Table Of Contents Page, PNAS Volume 119, Number 26
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Letters
Brief Reports
Sea ice levies an impost on maritime navigability in the Arctic, but ice cover diminution
due to anthropogenic climate change is generating expectations for improved accessibility
in coming decades. Projections of sea ice cover retreating preferentially ...
Excess mortality associated with the COVID-19 pandemic has led many to experience
the loss of family members, with significant negative outcomes. We quantify the extent
to which these population-wide rates of kin loss represent a departure from levels
...
Physical Sciences
Applied Physical Sciences
Detailed characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
transmission across different settings can help design less disruptive interventions.
We used real-time, privacy-enhanced mobility data in the New York City, NY and ...
There are still significant knowledge gaps in understanding the intrusion and retention
of exogeneous particles into the central nervous system (CNS). Here, we uncovered
various exogeneous fine particles in human cerebrospinal fluids (CSFs) and identified
...
Accurate measurements of the size and quantity of aerosols generated by various human
activities in different environments are required for efficacious mitigation strategies
and accurate modeling of respiratory disease transmission. Previous studies of ...
Applied Mathematics
Large-scale measurements linking genetic background to biological function have driven
a need for models that can incorporate these data for reliable predictions and insight
into the underlying biophysical system. Recent modeling efforts, however, ...
Biophysics And Computational Biology
Biodiversity is often attributed to a dynamic equilibrium between the immigration
and extinction of species. This equilibrium forms a common basis for studying ecosystem
assembly from a static reservoir of migrants—the mainland. Yet, natural ecosystems
...
The high-dimensional character of most biological systems presents genuine challenges
for modeling and prediction. Here we propose a neural network–based approach for dimensionality
reduction and analysis of biological gene expression data, using, as a ...
Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy
and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm
interphase chromosome structure, which is present throughout the nucleus. ...
Chemistry
Proton-coupled electron transfer (PCET) is key to the activation of the blue light
using flavin (BLUF) domain photoreceptors. Here, to elucidate the photocycle of the
central FMN-Gln-Tyr motif in the BLUF domain of OaPAC, we eliminated the intrinsic
...
Solar-driven bioelectrosynthesis represents a promising approach for converting abundant
resources into value-added chemicals with renewable energy. Microorganisms powered
by electrochemical reducing equivalents assimilate CO2, H2O, and N2 building ...
The carbon-neutral synthesis of syngas from CO2 and H2O powered by solar energy holds grand promise for solving critical issues such as
global warming and the energy crisis. Here we report photochemical reduction of CO2 with H2O into syngas using core/...
Deficiencies of the transmembrane iron-transporting protein ferroportin (FPN1) cause
the iron misdistribution that underlies ferroportin disease, anemia of inflammation,
and several other human diseases and conditions. A small molecule natural product,
...
Environmental Sciences
The 2015/16 El Niño brought severe drought and record-breaking temperatures in the
tropics. Here, using satellite-based L-band microwave vegetation optical depth, we
mapped changes of above-ground biomass (AGB) during the drought and in subsequent
years ...
Physics
Solid molecular hydrogen has been predicted to be metallic and high-temperature superconducting
at ultrahigh hydrostatic pressures that push current experimental limits. Meanwhile,
little is known about the influence of nonhydrostatic conditions on its ...
Social Sciences
Economic Sciences
We use event study models based on staggered summer vacations in Germany to estimate
the effect of school reopenings after the summer of 2021 on the spread of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2). Estimations are based on daily ...
Political Sciences
Although experiments show that exposure to factual information can increase factual
accuracy, the public remains stubbornly misinformed about many issues. Why do misperceptions
persist even when factual interventions generally succeed at increasing the ...
Psychological And Cognitive Sciences
Neural plasticity in subareas of the rodent amygdala is widely known to be essential
for Pavlovian threat conditioning and safety learning. However, less consistent results
have been observed in human neuroimaging studies. Here, we identify and test three
...
Biological Sciences
Agricultural Sciences
The regulatory process for assessing the risks of pesticides to bees relies heavily
on the use of the honeybee, Apis mellifera, as a model for other bee species. However, the validity of using A. mellifera as a surrogate for other Apis and non-Apis bees ...
Anthropology
Human between-group interactions are highly variable, ranging from violent to tolerant
and affiliative. Tolerance between groups is linked to our unique capacity for large-scale
cooperation and cumulative culture, but its evolutionary origins are ...
Applied Biological Sciences
Accurate measurements of the size and quantity of aerosols generated by various human
activities in different environments are required for efficacious mitigation strategies
and accurate modeling of respiratory disease transmission. Previous studies of ...
Over half the world’s population is at risk for viruses transmitted by Aedes mosquitoes, such as dengue and Zika. The primary vector, Aedes aegypti, thrives in urban environments. Despite decades of effort, cases and geographic range
of Aedes-borne ...
Biochemistry
All kingdoms of life produce essential nicotinamide dinucleotide NADP(H) using NAD
kinases (NADKs). A panel of published NADK structures from bacteria, eukaryotic cytosol,
and yeast mitochondria revealed similar tetrameric enzymes. Here, we present the ...
Bacterial tyrosine kinases (BY-kinases) comprise a family of protein tyrosine kinases
that are structurally distinct from their functional counterparts in eukaryotes and
are highly conserved across the bacterial kingdom. BY-kinases act in concert with
...
CRISPR diagnostics based on nucleic acid amplification faces barriers to its commercial
use, such as contamination risks and insufficient sensitivity. Here, we propose a
robust solution involving optochemical control of CRISPR RNA (crRNA) activation in
...
Biophysics And Computational Biology
Large-scale measurements linking genetic background to biological function have driven
a need for models that can incorporate these data for reliable predictions and insight
into the underlying biophysical system. Recent modeling efforts, however, ...
Phase-separated biomolecular condensates that contain multiple coexisting phases are
widespread in vitro and in cells. Multiphase condensates emerge readily within multicomponent
mixtures of biomolecules (e.g., proteins and nucleic acids) when the ...
Allostery is the phenomenon of coupling between distal binding sites in a protein.
Such coupling is at the crux of protein function and regulation in a myriad of scenarios,
yet determining the molecular mechanisms of coupling networks in proteins remains
...
Voltage-sensing phosphatase (VSP) consists of a voltage sensor domain (VSD) and a
cytoplasmic catalytic region (CCR), which is similar to phosphatase and tensin homolog
(PTEN). How the VSD regulates the innate enzyme component of VSP remains unclear.
Here,...
The association between two intrinsically disordered proteins (IDPs) may produce a
fuzzy complex characterized by a high binding affinity, similar to that found in the
ultrastable complexes formed between two well-structured proteins. Here, using coarse-...
Hearing depends on intricate morphologies and mechanical properties of diverse inner
ear cell types. The individual contributions of various inner ear cell types into
mechanical properties of the organ of Corti and the mechanisms of their integration
are ...
Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by
a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the
receptor, the TOM complex components, Tom 20, Tom22, and Tom70, recognize the presequence
...
Protein aggregation into amyloid fibrils is the archetype of aberrant biomolecular
self-assembly processes, with more than 50 associated diseases that are mostly uncurable.
Understanding aggregation mechanisms is thus of fundamental importance and goes in
...
While biofilms formed by bacteria have received great attention due to their importance
in pathogenesis, much less research has been focused on the biofilms formed by archaea.
It has been known that extracellular filaments in archaea, such as type IV pili,...
Proton-coupled electron transfer (PCET) is key to the activation of the blue light
using flavin (BLUF) domain photoreceptors. Here, to elucidate the photocycle of the
central FMN-Gln-Tyr motif in the BLUF domain of OaPAC, we eliminated the intrinsic
...
Cell Biology
Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy
and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm
interphase chromosome structure, which is present throughout the nucleus. ...
Excess bone loss due to increased osteoclastogenesis is a significant clinical problem.
Intraflagellar transport (IFT) proteins have been reported to regulate cell growth
and differentiation. The role of IFT80, an IFT complex B protein, in osteoclasts (...
Angiogenesis contributes fundamentally to embryonic development, tissue homeostasis,
and wound healing. Basic fibroblast growth factor (FGF2) is recognized as the first
proangiogenic molecule discovered, and it facilitates angiogenesis by activating FGF
...
As a sedentary epithelium turns motile during wound healing, morphogenesis, and metastasis,
the Golgi apparatus moves from an apical position, above the nucleus, to a basal position.
This apical-to-basal repositioning of Golgi is critical for epithelial ...
Macroautophagy promotes cellular homeostasis by delivering cytoplasmic constituents
to lysosomes for degradation [Mizushima, Nat. Cell Biol. 20, 521–527 (2018)]. However, while most studies have focused on the mechanisms of
protein degradation during this ...
Proper orientation of the mitotic spindle plays a crucial role in embryos, during
tissue development, and in adults, where it functions to dissipate mechanical stress
to maintain tissue integrity and homeostasis. While mitotic spindles have been shown
to ...
Mechanisms of defense against ferroptosis (an iron-dependent form of cell death induced
by lipid peroxidation) in cellular organelles remain poorly understood, hindering
our ability to target ferroptosis in disease treatment. In this study, metabolomic
...
In the metazoan S phase, coordinated firing of clusters of origins replicates different
parts of the genome in a temporal program. Despite advances, neither the mechanism
controlling timing nor that coordinating firing of multiple origins is fully ...
Developmental Biology
Delineating gene regulatory networks that orchestrate cell-type specification is a
continuing challenge for developmental biologists. Single-cell analyses offer opportunities
to address these challenges and accelerate discovery of rare cell lineage ...
Ecology
Modeling fire spread as an infection process is intuitive: An ignition lights a patch
of fuel, which infects its neighbor, and so on. Infection models produce nonlinear
thresholds, whereby fire spreads only when fuel connectivity and infection probability
...
Physiological performance declines precipitously at high body temperature (Tb), but little attention has been paid to adaptive variation in upper Tb limits among endotherms. We hypothesized that avian maximum tolerable Tb (Tbmax) has evolved in response ...
Biodiversity is often attributed to a dynamic equilibrium between the immigration
and extinction of species. This equilibrium forms a common basis for studying ecosystem
assembly from a static reservoir of migrants—the mainland. Yet, natural ecosystems
...
Environmental Sciences
Severe deterioration of water quality in lakes, characterized by overabundance of
algae and declining dissolved oxygen in the deep lake (DOB), was one of the ecological crises of the 20th century. Even with large reductions
in phosphorus loading, termed “...
Nonpharmaceutical interventions (NPIs) such as mask wearing can be effective in mitigating
the spread of infectious diseases. Therefore, understanding the behavioral dynamics
of NPIs is critical for characterizing the dynamics of disease spread. ...
Evolution
Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae,
renowned for having evolved male pregnancy. Comprising three known species, seadragons
are widely recognized and admired for their fantastical body forms and coloration,
and ...
Genetics
Discovery of deafness genes and elucidating their functions have substantially contributed
to our understanding of hearing physiology and its pathologies. Here we report on
DNA variants in MINAR2, encoding membrane integral NOTCH2-associated receptor 2, ...
Immunology And Inflammation
During viral infection, sensing of viral RNA by retinoic acid–inducible gene-I–like
receptors (RLRs) initiates an antiviral innate immune response, which is mediated
by the mitochondrial adaptor protein VISA (virus-induced signal adaptor; also known
as ...
Immune checkpoint inhibitors (ICIs) are essential components of the cancer therapeutic
armamentarium. While ICIs have demonstrated remarkable clinical responses, they can
be accompanied by immune-related adverse events (irAEs). These inflammatory side ...
Mitochondrial calcium uniporter promotes phagocytosis-dependent activation of the NLRP3 inflammasome
Mitochondria, a highly metabolically active organelle, have been shown to play an
essential role in regulating innate immune function. Mitochondrial Ca2+ uptake via the mitochondrial Ca2+ uniporter (MCU) is an essential process regulating mitochondrial ...
Behçet’s disease (BD) is a chronic vasculitis characterized by systemic immune aberrations.
However, a comprehensive understanding of immune disturbances in BD and how they contribute
to BD pathogenesis is lacking. Here, we performed single-cell and bulk ...
Tumor infiltration by T cells profoundly affects cancer progression and responses
to immunotherapy. However, the tumor immunosuppressive microenvironment can impair
the induction, trafficking, and local activity of antitumor T cells. Here, we investigated
...
Medical Sciences
Deficiencies of the transmembrane iron-transporting protein ferroportin (FPN1) cause
the iron misdistribution that underlies ferroportin disease, anemia of inflammation,
and several other human diseases and conditions. A small molecule natural product,
...
β-adrenergic receptor (β-AR) signaling plays predominant roles in modulating energy
expenditure by triggering lipolysis and thermogenesis in adipose tissue, thereby conferring
obesity resistance. Obesity is associated with diminished β3-adrenergic ...
Microbiology
One of the biggest challenges in microbiome research in environmental and medical
samples is to better understand functional properties of microbial community members
at a single-cell level. Single-cell isotope probing has become a key tool for this
...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolves rapidly under
the pressure of host immunity, as evidenced by waves of emerging variants despite
effective vaccinations, highlighting the need for complementing antivirals. We report
that ...
Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is
moderated by complex interactions between trees and soil microorganisms. However,
existing methods limit our ability to predict how changes in environmental conditions
...
Host genetic resistance to viral infection controls the pathogenicity and epidemic
dynamics of infectious diseases. Refrex-1 is a restriction factor against feline leukemia
virus subgroup D (FeLV-D) and an endogenous retrovirus (ERV) in domestic cats (ERV-...
Construction and remodeling of the bacterial peptidoglycan (PG) cell wall must be
carefully coordinated with cell growth and division. Central to cell wall construction
are hydrolases that cleave bonds in peptidoglycan. These enzymes also represent ...
Human genetic variation associates with the composition of the gut microbiome, yet
its influence on clinical traits remains largely unknown. We analyzed the consequences
of nearly a thousand gut microbiome-associated variants (MAVs) on phenotypes reported
...
Massively parallel measurements of dominant-negative inhibition by protein fragments
have been used to map protein interaction sites and discover peptide inhibitors. However,
the underlying principles governing fragment-based inhibition have thus far ...
Neuroscience
Neural plasticity in subareas of the rodent amygdala is widely known to be essential
for Pavlovian threat conditioning and safety learning. However, less consistent results
have been observed in human neuroimaging studies. Here, we identify and test three
...
The current dominant view of the hippocampus is that it is a navigation “device” guided
by environmental inputs. Yet, a critical aspect of navigation is a sequence of planned,
coordinated actions. We examined the role of action in the neuronal ...
Retromer is a heteropentameric complex that plays a specialized role in endosomal
protein sorting and trafficking. Here, we report a reduction in the retromer proteins—vacuolar
protein sorting 35 (VPS35), VPS26A, and VPS29—in patients with amyotrophic ...
VEGF was initially discovered due to its angiogenic activity and therefore named “vascular
endothelial growth factor.” However, its more recently discovered neurotrophic activity
may be evolutionarily more ancient. Our previous work showed that all the ...
Pharmacology
The brain microcirculation is increasingly viewed as a potential target for disease-modifying
drugs in the treatment of Alzheimer’s disease patients, reflecting a growing appreciation
of evidence that cerebral blood flow is compromised in such patients. ...
Physiology
Both chronic obstructive pulmonary disease (COPD) and asthma are severe respiratory
diseases. Bitter receptor–mediated bronchodilation is a potential therapy for asthma,
but the mechanism underlying the agonistic relaxation of airway smooth muscle (ASM)
...
Plant Biology
Plants use photoperiodism to activate flowering in response to a particular daylength.
In rice, flowering is accelerated in short-day conditions, and even a brief exposure
to light during the dark period (night-break) is sufficient to delay flowering. ...
Asian rice (Oryza sativa L.) is consumed by more than half of the world's population. Despite its global importance,
the process of early rice domestication remains unclear. During domestication, wild
rice (Oryza rufipogon Griff.) acquired non-seed-...
Psychological And Cognitive Sciences
The influence of prior knowledge on memory is ubiquitous, making the specific mechanisms
of this relationship difficult to disentangle. Here, we show that expert knowledge
produces a fundamental shift in the way that interitem similarity (i.e., the ...
A prominent and robust finding in cognitive neuroscience is the strengthening of memories
during nonrapid eye movement (NREM) sleep, with slow oscillations (SOs;<1Hz) playing
a critical role in systems-level consolidation. However, NREM generally shows a ...
Diffusion tractography allows identification and measurement of structural tracts
in the human brain previously associated with motivated behavior in animal models.
Recent findings indicate that the structural properties of a tract connecting the
midbrain ...
Systems Biology
Collective behaviors require coordination among a group of individuals. As a result,
individuals that are too phenotypically different from the rest of the group can be
left out, reducing heterogeneity, but increasing coordination. If individuals also
...
The high-dimensional character of most biological systems presents genuine challenges
for modeling and prediction. Here we propose a neural network–based approach for dimensionality
reduction and analysis of biological gene expression data, using, as a ...
Correction
SI Correction
Cover image: Pictured is a leafy seadragon (Phycodurus eques). Clayton M. Small, Susan Bassham, et al. analyzed annotated genomes of P. eques and a weedy seadragon (Phyllopteryx taeniolatus) to explore the genetics of seadragons’ unique traits, such as their elaborate, leaf-like appendages. The authors identified several genomic features specific to seadragons, including a high density of repetitive DNA, recent expansion of gene families, and loss of highly conserved genetic pathways. The results provide insight into seadragon evolution and a resource for conservation studies of seadragons and their relatives. See the article by Small, Bassham, et al., e2119602119. Image credit: Graham Short (California Academy of Sciences, San Francisco, CA).
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