Table Of Contents Page, PNAS Volume 121, Number 6
This Week in PNAS
Inner Workings
QnAs
Commentary
Physical Sciences
Applied Physical Sciences
Proteins play a central role in biology from immune recognition to brain activity.
While major advances in machine learning have improved our ability to predict protein
structure from sequence, determining protein function from its sequence or structure
...
It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection
leads to the strong but ineffective inflammatory response that characterizes severe
Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse ...
Invisibility, a fascinating ability of hiding objects within environments, has attracted
broad interest for a long time. However, current invisibility technologies are still
restricted to stationary environments and narrow band. Here, we experimentally ...
As a prototypical photocatalyst, TiO has been extensively studied. An interesting yet puzzling experimental fact was that
P25—a mixture of anatase and rutile TiO—outperforms the individual phases; the origin of this mysterious fact, however, remains
...
We report on the collective response of an assembly of chemomechanical Belousov-Zhabotinsky
(BZ) hydrogel beads. We first demonstrate that a single isolated spherical BZ hydrogel
bead with a radius below a critical value does not oscillate, whereas an ...
Biophysics and Computational Biology
A central challenge in the study of intrinsically disordered proteins is the characterization
of the mechanisms by which they bind their physiological interaction partners. Here,
we utilize a deep learning–based Markov state modeling approach to ...
In various biological systems, information from many noisy molecular receptors must
be integrated into a collective response. A striking example is the thermal imaging
organ of pit vipers. Single nerve fibers in the organ reliably respond to milli-Kelvin
(...
Spontaneously occurring miniature excitatory postsynaptic currents (mEPSCs) are fundamental
electrophysiological events produced by quantal vesicular transmitter release at synapses.
Their analysis can provide important information regarding pre- and ...
Among the long-standing efforts to elucidate the physical mechanisms of protein–ligand
catch bonding, particular attention has been directed at the family of selectin proteins.
Selectins exhibit slip, catch–slip, and slip–catch–slip bonding, with minor ...
Computational models of evolution are valuable for understanding the dynamics of sequence
variation, to infer phylogenetic relationships or potential evolutionary pathways
and for biomedical and industrial applications. Despite these benefits, few have ...
Chemistry
Atomically dispersed catalysts are a promising alternative to platinum group metal
catalysts for catalyzing the oxygen reduction reaction (ORR), while limited durability
during the electrocatalytic process severely restricts their practical application.
...
The incorporation of multiple metal ions in metal–organic frameworks (MOFs) through
one-pot synthesis can induce unique properties originating from specific atomic-scale
spatial apportionment, but the extraction of this crucial information poses ...
Memristive devices, electrical elements whose resistance depends on the history of
applied electrical signals, are leading candidates for future data storage and neuromorphic
computing. Memristive devices typically rely on solid-state technology, while ...
Metal-organic frameworks (MOFs) are superior ion adsorbents for selectively capturing
toxic ions from water. Nevertheless, they have rarely been reported to have lithium
selectivity over divalent cations due to the well-known flexibility of MOF framework
...
SO2 (Sulfur dioxide) is the major precursor to the production of sulfuric acid (H2SO4), contributing to acid rain and atmospheric aerosols. Sulfuric acid formed from SO2 generates light-reflecting sulfate aerosol particles in the atmosphere. This property
...
Helical sulfonyl-γ-AApeptides modulating Aβ oligomerization and cytotoxicity by recognizing Aβ helix
In contrast to prevalent strategies which make use of β-sheet mimetics to block Aβ
fibrillar growth, in this study, we designed a series of sulfonyl-γ-AApeptide helices
that targeted the crucial α-helix domain of Aβ13-26 and stabilized Aβ conformation
to ...
Relating the macroscopic properties of protein-based materials to their underlying
component microstructure is an outstanding challenge. Here, we exploit computational
design to specify the size, flexibility, and valency of de novo protein building blocks,...
Molecular understanding of the vertebrate Organizer, a tissue center critical for
inductive signaling during gastrulation, has so far been mostly limited to transcripts
and a few proteins, the latter due to limitations in detection and sensitivity. The
...
Computer Sciences
We present an accreditation protocol for analogue, i.e., continuous-time, quantum
simulators. For a given simulation task, it provides an upper bound on the variation
distance between the probability distributions at the output of an erroneous and error-...
Earth, Atmospheric, and Planetary Sciences
Amplified warming of high latitudes and rapid thaw of frozen ground threaten permafrost
carbon stocks. The presence of permafrost modulates water infiltration and flow, as
well as sediment transport, on soil-mantled slopes, influencing the balance of ...
We present improved estimates of air–sea CO2 exchange over three latitude bands of the Southern Ocean using atmospheric CO2 measurements from global airborne campaigns and an atmospheric 4-box inverse model
based on a mass-indexed isentropic coordinate (M...
Industrial and environmental granular flows commonly exhibit a phenomenon known as
“granular segregation,” in which grains separate according to physical characteristics
(size, shape, density), interfering with industrial applications (cement mixing, ...
It is generally accepted that aragonite crystals of biogenic origin are characterized
by significantly higher twin densities compared to samples formed during geological
processes. Based on our single crystal X-ray diffraction (SCXRD) and transmission
...
The assumption that vegetation improves air quality is prevalent in scientific, popular,
and political discourse. However, experimental and modeling studies show the effect
of green space on air pollutant concentrations in urban settings is highly ...
Engineering
Shape transformation, a key mechanism for organismal survival and adaptation, has
gained importance in developing synthetic shape-shifting systems with diverse applications
ranging from robotics to bioengineering. However, designing and controlling ...
Ultralight architected materials enabled by advanced manufacturing processes have
achieved density-normalized strength and stiffness properties that are inaccessible
to bulk materials. However, the majority of this work has focused on static loading
and ...
Oxygen evolution reaction (OER) is the pivotal obstacle of water splitting for hydrogen
production. Dual-sites catalysts (DSCs) are considered exceeding single-site catalysts
due to the preternatural synergetic effects of two metals in OER. However, ...
Physics
We present an accreditation protocol for analogue, i.e., continuous-time, quantum
simulators. For a given simulation task, it provides an upper bound on the variation
distance between the probability distributions at the output of an erroneous and error-...
Innovation and obsolescence describe dynamics of ever-churning and adapting social
and biological systems, concepts that encompass field-specific formulations. We formalize
the connection with a reduced model of the dynamics of the “space of the possible”
...
High pressure has triggered various novel states/properties in condensed matter, as
the most representative and dramatic example being near-room-temperature superconductivity
in highly pressured hydrides (~200 GPa). However, the mechanism of ...
Electrostatic forces in solutions are highly relevant to a variety of fields, ranging
from electrochemical energy storage to biology. However, their manifestation in concentrated
electrolytes is not fully understood, as exemplified by counterintuitive ...
Social Sciences
Demography
Taking stock of individuals’ perceived family ideals is particularly important in
the current moment given unprecedented fertility declines and the diversification
of households in advanced industrial societies. Study participants in urban China,
Japan, ...
Political Sciences
In the United States, estimates of excess deaths attributable to the COVID-19 pandemic
have consistently surpassed reported COVID-19 death counts. Excess deaths reported
to non-COVID-19 natural causes may represent unrecognized COVID-19 deaths, deaths
...
Social Sciences
Understanding and predicting the emergence and evolution of cultural tastes manifested
in consumption patterns is of central interest to social scientists, analysts of culture,
and purveyors of content. Prior research suggests that taste preferences ...
Biological Sciences
Applied Biological Sciences
Fibroblast growth factor receptor (FGFR) kinase inhibitors have been shown to be effective
in the treatment of intrahepatic cholangiocarcinoma and other advanced solid tumors
harboring FGFR2 alterations, but the toxicity of these drugs frequently leads to ...
Biochemistry
A missense variant in patatin-like phospholipase domain-containing protein 3 [PNPLA3(I148M)]
is the most impactful genetic risk factor for fatty liver disease (FLD). We previously
showed that PNPLA3 is ubiquitylated and subsequently degraded by ...
Helical sulfonyl-γ-AApeptides modulating Aβ oligomerization and cytotoxicity by recognizing Aβ helix
In contrast to prevalent strategies which make use of β-sheet mimetics to block Aβ
fibrillar growth, in this study, we designed a series of sulfonyl-γ-AApeptide helices
that targeted the crucial α-helix domain of Aβ13-26 and stabilized Aβ conformation
to ...
The synthesis of proteins as encoded in the genome depends critically on translational
fidelity. Nevertheless, errors inevitably occur, and those that result in reading
frame shifts are particularly consequential because the resulting polypeptides are
...
Neurotransmitter receptors are essential components of synapses for communication
between neurons in the brain. Because the spatiotemporal expression profiles and dynamics
of neurotransmitter receptors involved in many functions are delicately governed in
...
Biophysics and Computational Biology
Proteins play a central role in biology from immune recognition to brain activity.
While major advances in machine learning have improved our ability to predict protein
structure from sequence, determining protein function from its sequence or structure
...
A central challenge in the study of intrinsically disordered proteins is the characterization
of the mechanisms by which they bind their physiological interaction partners. Here,
we utilize a deep learning–based Markov state modeling approach to ...
Relating the macroscopic properties of protein-based materials to their underlying
component microstructure is an outstanding challenge. Here, we exploit computational
design to specify the size, flexibility, and valency of de novo protein building blocks,...
During cell division, precise and regulated distribution of cellular material between
daughter cells is a critical step and is governed by complex biochemical and biophysical
mechanisms. To achieve this, membraneless organelles and condensates often ...
Amino acid mutations that lower a protein’s thermodynamic stability are implicated
in numerous diseases, and engineered proteins with enhanced stability can be important
in research and medicine. Computational methods for predicting how mutations perturb
...
Cell Biology
Mucins are large, highly glycosylated extracellular matrix proteins that line and
protect epithelia of the respiratory, digestive, and urogenital tracts. Previous work
has shown that mucins form large, interconnected polymeric networks that mediate their
...
Rett syndrome (RTT) is a devastating neurodevelopmental disorder primarily caused
by mutations in the methyl-CpG binding protein 2 (Mecp2) gene. Here, we found that
inhibition of Receptor-Interacting Serine/Threonine-Protein Kinase 1 (RIPK1) kinase
...
Cancer is a leading cause of mortality in humans, but the efficacy of current treatments
for many cancers is limited, as they lack unique mechanistically defined targets.
Here, we show that, upon malignant transformation, aggressive oncocells generate a
...
Developmental Biology
Molecular understanding of the vertebrate Organizer, a tissue center critical for
inductive signaling during gastrulation, has so far been mostly limited to transcripts
and a few proteins, the latter due to limitations in detection and sensitivity. The
...
Congenital anomalies of the lower genitourinary (LGU) tract are frequently comorbid
due to genetically linked developmental pathways, and are among the most common yet
most socially stigmatized congenital phenotypes. Genes involved in sexual ...
Ecology
Protected areas are of paramount relevance to conserving wildlife and ecosystem contributions
to people. Yet, their conservation success is increasingly threatened by human activities
including habitat loss, climate change, pollution, and species ...
Microbial interactions are key to maintaining soil biodiversity. However, whether
negative or positive associations govern the soil microbial system at a global scale
remains virtually unknown, limiting our understanding of how microbes interact to
...
Self-organized spatial patterns are a common feature of complex systems, ranging from
microbial communities to mussel beds and drylands. While the theoretical implications
of these patterns for ecosystem-level processes, such as functioning and resilience,...
Microbial systems appear to exhibit a relatively high switching capacity of moving
back and forth among few dominant communities (taxon memberships). While this switching
behavior has been mainly attributed to random environmental factors, it remains ...
How individual animals respond to climate change is key to whether populations will
persist or go extinct. Yet, few studies investigate how changes in individual behavior
underpin these population-level phenomena. Shifts in the distributions of migratory
...
Environmental Sciences
The assumption that vegetation improves air quality is prevalent in scientific, popular,
and political discourse. However, experimental and modeling studies show the effect
of green space on air pollutant concentrations in urban settings is highly ...
Human–wildlife conflict is an important factor in the modern biodiversity crisis and
has negative effects on both humans and wildlife (such as property destruction, injury,
or death) that can impede conservation efforts for threatened species. Effectively
...
Evolution
Identifying the genetic basis of local adaptation and fitness trade-offs across environments
is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic
response for surviving seasonal freezing, and costs of acclimation may be a ...
Germline colonization by retroviruses results in the formation of endogenous retroviruses
(ERVs). Most colonization’s occurred millions of years ago. However, in the Australo-Papuan
region (Australia and New Guinea), several recent germline colonization ...
Genetics
Heterochromatin, defined by histone H3 lysine 9 methylation (H3K9me), spreads across
large domains and can be epigenetically inherited in a self-propagating manner. Heterochromatin
propagation depends upon a read–write mechanism, where the Clr4/Suv39h ...
Immunology and Inflammation
It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection
leads to the strong but ineffective inflammatory response that characterizes severe
Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse ...
Optic neuropathies, characterized by injury of retinal ganglion cell (RGC) axons of
the optic nerve, cause incurable blindness worldwide. Mesenchymal stem cell–derived
small extracellular vesicles (MSC-sEVs) represent a promising “cell-free” therapy
for ...
Persistent antigen exposure results in the differentiation of functionally impaired,
also termed exhausted, T cells which are maintained by a distinct population of precursors
of exhausted T (TPEX) cells. T cell exhaustion is well studied in the context ...
Immune-mediated necrotizing myopathy (IMNM) is an autoimmune disorder associated with
the presence of autoantibodies, characterized by severe clinical presentation with
rapidly progressive muscular weakness and elevated levels of creatine kinase, while
...
Impaired expression of MHC (major histocompatibility complex) class I in cancers constitutes
a major mechanism of immune evasion. It has been well documented that the low level
of MHC class I is associated with poor prognosis and resistance to checkpoint ...
Staphylococcus aureus skin colonization and eosinophil infiltration are associated with many inflammatory
skin disorders, including atopic dermatitis, bullous pemphigoid, Netherton’s syndrome,
and prurigo nodularis. However, whether there is a ...
The NOD-like receptor (NLR) family pyrin domain containing 6 (NLRP6) serves as a sensor
for microbial dsRNA or lipoteichoic acid (LTA) in intestinal epithelial cells (IECs),
and initiating multiple pathways including inflammasome pathway and type I ...
Medical Sciences
Resistance to neoadjuvant chemotherapy leads to poor prognosis of locally advanced
rectal cancer (LARC), representing an unmet clinical need that demands further exploration
of therapeutic strategies to improve clinical outcomes. Here, we identified a ...
Microbiology
Microbial dissimilatory sulfate reduction (DSR) is a key process in the Earth biogeochemical
sulfur cycle. In spite of its importance to the sulfur and carbon cycles, industrial
processes, and human health, it is still not clear how reduction of sulfate ...
Microbiota-centric interventions are limited by our incomplete understanding of the
gene functions of many of its constituent species. This applies in particular to small
RNAs (sRNAs), which are emerging as important regulators in microbiota species yet
...
Coastal Antarctic marine ecosystems are significant in carbon cycling because of their
intense seasonal phytoplankton blooms. Southern Ocean algae are primarily limited
by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12). Micronutrient ...
Several structured noncoding RNAs in bacteria are essential contributors to fundamental
cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities
to uncover and explore biochemical mechanisms relevant to other major and ...
Neuroscience
In various biological systems, information from many noisy molecular receptors must
be integrated into a collective response. A striking example is the thermal imaging
organ of pit vipers. Single nerve fibers in the organ reliably respond to milli-Kelvin
(...
Spontaneously occurring miniature excitatory postsynaptic currents (mEPSCs) are fundamental
electrophysiological events produced by quantal vesicular transmitter release at synapses.
Their analysis can provide important information regarding pre- and ...
Ionotropic glutamate receptors (iGluRs) mediate excitatory signals between cells by
binding neurotransmitters and conducting cations across the cell membrane. In the
mammalian brain, most of these signals are mediated by two types of iGluRs: AMPA and
NMDA ...
The hippocampal formation is crucial for learning and memory, with submodule CA3 thought
to be the substrate of pattern completion. However, the underlying synaptic and computational
mechanisms of this network are not well understood. Here, we perform ...
The N6-methyladenosine (m6A) modification of RNA is an emerging epigenetic regulatory mechanism that has been
shown to participate in various pathophysiological processes. However, its involvement
in modulating neuropathic pain is still poorly understood. ...
Recent studies have indicated somatosensory cortex involvement in motor learning and
retention. However, the nature of its contribution is unknown. One possibility is
that the somatosensory cortex is transiently engaged during movement. Alternatively,
...
Visually guided reaching, a regular feature of human life, comprises an intricate
neural control task. It includes identifying the target’s position in 3D space, passing
the representation to the motor system that controls the respective appendages, and
...
Cortical inhibitory interneurons (cINs) are born in the ventral forebrain and migrate
into the cortex where they make connections with locally produced excitatory glutamatergic
neurons. Cortical function critically depends on the number of cINs, which is ...
Physiology
Efficient removal of fibrillar collagen is essential for adaptive subcutaneous adipose
tissue (SAT) expansion that protects against ectopic lipid deposition during weight
gain. Here, we used mice to further define the mechanism for this collagenolytic ...
Plant Biology
Root development is tightly controlled by light, and the response is thought to depend
on signal transmission from the shoot. Here, we show that the root apical meristem
perceives light independently from aboveground organs to activate the light-regulated
...
Light plays a central role in plant growth and development, providing an energy source
and governing various aspects of plant morphology. Previous study showed that many
polyadenylated full-length RNA molecules within the nucleus contain unspliced introns
...
Sustainability Science
Protected areas are of paramount relevance to conserving wildlife and ecosystem contributions
to people. Yet, their conservation success is increasingly threatened by human activities
including habitat loss, climate change, pollution, and species ...
Human–wildlife conflict is an important factor in the modern biodiversity crisis and
has negative effects on both humans and wildlife (such as property destruction, injury,
or death) that can impede conservation efforts for threatened species. Effectively
...
Corrections
Cover image: Pictured are colonies of the Antarctic phytoplankton Phaeocystis antarctica. Deepa Rao et al. used laboratory cultures and comparative omics to characterize the vitamin requirements of P. antarctica, which absorbs significant amounts of atmospheric carbon during seasonal algal blooms in the Southern Ocean. The authors found that P. antarctica is not dependent on the availability of vitamin B12 for growth as was previously hypothesized. The results could provide insight into the ecological dynamics and responses of marine microbes to changes in micronutrient availability driven by climate change. See the article by Rao et al. e2204075121. Image credit: Dawn Moran.
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