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Table of Contents — August 13, 2024, 121 (33) | PNAS

Table Of Contents Page, PNAS Volume 121, Number 33

PNAS August 13, 2024

This Week in PNAS

Inner Workings

QnAs

Retrospective

Commentaries

Letters

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 ...
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 ...

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

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

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 ...

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