuoles of ...
Neuroscience
When making decisions in a cluttered world, humans and other animals often have to
hold multiple items in memory at once—such as the different items on a shopping list.
Psychophysical experiments in humans and other animals have shown remembered stimuli
...
Adolescent development of human brain structural and functional networks is increasingly
recognized as fundamental to emergence of typical and atypical adult cognitive and
emotional proodal magnetic resonance imaging (MRI) data collected from N 300 ...
X-linked dystonia–parkinsonism (XDP) is a severe neurodegenerative disorder resulting
from an inherited intronic SINE-Alu-VNTR (SVA) retrotransposon in the TAF1 gene that causes dysregulation of TAF1 transcription. The specific mechanism underlying this ...
Pharmacology
Brain rhythms provide the timing for recruitment of brain activity required for linking
together neuronal ensembles engaged in specific tasks. The γ-oscillations (30 to 120
Hz) orchestrate neuronal circuits underlying cognitive processes and working ...
Physiology
Connexin hemichannels were identified as the first members of the eukaryotic large-pore
channel family that mediate permeation of both atomic ions and small molecules between
the intracellular and extracellular environments. The conventional view is that ...
Plant Biology
Transcription factor ELONGATED HYPOCOTYL5 (HY5) is the central hub for seedling photomorphogenesis.
E3 ubiquitin (Ub) ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) inhibits HY5 protein
accumulation through ubiquitination. However, the process of HY5 ...
Plants employ distinct mechanisms to respond to environmental changes. Modification
of mRNA by N 6-methyladenosine (m6A), known to affect the fate of mRNA, may be one such mechanism to reprogram mRNA
processing and translatability upon stress. However, it ...
Sustainability Science
The Amazon forest contains globally important carbon stocks, but in recent years,
atmospheric measurements suggest that it has been releasing more carbon than it has
absorbed because of deforestation and forest degradation. Accurately attributing the
...
Corrections
SI Correction
Cover image: Pictured is a wafer-scale, flexible spectrometer array. Chunyu You et al. fabricated miniaturized spectrometers with a resolution of around 2.5 nanometers using complementary metal-oxide-semiconductor (CMOS) methods. Using a self-adapting algorithm, the authors circumvented the need for manual tuning of processing algorithm parameters. According to the authors, the CMOS production process and self-referencing algorithms may help reduce the cost of spectrometers for use in applications such as machine vision, environmental monitoring, and medical diagnostics. See the article by You et al. e2403950121. Image credit: Chunyu You, Ningge Huang, and Yongfeng Mei.
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