Table Of Contents Page, PNAS Volume 122, Number 49
This Week in PNAS
Core Concepts
QnAs
Commentaries
Perspective
In response to challenges posed by climate change, rice farming emerges as a strategic
adaptation in the agriculture sector in the northeastern United States. Cultivating
rice can diversify farming practices, create new sources of income, improve water
...
Letters
Brief Reports
Fisheries are critical for sustaining waterfront communities. However, subsistence
fishing is not well understood in the United States, despite its potential contributions
to health and culture. We piloted a multivariable construct to classify subsistence
...
The competition–colonization trade-off is a possible explanation for coexistence of
species in a metacommunity context that has been intensively studied for decades.
Nonetheless, questions about the ubiquity and generality of the mechanism remain.
The ...
Physical Sciences
Applied Mathematics
We investigate a randomly evolving process of subgraphs in an underlying host graph
using the spectral theory of semigroups related to the Tsetlin library and hyperplane
arrangements. Starting with some initial subgraph, at each iteration, we apply a ...
Transmission dynamics of infectious diseases are often studied using compartmental
mathematical models, which are commonly represented as systems of autonomous ordinary
differential equations. A key step in the analysis of such models is to identify ...
Applied Physical Sciences
Biomolecular condensates play a crucial role in the spatial organization of living
matter. These membrane-less organelles, resulting from liquid–liquid phase separation,
operate far from thermodynamic equilibrium, with their size and stability influenced
...
Structural coloration offers many advantages over conventionally used pigment-based
colors due to their nontoxic, fade-resistant, and environmentally friendly nature.
These colors arise from the structural arrangements of colorless materials at the
...
Biology is teeming with intricate molecular structures whose geometries are inextricably
linked to their function. A prototypical example is the helical bacterial flagellum,
a complex curved crystalline assembly of proteins that the bacterium uses to ...
The primary challenge hindering widespread adoption of lithium (Li) anodes is the
safety risks of short circuits owing to the penetration of Li whiskers, where their
mechanical property plays a crucial role. However, measurement of the overall Young’s
...
Despite significant advances in characterizing the highly nonconvex landscapes of
constraint satisfaction problems, the good performance of certain algorithms in solving
hard combinatorial optimization tasks remains poorly understood. This gap in ...
Zeolites are crystalline, microporous silicates widely used in catalysis and separations,
yet the molecular mechanisms of their formation remain unresolved. Experiments indicate
that hydrothermal synthesis of silica zeolites from clear solution proceeds ...
Preclinical shortwave infrared/near-infrared II (SWIR/NIR-II, 1,000 to 3,000 nm) fluorescence
imaging has shown superior contrast, resolution, and penetration depth compared to
traditional near-infrared I (NIR-I, 700 to 900 nm) imaging, owing to reduced ...
Astronomy
NASA’s OSIRIS-REx mission characterized the asteroid Bennu and delivered pristine
samples of its regolith to Earth. Coordinated analyses of this primitive, carbonaceous
material are elucidating the abiotic formation and inventory of prebiotic organic
...
Biophysics and Computational Biology
Cone opsins enable daylight vision and color discrimination. Like their dim-light
cousin rhodopsin (Rho) found in rod cells, they use a covalently attached retinal
ligand to sense light and initiate visual phototransduction by activating G proteins.
...
Predicting the outcomes of species invasions is a central goal of ecology, a task
made especially challenging due to ecological feedbacks. To address this, we develop
a general theory of ecological invasions applicable to a wide variety of ecological
...
Chemistry
Catalytic CO2 reduction into value-added products is an energy-intensive process and typically
relies on molecular hydrogen as reductant. Coupling CO2 reduction with propane dehydrogenation for in situ hydrogen generation presents a
sustainable ...
The mechanisms of molecular processes can be characterized by following the minimum
free energy pathway (MFEP) on the underlying multidimensional conformational landscapes.
Despite recent advancements in enhanced sampling algorithms, obtaining a converged
...
Earth, Atmospheric, and Planetary Sciences
The abiotic production of sulfur-containing biomolecules under mild and globally relevant
conditions has been an elusive endeavor in prebiotic chemistry experiments. As a result,
a disconnect has emerged between understanding the origins of life and the ...
Marine shallow cumulus clouds have long caused large uncertainty in climate projections.
Such “trade cumuli” frequently organize into mesoscale (10 to 500 km) structures,
through two processes that couple the clouds to shallow mesoscale circulations: i)
...
Wildfire activity has increased dramatically in the western United States over the
last three decades, having a significant impact on air quality and human health. However,
quantifying the drivers of trends in wildfires and subsequent smoke concentrations
...
Simple binary oxide glasses can exhibit a compression behavior distinct from that
of their crystalline counterparts. In this study, we employed high-pressure X-ray
absorption spectroscopy, coupled to the diamond anvil cell, to investigate in detail
local ...
The long-term climate of Earth alternates between warmer and cooler periods, for which
atmospheric CO2 content is often viewed as a primary control. Although silicate weathering feedback
governs this long-term equilibrium, the partitioning of carbonate ...
Subduction zones transport significant amounts of water into Earth’s mantle, primarily
through hydrous minerals such as lawsonite. However, the seismic detectability of
lawsonite-bearing oceanic crust at mantle depths remains uncertain. To address this
...
The Lomagundi–Jatuli Event (LJE), Earth’s most pronounced and prolonged positive carbon
isotope excursion, followed the Great Oxidation Event and remains enigmatic in origin.
We present a Pb–Pb isochron age of 2,194 ± 5 Ma for black shales from the ...
Physics
We present the time-dependent Quantum Geometric Tensor (tQGT) as a comprehensive tool
for capturing the geometric character of insulators observable within linear response.
We show that tQGT describes the zero-point motion of bound electrons and acts as a
...
Social Sciences
Political Sciences
Declining confidence in public institutions afflicts many democracies, a trend apparently
exacerbated by backsliding leaders. These are leaders who gradually undermine the
institutions that sustain democratic competition and accountability. Does the ...
Psychological and Cognitive Sciences
Why and when do people draw upon religious and supernatural solutions to problems?
Cognitive scientists and anthropologists have proposed a range of answers, stressing
religion and ritual’s capacity to alleviate anxiety, create a sense of order, or ...
Biological Sciences
Agricultural Sciences
To understand the biological function of genomic regions, vast molecular data have
been generated to annotate mammalian genomes. However, how to effectively use such
extensive information to improve the mapping and prediction of complex traits, including
...
Biochemistry
The genomes of various RNA viruses and a subset of human genes contain structured
RNA elements termed internal ribosomal entry sites (IRESs) to initiate translation
in a cap-independent manner. The well-studied IRES from Hepatitis C virus (HCV) binds
to ...
RAD51AP1 is an emergent key factor in homologous recombination (HR), the major pathway
for accurate repair of DNA double-strand breaks, and in alternative lengthening of
telomeres (ALT). Depletion of RAD51AP1 diminishes HR and overexpression is common
in ...
IMP dehydrogenase (IMPDH) controls a key regulatory node in purine biosynthesis. Gain-of-function
mutations in human IMPDH2 are associated with neurodevelopmental disorders and neuromuscular
symptoms including dystonia, but the developmental mechanisms ...
Phosphate is often a limiting resource, directly affecting the availability of key
biomolecules such as nucleotides. To cope with phosphate scarcity, bacteria have evolved
enzymes that utilize alternative phosphorus compounds, including phosphite (Pt). ...
Biophysics and Computational Biology
High-resolution studies in structural biology are often limited by the challenges
of crystallization and low contrast in the cellular native environment. The exquisite
labeling specificity of fluorescence microscopy gets around these issues and allows
...
Although histologically normal, esophageal preneoplastic cells harbor early genetic
alterations and likely exhibit lineage plasticity. However, their origins and trajectories
remain unclear. To address this, we combined genetic barcoding with single-cell ...
Escherichia coli swims using helical flagellar filaments driven at their base by a rotary motor. Torque-generating
“stator” units drive the bacterial flagellar motor by transmitting mechanical power
to a cytoplasmic “rotor,” the C-ring. Each stator unit ...
Currently approved vaccines for the prevention of malaria provide only partial protection
against disease due to high variability in the quality of induced antibodies. These
vaccines present the unstructured central repeat region, as well as the C-...
The development of a zygote into a functional organism requires that this single progenitor
cell gives rise to numerous distinct cell types. Attempts to exhaustively tabulate
the interactions within developmental signaling networks that coordinate these ...
Cell Biology
Cilia are hair-like organelles that protrude from the cell surface. In mammals, tracheal
multiciliated cells (MCCs) play an important role in elimination of hazardous microorganisms
by driving a unidirectional mucus flow. Although uniform orientation of ...
Tight junctions seal the paracellular space between epithelial cells, with their claudin
(CLDN) composition dictating epithelial permeability properties. In kidney thick ascending
limbs, calcium is reabsorbed paracellularly through a meshwork of CLDN16 ...
Endoplasmic reticulum–associated degradation (ERAD) is a quality control process which
removes misfolded proteins from the ER. The central component of the most conserved
ERAD system is an integral membrane ubiquitin ligase called Hrd1. The Hrd1 ligase
...
Cardiac calcification, often seen in age-related diseases, impairs heart function,
yet its association with malignant tumors remains largely overlooked. Our study revealed
that pericardial calcification (PC) occurs in up to 80% of breast cancer patients
...
Triple-negative breast cancer (TNBC) is a highly aggressive and metastatic form of
breast cancer that lacks an effective targeted therapy. To identify potential therapeutic
targets, we investigated the phosphohistidine phosphatase, LHPP, which has been ...
Pancreatic ductal adenocarcinoma (PDAC) has one of the lowest cancer survival rates.
Recent studies using RAS inhibitors have opened the door to more efficacious therapies,
although their beneficial effect is still limited mainly due to the rapid ...
Signaling by luteinizing hormone (LH) in the outer granulosa cells of mammalian ovarian
follicles causes meiosis to resume in the oocyte, located ~10 cell layers away, preparing
the oocyte for ovulation and fertilization. This long-distance communication ...
Developmental Biology
Cranial neural crest cells (NCCs) undergo dynamic processes during embryonic development,
including delamination from the neural tube by epithelial-to-mesenchymal transition
(EMT), migration to the periphery, condensation via mesenchymal-to-epithelial ...
During vertebrate embryogenesis, hematopoietic stem and progenitor cells (HSPCs) originate
from hemogenic endothelium (HE) in the dorsal aorta through endothelial-to-hematopoietic
transition (EHT). While basal inflammation is essential for this process, ...
Evolution
Gene duplication followed by adaptation to new selection pressures has been proposed
to be of central importance in the evolution of venom toxins. Coupling high-quality
genome data with quantitative bioactivity readouts can be used to understand how venom
...
Genetics
Ribosomes catalyze all protein synthesis, and mutations altering their levels and
function underlie many developmental diseases and cancer. Historically considered
to be invariant machines, ribosomes differ in composition between tissues and developmental
...
Immunology and Inflammation
IgG is a key to adaptive immunity and a critical platform for drug design. Sialic
acid on the conserved glycan within the Fc domain is believed to promote anti-inflammatory
IgG function; however, regulation of sialylation remains poorly defined. We ...
Glucose is catabolized by two major metabolic pathways, glycolysis and the oxidative
pentose phosphate pathway (oxPPP). The oxPPP generates nicotinamide adenine dinucleotide
phosphate (NADPH) at two steps, glucose-6-phosphate dehydrogenase (G6PD), the ...
Foxp3+ regulatory T cells (Tregs) heavily infiltrate malignant tumors and restrict antitumor
immunity. These tumor-infiltrating Tregs (TI-Tregs) adopt a distinct phenotype by
expressing a unique set of genes. This TI-Treg gene expression signature is ...
Medical Sciences
HOXB13 is a lineage-specific transcription factor that plays a critical role in initiation
and progression of prostate cancer (PCa). While most research has focused on the role
of HOXB13 on androgen receptor (AR) activity, here we demonstrate that HOXB13 ...
This study reanalyzed endothelial cell (EC) gene expression in the mouse aorta utilizing
eight single-cell RNA-sequencing datasets. Contrary to the assumption that all ECs
originated from the luminal surface, we identified two distinct sites of origin: ...
Studying the lineage commitment and differentiation potential of long-term hematopoietic
stem cells (LT-HSCs) is important to understand the dynamics of hematopoiesis. A central
question concerns which hematopoietic stem and progenitor cell populations ...
Microbiology
During Mycobacterium tuberculosis infections bacteria are engulfed by macrophages, a main line of defense against invading
pathogens. Upon activation, macrophages increase glycolysis, producing the antibacterial
aldehyde methylglyoxal. To test whether ...
Evidence is emerging that perturbed postnatal gut microbiota development is causally
related to childhood undernutrition. Clinical trials in undernourished Bangladeshi
children found that a polysaccharide-rich, microbiota-directed complementary food
(MDCF-...
Endogenous retroviruses (ERV) represent 8 to 10% of mammalian genome. While most ERV
are defective, a few retroviral genes, such as the envelope syncytins, were exapted
during evolution and likely contributed to the emergence of placental mammals. We
have ...
Bacterial biofilms are resilient multicellular communities that underlie persistent
infections and environmental survival. Dispersal from biofilms is a pivotal event
for transmission and pathogenesis, yet the host signals and bacterial mechanisms ...
Signal transduction by histidine kinases (HKs) is nearly ubiquitous in bacterial species.
HKs can either sense ligands directly or indirectly via a cognate solute-binding protein
(SBP). The molecular basis for SBP-dependent signal reception, however, ...
Bacterial small RNAs (sRNAs) derived from mRNA 3′ untranslated regions (3′ UTRs) have
emerged as important regulators of gene expression, yet their evolutionary origins
and functional diversification remain poorly understood compared to the protein-coding
...
Biotin is an essential enzyme cofactor for intermediary metabolism, and its importance
is reflected by the multiplicity of bacterial pathways to its universal precursor,
pimelic acid. Here, we report identification of a fourth pimeloyl pathway in the rare
...
Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular
processes by cycling between active and inactive states through nucleotide binding
and hydrolysis. These mechanisms were long thought to rely exclusively on ATPase or
...
Human norovirus (HuNoV) is the leading cause of gastroenteritis. However, the lack
of a reverse genetics system for infectious HuNoV has hindered the development of
antivirals and vaccines. Herein, we established a reverse genetics system for infectious
...
Guanidine is well known as a denaturing agent. However, recent studies have demonstrated
both the widespread synthesis of guanidine, e.g., in plants and mammals, as well as
the widespread occurrence of guanidine metabolism in bacteria, suggesting a ...
Hepatitis E virus (HEV), the causative agent of hepatitis E, is threatening public
health globally. Due to the shortage of efficient in vitro cell culture systems and
in vivo model, the viral replication and pathogenesis mechanisms remain largely unknown.
...
Neuroscience
Internal bodily signals, notably the heartbeat, influence our perception of the external
world—but the nature of this influence remains unclear. Different frameworks, originating
in opposing views of the function of interoception, have developed largely ...
Gene expression in the brain is typically evaluated using invasive biopsy or postmortem
histology. Serum markers provide an alternative way to monitor the brain, but relatively
few such markers exist. Additionally, the origin of serum markers often cannot ...
In the vertebrate retina, short wavelength-sensitive S-cones and their downstream
interneurons play unique roles in both image forming and non-image-forming vision.
Due to their conserved relative rarity in the retina and the high density of rods
found in ...
Pharmacology
Cone opsins enable daylight vision and color discrimination. Like their dim-light
cousin rhodopsin (Rho) found in rod cells, they use a covalently attached retinal
ligand to sense light and initiate visual phototransduction by activating G proteins.
...
Physiology
Higher exercise capacity and regular exercise training improve cancer prognosis at
all stages of disease. However, the metabolic adaptations to aerobic exercise training
that mediate tumor–host interactions are poorly understood. Here, we demonstrate that
...
Proper endometrial function is critical for establishing and maintaining healthy pregnancies,
as well as preventing the pathogenesis of conditions such as endometrial hyperplasia
and endometrial cancer. The TGFβ signaling pathway regulates key aspects of ...
Plant Biology
Genomic integrity is constantly challenged by transcription/replication conflicts,
a major source of replication stress and instability across all life forms. While
extensive studies have elucidated mechanisms for resolving transcription/replication
...
The quiescent center (QC) resides in a reversible G0 state in which cells are not actively dividing and yet retain their proliferation
competence upon stimulation. How this quiescent state is molecularly defined and stably
maintained is a fascinating ...
Psychological and Cognitive Sciences
Neurofluids, including cerebrospinal fluid (CSF) and interstitial fluid, circulate
through regulated central nervous system pathways to clear cerebral waste and support
brain health, with elevated CSF flow hyperdynamicity and regurgitation through the
...
Conscious awareness refers to the subjective experience of perceiving, thinking, and
feeling and the ability to report these experiences. These perceptions and thoughts
are experienced as bound to an individual self. A fundamental aspect of this self-...
Systems Biology
Predicting the outcomes of species invasions is a central goal of ecology, a task
made especially challenging due to ecological feedbacks. To address this, we develop
a general theory of ecological invasions applicable to a wide variety of ecological
...
Corrections
Cover image: Pictured is a Drosophila ovary with a hypomorphic mutation, showing ribosomal protein (RP) S6 phosphorylation in magenta, DNA in blue, and cell membranes in cyan. Katarina Grobicki et al. used a Drosophila melanogaster model to investigate the function of 11 RP paralogues, which have been hypothesized to alter the function of ribosomes in different tissues. Genetic analysis indicated that the majority of RP paralogues were not required for development or fertility in D. melanogaster. The results suggest that RP paralogues do not provide specialized functions and may instead sustain ribosome levels during development. See the article by Grobicki et al. e2506642122. Image credit: Katarina Grobicki.
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